THERMODYNAMICS FUNDAMENTALS AND ITS APPLICATION IN SCIENCE

Edited by Ricardo Morales-Rodriguez

Thermodynamics Fundamentals and Its Application in Science http://dx.doi.org/10.5772/2615 Edited by Ricardo Morales-Rodriguez
Contributors Ahmet Grses, Mehtap Ejder-Korucu, Nikolai Bazhin, Yi Fang, Bohdan Hejna, A. Plastino, Evaldo M. F. Curado, M. Casas, Zdeka Kolsk, Milan Zbransk, Alena Randov, Ronald J. Bakker, Elisabeth Blanquet, Ioana Nuta, Lin Li, Rza Atav, L.E. Panin, Yu Liu, Kui Wang, Philippe Vieillard, Nong-Moon Hwang, Jae-Soo Jung, Dong-Kwon Lee, Vasiliy Fefelov, Vitaly Gorbunov, Alexander Myshlyavtsev, Marta Myshlyavtseva, Adela Ionescu, Paiguy Armand Ngouateu Wouagfack, Rn Tchinda, Raul Mluan, Pedro Gmez Vilda, Xuejing Hou, Harvey J.M. Hou, C.A.S. Silva, Hui-Zhen Fu, Yuh-Shan Ho

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Publishing Process Manager Marina Jozipovic Typesetting InTech Prepress, Novi Sad Cover InTech Design Team First published September, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Thermodynamics Fundamentals and Its Application in Science, Edited by Ricardo Morales-Rodriguez p. cm. ISBN 978-953-51-0779-8

Contents
Preface IX Section 1 Chapter 1 Classical Thermodynamics 1 A View from the Conservation of Energy to Chemical Thermodynamic 3 Ahmet Grses and Mehtap Ejder-Korucu Useful Work and Gibbs Energy 29 Nikolai Bazhin Statistical Thermodynamics 45 Gibbs Free Energy Formula for Protein Folding 47 Yi Fang Information Capacity of Quantum Transfer Channels and Thermodynamic Analogies 83 Bohdan Hejna Thermodynamics Microscopic Connotations 119 A. Plastino, Evaldo M. F. Curado and M. Casas Property Prediction and Thermodynamics 133 Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 135 Zdeka Kolsk, Milan Zbransk and Alena Randov Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 163 Ronald J. Bakker Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 191 Elisabeth Blanquet and Ioana Nuta

Chapter 2

Section 2 Chapter 3

Chapter 4

Chapter 5

Section 3 Chapter 6

Chapter 7

Chapter 8

VI

Contents

Section 4 Chapter 9

Material and Products 215 Application of Thermodynamics and Kinetics in Materials Engineering 217 Lin Li Thermodynamics of Wool Dyeing 247 Rza Atav Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 263 L.E. Panin Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 305 Yu Liu and Kui Wang Thermodynamics of Hydration in Minerals: How to Predict These Entities 339 Philippe Vieillard Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 371 Nong-Moon Hwang, Jae-Soo Jung and Dong-Kwon Lee Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 389 Vasiliy Fefelov, Vitaly Gorbunov, Alexander Myshlyavtsev and Marta Myshlyavtseva Non-Equilibrium Thermodynamics 417 Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 419 Adela Ionescu ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 445 Paiguy Armand Ngouateu Wouagfack and Rn Tchinda Thermodynamics in Diverse Areas 461 Thermodynamics of Microarray Hybridization 463 Raul Mluan and Pedro Gmez Vilda Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 483 Xuejing Hou and Harvey J.M. Hou

Chapter 10

Chapter 11

Chapter 12

Chapter 13

Chapter 14

Chapter 15

Section 5 Chapter 16

Chapter 17

Section 6 Chapter 18

Chapter 19

Contents

VII

Chapter 20

Fuzzy Spheres Decays and Black Hole Thermodynamics 501 C.A.S. Silva Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 519 Hui-Zhen Fu and Yuh-Shan Ho

Chapter 21

Preface
This book is a result of a careful selection of scientific contributions involved in the thermodynamic area and it is titled Thermodynamics - Fundamentals and Its Application in Science. Thermodynamics is very important for the description of phenomena in different fields on science. Therefore, this book contains chapters describing the fundamentals and the diverse applications in different areas under development, which allow the access of different kind of readers; for instance, bachelor and postgraduate students, researchers, etc. The book is divided in six sections and the classification was done according to the purpose, relevance and approaches employed in the development of the contributions. The first section describes the classical thermodynamics, where firstly an overview about classical thermodynamics considering diverse fundamental concepts of the area is described. This section also has a contribution presenting the mechanism of useful work and heat production in reversible systems. The second section includes some chapters based on statistical mechanics, for instance, one of the chapters described the protein folding phenomena based on Gibbs free energy through the use of quantum mechanics, topic of high importance currently. On the other hand, another of the contributions in this section describes the information capacity of quantum transfer channels and thermodynamics analogies. The last chapter of this section introduces some axioms which allow one to derive the MaxEnt equations and viceversa, giving an alternative foundation for equilibriums statistical mechanics. The property prediction in thermodynamics is presented in the following section. A chapter explaining the use and implementation of group contribution methods for property prediction of organic compounds is firstly described. The description of pure gases and multi/component fluid systems is presented in another chapter, which in fact used a modified version of the Van der Waals equation. The last chapter is this section illustrates the interest area of macroscopic modelling on the thermodynamics simulation and gives some interesting examples in different domains in the material and product design areas employing some predicted properties. The fourth section contains the application of some thermodynamic insights in the material and products area. One of the chapters introduces some computational

Preface

results on the designing of advances material. A wool dyeing phenomenon described by thermodynamics is presented in another contribution. On the other hand, some authors talk about nanostructural transition in biological membranes under the action of steroid hormones. In this section, a chapter highlighting the importance of improving the understanding of molecular recognition mechanics in supramolecular systems and the design and synthesis of new supramolecular systems based on different kinds of cyclodextrins is also presented. The use of thermodynamics in the mineral field is presented describing the hydration of minerals providing several relationships illustrated by examples exhibiting great variability closely related to the chemical and physical compound properties. The synthesis of monodisperse nanoparticles is also described in one of the chapters of this section, relying on thermodynamics and kinetic basis. The last chapter of the section talks about thermodynamics of lattice gas models of multisite adsorption. A section with chapters presenting non equilibrium approach is the fifth section of the book. One of the chapters talks about the influence of certain parameters on excitable media behaviour, specifically describing the turbulent mixing. Moreover, the other chapter of this section presents an analytical method developed to achieve the performance optimization of irreversible three-heat-sources absorption refrigeration models having finite-rate of heat transfer, heat leakage and internal irreversibility based on an objective function named ecological coefficient performance (ECOP). The last section contains some chapters talking about diverse applications of thermodynamics. For instance, one chapter discusses the importance of thermodynamics in microarrays hybridization, due to thermodynamics factors affect molecular interaction which in fact are not taken into account for the estimation of genetic expression in current algorithms. Another chapter describes a case study probing thermodynamics of electron transfer in photosystems using a combination of molecular genetics and sophisticated biophysical techniques, in particular, pulsed photoacoustic spectroscopy. The other chapter of this section address the black hole thermodynamics in the context of topology change, as conceived for some classes of quantum spaces called fuzzy spheres. The last chapter of the section and book shows a bibliometric study about thermodynamic contributions giving a general picture about the number of papers, institutions and countries working on certain thermodynamic topics as well as the quality of the paper by their citations. It is expected that the collections of these chapters contributes to the state of the art in the thermodynamics area, which not only involve the fundamentals of thermodynamics, but moreover, consider the wide applications of this area in several fields. Ricardo Morales-Rodriguez Technical University of Denmark, Denmark

Section 1

Classical Thermodynamics

Chapter 1

A View from the Conservation of Energy to Chemical Thermodynamics

Ahmet Grses and Mehtap Ejder-Korucu
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51383

1. Introduction
According to the conservation of energy law, energy, which is the capacity to do work or to supply heat, can be neither created nor destroyed; it can only be converted from one form into another. For example, the water in a reservoir of dam has potential energy because of its height above the outlet stream but has no kinetic energy because it is not moving. As the water starts to fall over the dam, its height and potential energy, (Ep) is energy due to position or any other form of stored energy, decrease while its velocity and kinetic energy, (EK) is the energy related to the motion of an object with mass m and velocity v, increase. The total of potential energy plus kinetic energy always remains constant. When the water reaches the bottom and dashes against the rocks or drives the turbine of a generator, its kinetic energy is converted to other forms of energy-perhaps into heat that raises the temperature of the water or into electrical energy [6]. If any fuel is burned in an open medium, its energy is lost almost entirely as heat, whereas if it is burned in a car engine; a portion of the energy is lost as work to move the car, and less is lost as heat. These are also typical examples of the existence of the law.

Figure 1. Some examples showing the existence of the conservation of energy law
2012 Grses and Ejder-Korucu, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

4 Thermodynamics Fundamentals and Its Application in Science

It is thought that the summation of the introduction as a detailed concept map related with the conservation of energy would be better. This map in Fig.2 presents a concise view for many concepts of thermodynamics and their relations.

Figure 2. A concept map for the conservation of energy law

The macroscopic part of universe under study in thermodynamics is called the system. The parts of the universe that can interact with the system are called the surroundings [5]. In order to describe the thermodynamic behavior of a physical system, the interaction between the system and its surroundings must be understood. Thermodynamic systems are thus classified into three main types according to the way they interact with the surroundings (Fig.3); open system: matter and energy can be exchanged with the surroundings; closed system: can exchange energy but not matter with the surroundings and isolated system: cannot exchange matter or energy with the surroundings [4, 5]. Addition, a boundary that does permit energy transfer as heat (such as steel and glass) is called diathermic and a boundary that does not permit energy transfer as heat is called adiabatic [1;4]. The system may be homogeneous or heterogeneous. An exact definition is difficult, but it is convenient to define a homogeneous system as one whose properties are the same in all parts, or at least their spatial variation is continuous. A heterogeneous system consists of

A View from the Conservation of Energy to Chemical Thermodynamics 5

two or more distinct homogeneous regions or phases, which are separated from one another by surfaces of discontinuity [4].

Figure 3. Systems and their surroundings; (a) open system (b) closed system and (c) isolated system.

Heating is a process in which the temperature of system, separated with diathermic border from its surrounding, is increased. This process leads to passing system from a state of lower energy to higher one. Heating process based on the energy difference between system and its surrounding provides identify of an important property which indicates the flow direction of energy. This property is called temperature. Temperature is a physical property of matter that quantitatively expresses the common notions of hot and cold. Objects of low temperature are cold, while various degrees of higher temperatures are referred to as warm or hot. Heat spontaneously flows from bodies of a higher temperature to bodies of lower temperature, at a rate that increases with the temperature difference and the thermal conductivity. No heat will be exchanged between bodies at same temperature; such bodies are said to be in "equilibrium. On the other hand, kinetic energy associated with the random motion of particles is called thermal energy, and the thermal energy of a given material is proportional to temperature. However, the magnitude of thermal energy in a sample also depends on the number of particles in the sample and so it is an extensive property. The water in a swimming pool and a cup of water taken from the pool has the same temperature, so their particles have the same average kinetic energy. The water in the pool has much more thermal energy than the water in the cup, simply because there are a larger number of molecules in the pool. A large number of particles at a given temperature have a higher total energy than a small number of particles at the same temperature [7]. Quantitatively, temperature which is an intensive property is measured with thermometers, which may be calibrated to a variety of temperature scales [9]. If two thermodynamic systems, A and B, each of which is in thermal equilibrium independently, are brought into thermal contact, one of two things will take place: either a flow of heat from one system to the other or no thermodynamic process will result. In the latter case the two systems are said to be in thermal equilibrium with respect to each other [11]. When same treatment has been repeated other system, C, if there is thermal equilibrium between B and C; the condition of thermodynamic equilibrium between them may be symbolically represented as follows,

6 Thermodynamics Fundamentals and Its Application in Science

If A B and B C
This observation has also been schematically shown in Fig.4

(1)

Figure 4. A schematic presentation of the zeroth law of thermodynamics.

Based on preceding observations, some of the physical properties of the system B (Thermometer) can be used as a measure of the temperature, such as the volume of a fixed amount of a liquid merqury or any alcohol under standard atmospheric pressure. The zeroth law of thermodynamics is the assurance of the existence of a property called the temperature [11]. The zeroth law allows us to assert the existence of temperature as a state function. Having defined temperature, how do we measure it? Of course, you are familiar with the process of putting a liquid-mercury thermometer in contact with a system, waiting until the volume change of the mercury has ceased, indicating that thermal equilibrium between the thermometer and the system has been reached [5]. It is necessary to know four common different temperature scales, namely Fahrenheit (0F), Celsius (0C), Kelvin (K) and Rankine (0R). To convert these scales one another can be used the following equations [9,10].

T/K

/ 0 C 273.15

(2) (3)

oR 459.67 oF oC 32 oR K oF 1.8 1.8

2. The first law of thermodynamic (the conservation of energy)

In thermodynamics, the total energy of a system is called its internal energy, U. The internal energy is the total kinetic and potential energies of the particles in the system. It is denoted by U the change in internal energy when a system changes from an initial state i with internal energy Ui to a final state of internal energy Uf :

U f Ui U

(4)

The internal energy is a state function in the sense that its value depends only on the current state of the system and is independent of how that state has been prepared. In other words, internal energy is a function of the properties as variables that determine the current state of

A View from the Conservation of Energy to Chemical Thermodynamics 7

the system. Changing any one of the state variables, such as the pressure and temperature, results in a change in internal energy. The internal energy is a state function that has consequences of the greatest importance. The internal energy is an extensive property of a system and is measured in joules (1 J = 1 kg m2 s2). The molar internal energy, Um, is the internal energy divided by the amount of substance in a system, Um = U/n; it is an intensive property and commonly reported in kilojoules per mole (kJ mol1) [12]. A particle has a certain number of motional degrees of freedom, such as the ability to translate (the motion of its centre of mass through space), rotate around its centre of mass, or vibrate (as its bond lengths and angles change, leaving its centre of mass unmoved). Many physical and chemical properties depend on the energy associated with each of these modes of motion. For example, a chemical bond might break if a lot of energy becomes concentrated in it, for instance as vigorous vibration. According to it, the average energy of each quadratic contribution to the energy is 1/2 kT. The mean energy of the atoms free to move in three dimensions is kT and the total energy of a monatomic perfect gas is NkT, or nRT (because N = nNA and R = NAk , NA: Avogadro's number and k: Boltzman's constant). I t can therefore be written;

Um T Um 0 RT monatomic gas; translation only

(5)

where Um(0) is the molar internal energy at T = 0, when all translational motions have ceased and the sole contribution to the internal energy arises from the internal structure of the atoms. This equation shows that the internal energy of a perfect gas increases linearly with temperature. At 25C, 3/2 RT = 3.7 kJ mol1, so translational motion contributes about 4 kJ mol1 to the molar internal energy of a gaseous sample of atoms or molecules. When the gas consists of molecules, we need to take into account the effect of rotation and vibration. A linear molecule, such as N2 and CO2, can rotate around two axes perpendicular to the line of the atoms, so it has two rotational modes of motion, each contributing a term 1/2 kT to the internal energy. Therefore, the mean rotational energy is kT and the rotational contribution to the molar internal energy is RT.

Um T Um 0 5 / 2 RT linear molecule ; translation and rotation only

(6)

A nonlinear molecule, such as CH4 or H2O, can rotate around three axes and, again, each mode of motion contributes a term 1/2 kT to the internal energy. Therefore, the mean rotational energy is 3/2 kT and there is a rotational contribution of 3/2 RT to the molar internal energy. That is,

Um T Um 0 3RT nonlinear molecule; translation and rotation only

(7)

The internal energy now increases twice as rapidly with temperature compared with the monatomic gas. Another way: for a gas consisting of 1 mol of nonlinear molecules to undergo the same rise in temperature as 1 mol of monatomic gas, twice as more energy must be supplied. Molecules do not vibrate significantly at room temperature and, as a first

8 Thermodynamics Fundamentals and Its Application in Science

approximation; the contribution of molecular vibrations to the internal energy is negligible except for very large molecules such as polymers and biological macromolecules. None of the expressions we have been derived depends on the volume occupied by the molecules: there are no intermolecular interactions in a perfect gas, so the distance between the molecules has no effect on the energy. That is, the internal energy of a perfect gas is independent of the volume it occupies. The internal energy of interacting molecules in condensed phases also has a contribution from the potential energy of their interaction. However, no simple expressions can be written down in general. Nevertheless, the crucial molecular point is that, as the temperature of a system is raised, the internal energy increases as the various modes of motion become more highly excited [12]. By considering how the internal energy varies with temperature when the pressure of the system is kept constant; many useful results and also some unfamiliar quantities can be obtained. If it is divided both sides of eqn ((dU = (U/V)T dV + (U/T) v dT ) ((U/V)T = T and T called as the internal pressure ; (U/T) v = Cv and it is called as heat capacity at constant volume )) by dT and impose the condition of constant pressure on the resulting differentials, so that dU/dT on the left becomes (U/T)p, So;

U / T p

T V / T p Cv

(8)

It is usually sensible in thermodynamics to inspect the output of a manipulation like this to see if it contains any recognizable physical quantity. The differential coefficient on the right in this expression is the slope of the plot of volume against temperature (at constant pressure). This property is normally identified as thermal expansion coefficient, , of a substance, which is defined as

1 / V V / T p

(9)

When it is introduced the definition of into the equation for (U/T)p = T V + Cv ,this equation is entirely general (provided the system is closed and its composition is constant). It expresses the dependence of the internal energy on the temperature at constant pressure in terms of Cv, which can be measured in one experiment, in terms of , which can be measured in another, and in terms of the quantity T, for a perfect gas, T = 0, so

Cv U / T p

(10)

That is, the constant-volume heat capacity of a perfect gas is equal to the slope of a plot of internal energy against temperature at constant pressure as well as (by definition) to the slope at constant volume. It can also be predicted that the change of internal energy with temperature at constant pressure means a total energy change raised from increase in both energy of kinetics and potential energy of particles in higher temperature. The translational motion of particles against constant external pressure will lead to expansion, but thermal expansion characteristics of substance control its magnitude. Thus, we can see that heating in constant volume only changes internal energy as qv (U = qv), whereas its change in

A View from the Conservation of Energy to Chemical Thermodynamics 9

constant pressure additionally includes changing of potential energy of particles due to translation motion. That is, changes in constant pressure require a different definition of the transferred energy [12].

3. From conservation of energy to heat and work

It has been found experimentally that the internal energy of a system may be changed either by doing work on the system or by heating it. Whereas we may know how the energy transfer has occurred (because we can see if a weight has been raised or lowered in the surroundings, indicating transfer of energy by doing work, or if ice has melted in the surroundings, indicating transfer of energy as heat), the system is blind to the mode employed. Heat and work are equivalent ways of changing a systems internal energy. It is also found experimentally that, if a system is isolated from its surroundings, then no change in internal energy takes place. This summary of observations is now known as the First Law of thermodynamics or the Conservation of Energy and is expressed as follows [1;12]. The internal energy of an isolated system is constant.

U 0

(11)

A system cannot be used to do work, leave it isolated, and then come back expecting to find it restored to its original state with the same capacity for doing work. The experimental evidence for this observation is that no perpetual motion machine, a machine that does work without consuming fuel or using some other source of energy, has ever been built. These remarks may be summarized as follows. If we write w for the work done on a system, q for the energy transferred as heat to a system, and U for the resulting change in internal energy, and then it follows that
U q w

(12)

Equation summarizes the equivalence of heat and work and the fact that the internal energy is constant in an isolated system (for which q = 0 and w = 0). The equation states that the change in internal energy of a closed system is equal to the energy that passes through its boundary as heat or work. It employs the acquisitive convention, in which w and q are positive if energy is transferred to the system as work or heat and are negative if energy is lost from the system. In other words, we view the flow of energy as work or heat from the systems perspective [1;12]. Heat (q) Heat flows by virtue of a temperature difference. Heat will flow until temperature gradients disappear [8]. When a heater is immersed in a beaker of water (the system), the capacity of the system to do work increases because hot water can be used to do more work than cold water [1]. An exothermic process is a process that releases energy as heat. All combustion reactions are exothermic. An endothermic process is a process that absorbs energy as heat. An example of an endothermic process is the vaporization of water. An endothermic process in a diathermic container results in energy flowing into the system as heat. An exothermic

10 Thermodynamics Fundamentals and Its Application in Science

process in a similar diathermic container results in a release of energy as heat into the surroundings. If an endothermic process in nature was taken place by a system divided an adiabatic boundary from its surroundings, a lowering of temperature of the system results; conversely if the process is exothermic, temperature rises [1]. These are the expected results of conversation of energy. Work (w) Energy is the essence of our existence as individuals and as a society. Just as energy is important to our society on a macroscopic scale, it is critically important to each living organism on a microscopic scale. The living cell is a miniature chemical factory powered by energy from chemical reactions. The process of cellular respiration extracts the energy stored in sugars and other nutrients to drive the various tasks of the cell. Although the extraction process is more complex and more subtle, the energy obtained from fuel molecules by the cell is the same as would be obtained from burning the fuel to power an internal combustion engine [3]. The fundamental physical property in thermodynamics is work is done when an object is moved against an opposing force. Doing work is equivalent into raising a weight somewhere in the surrounding. An example of doing work is the expansion of a gas that pushes out a piston and raises a weight. A chemical reaction that derives an electric current through a resistance also does work, because the same current could be driven through a motor and used to raise a weight [1]. Work is the transferred energy by virtue of a difference in mechanical properties from a boundary between the system and the surroundings. There are many types of work; such as mechanical work, electrical work, magnetic work, and surface tension [8]. The SI unit of both heat and work (kg m2/s2) is given the name joule (J), after the English physicist James Prescott Joule (1818-1889) [6]. 1 J = 1 kg m2/s2 In addition to the SI unit joule, some chemists still use the unit calorie (cal). Originally defined as the amount of energy necessary to raise the temperature of 1 g of water by 1oC (specially, from 14.5 oC to 15.5 oC), one calorie is now defined as exactly 4,184 J [6]. The workenergy theorem In mechanics, the workenergy theorem demonstrates that the total work done on a system is transformed into kinetic energy. This is represented in a very simple and meaningful equation as follows: Wtotal Ek (13)

in which, Wtotal is the total work done on the system, including the work carried out by all the external forces (Wex), as well as the work developed by the internal forces within the system (Win). Thus;

A View from the Conservation of Energy to Chemical Thermodynamics 11

Wtotal Wex Win

(14)

Now, if the external work is separated into two terms, namely the work done by the external conservative forces (Wex,c), which are associated with an external potential energy (Ep,ex), and the non-conservative external work (Wnon-ex), the whole external work can be written as:

Wex Wex,c Wnonex

Ep,ex Wnonex

(15)

Similarly, the work developed by the internal forces within the system can be also expressed as the sum of a conservative work term plus the non-conservative internal work. Thus;

Win Win,c Wnonin

Ep,in Wnonin

(16)

Where, Ep,in is the internal potential energy of the system. As for the kinetic energy of a system, mechanics shows that it can be considered as consisting of two terms, as follows:
Ek 1 / 2 Mv 2CM Ek ,CM

(17)

M being the total mass of the system,vCM the velocity of its center of mass, and Ek,CM the kinetic energy of the system with respect to its center of mass. The first term on the right-hand side of equation above represents the kinetic energy of the center of mass of the system, as if it had the mass of the whole system. Thus, as the velocity vCM is taken with respect to an external reference frame, this first term can be called the external kinetic energy of the system (Ek,ex), whereas the second term would be its internal kinetic energy (Ek,in). Accordingly, the increase of the kinetic energy of a system can be written in the following way:

Ek Ek,ex Ek,in

(18)

Then, the substitution of equations 14, 15, 16 and 18 into equation 13 allows us to order terms as follows:

Wex Ep ,ex Ek ,ex Ep ,in Ek ,in Win

(19)

Equation 19 is a general developed expression of the workenergy theorem derived from mechanics. It should be noticed that, though it does not describe the details of the energetic terms, each of them is explicitly stated, which will be of great help both to define and to understand the contribution of thermodynamics when establishing the first law [17]. Reversibility and Reversible changes A reversible change in thermodynamics is a change that can be reversed by an infinitesimal modification of a variable. One example of reversibility that we have encountered already is the thermal equilibrium of two systems with the same temperature. The transfer of energy as heat between the two is reversible because, if the temperature of either system is lowered infinitesimally, then energy flows into the system with the lower temperature. If the

12 Thermodynamics Fundamentals and Its Application in Science

temperature of either system at thermal equilibrium is raised infinitesimally, then energy flows out of the hotter system. There is obviously a very close relationship between reversibility and equilibrium: systems at equilibrium are poised to undergo reversible change. Suppose a gas is confined by a piston and that the external pressure, pex, is set equal to the pressure, p, of the confined gas. Such a system is in mechanical equilibrium with its surroundings because an infinitesimal change in the external pressure in either direction causes changes in volume in opposite directions. If the external pressure is reduced infinitesimally, the gas expands slightly. If the external pressure is increased infinitesimally, the gas contracts slightly. In either case the change is reversible in the thermodynamic sense. If, on the other hand, the external pressure differs measurably from the internal pressure, then changing pex infinitesimally will not decrease it below the pressure of the gas, so will not change the direction of the process. Such a system is not in mechanical equilibrium with its surroundings and the expansion is thermodynamically irreversible [12]. To achieve reversible expansion we set pex equal to p at each stage of the expansion. In practice, this equalization could be achieved by gradually removing weights from the piston so that the downward force due to the weights always matches the changing upward force due to the pressure of the gas. When we set pex = p, eqn (dw = pexdV) becomes dw exdV p pdV reversible expansion work (20)

(Equations valid only for reversible processes are labeled with a subscript rev.) Although the pressure inside the system appears in this expression for the work, it does so only because pex has been set equal to p to ensure reversibility. The total work of reversible expansion from an initial volume Vi to a final volume Vf is therefore
w pdV
Vi Vf

(21)

The integral can be evaluated once it is known how the pressure of the confined gas depends on its volume [12]. At the isothermal, reversible expansion of a perfect gas, the work made by keeping the system in thermal contact with its surroundings can be stated as follows;
w V / Vi nRT dV / nRTln V f
Vi Vf

(22)

When the final volume is greater than the initial volume, as in an expansion, the logarithm in Eqn. 22 is positive and hence w < 0. In this case, the system has done work on the surroundings and there is a corresponding reduction in its internal energy, but due to there is a compensating influx of energy as heat, overall the internal energy is constant for the isothermal expansion of a perfect gas, which clearly indicates the Conservation of Energy Law. The equations also show that more work is done for a given change of volume when the temperature is increased: at a higher temperature the greater pressure of the confined

A View from the Conservation of Energy to Chemical Thermodynamics 13

gas needs a higher opposing pressure to ensure reversibility and the work done is correspondingly greater (Fig. 5) [12].

Figure 5. The work done by a perfect gas when it expands reversibly and isothermally is equal to the area under the isotherm p = nRT/V. The work done during the irreversible expansion against the same final pressure is equal to the rectangular area shown slightly darker. It can be seen that the reversible work is greater than the irreversible work [12].

Adiabatic changes We are now equipped to deal with the changes that occur when a perfect gas expands adiabatically. A decrease in temperature should be expected: because work is done but no heat enters the system, the internal energy decrease, and therefore the temperature of the working gas also decrease. In molecular terms, the kinetic energy of the particles decrease as work is done, so their average speed decreases, and hence the temperature decrease. This means that in the case of perfect gas, change in the distance between particles cannot be responsible for the changing of internal energy but the Conservation of Energy Law requires a measurable reduction in kinetic energy of particles, i.e. a reduction in their velocities. The change in internal energy of a perfect gas when the temperature is changed from Ti to T f and the volume is changed from Vi to Vf can be expressed as the sum of two steps (Fig. 6). In the first step, only the volume changes and the temperature is held constant at its initial value. However, because the internal energy of a perfect gas is independent of the volume the molecules occupy, the overall change in internal energy arises solely from the second step, the change in temperature at constant volume. Provided the heat capacity is independent of temperature, this change is

U CV T f Ti

CV T

(23)

Because the expansion is adiabatic, we know that q = 0; because U = q + w, it then follows that U = ad. The subscript ad denotes an adiabatic process. Therefore, by equating the two expressions we have obtained for U, we obtain Wad CV T (24)

14 Thermodynamics Fundamentals and Its Application in Science

Figure 6. To achieve a change of state from one temperature and volume to another temperature and volume, we may consider the overall change as composed of two steps. In the first step, the system expands at constant temperature; there is no change in internal energy if the system consists of a perfect gas. In the second step, the temperature of the system is reduced at constant volume. The overall change in internal energy is the sum of the changes for the two steps [12].

That is, the work done during an adiabatic expansion of a perfect gas is proportional to the temperature difference between the initial and final states. That is exactly what it can be expected on molecular grounds and according to Conversation of Energy, because the mean kinetic energy is proportional to T, so a change in internal energy arising from temperature alone is also expected to be proportional to T [12].

T f Ti Vi / V f

1/ c

(25)

where c = CV /R (CV :molar heat capacity in constant volume and R: universal gas constant). By raising each side of this expression to the power c, an equivalent expression is

ViTi c V f T f c This result is often summarized in the form VTc = constant

(26)

4. From the conservation of energy to heat transfer, heat capacity and the enthalpy
The process of heat moving from one object into another is called heat transfer. The difference in temperature defines the direction in which the heat flows when two objects come into contact; heat always flows from a hotter object at a higher temperature into a colder object at a lower temperature. Heat transfer which can mainly occur in three ways, namely conduction, convection and radiation changes the temperature of matter; it can also cause changes in phase or state [7]. When energy is added to a substance and no work is done, the temperature of the substance usually rises i.e. substance is heated; exception to the case in which a substance undergoes a change of state-also called a phase transition, such as vaporization/condensation,

A View from the Conservation of Energy to Chemical Thermodynamics 15

melting/freezing, and sublimation. The quantity of energy required to raise the temperature of given mass of a substance by some amount varies from one substance to another. The amount of increase also depends on the conditions in which heating takes place. Heat capacity (C) of a substance is the quantity of energy required to raise its temperature by 1C or 1 K. The heat capacity differs from substance to substance. In the case of a monatomic gas such as helium under constant volume, if it is assumed that no electronic or nuclear quantum excitations occur, each atom in the gas has only 3 degrees of freedom, all of a translational type. No energy dependence is associated with the degrees of freedom which define the position of the atoms. While, in fact, the degrees of freedom corresponding to the momenta of the atoms are quadratic, and thus contribute to the heat capacity. In the somewhat more complex case of a perfect gas of diatomic molecules, the presence of internal degrees of freedom is apparent. Table1 shows C v values for some mono and diatomic gases at 1 atm and 25C.
Monoatomic Gases He Ne Ar Kr Xe Cv (J/Kmol) Diatomic Gases H2 CO N2 Cl2 Br2 (vapor) Cv ( J/Kmol)

12.5 12.5 12.5 12.5 12.5

20.18 20.2 19.9 24.1 28.2

Table 1. C v values for some mono and diatomic gases at 1 atm and 25C.

From Table 1, it can be seen clearly that the heat capacities of all monoatomic gasses have exactly same values, but they are lower than those of diatomic gasses which include the contributions of translation vibration, and rotation. The heat capacity is directly proportional to the amount of substance. Heat capacity is an extensive property, meaning it is a physical property that scales with the size of a physical system .That means by doubling the mass of substance, heat capacity can be doubled. The heat required to increase the temperature from T1 to T2 of a substance can be calculated using the following equation.

Q C x T

(27)

The unit of heat capacity is JoC-1 or JK-1. For many experimental and theoretical purposes it is more convenient to report heat capacity as an intensive property, as an intrinsically characteristic property of a particular substance. This is most often accomplished by the specification of the property per a unit of mass. In science and engineering, such properties are often prefixed with the term specific. International standards now recommend that specific heat capacity always refer to division by mass. The units for the specific heat capacity are [C] = J/kg K in chemistry, the heat capacity is also often specified relative one mole, the unit for amount of substance, and is called the molar heat capacity, having the unit, J/mol K. For some considerations it is useful to specify the volume-specific heat capacity, commonly called volumetric heat capacity, which is the heat capacity per unit

16 Thermodynamics Fundamentals and Its Application in Science

volume and has SI units [S] = J/m3 K. This is used almost exclusively for liquids and solids, since for gasses it may be confused with specific heat capacity at constant volume. In thermodynamics, two types of heat capacities are defined; Cp, the heat capacity at constant pressure and C v, heat capacity at constant volume. The total energy of a system in thermodynamics is called internal energy which specifies the total kinetic and potential energy of particles in the system. Internal energy of a system can be changed either by doing work on the system or heating it as a result of the conversation of energy law. The internal energy of a substance increases when its temperature is increased. By considering the total change in internal energy of a substance which is heated at constant pressure, the difference between heat capacities at two different conditions can be meaningfully interpreted. Heat capacity in terms of derivative at constant volume is expressed as follows:
Cv

U / T v

(28)

The first law of thermodynamics argues that the internal energy of a system which is heated at constant-pressure differs from that at the constant-volume by the work needed to change the volume of the system to maintain constant pressure. This work arises in two ways: One is the work of driving back the atmosphere (external work); the other is the work of stretching the bonds in the material, including any weak intermolecular interactions (internal work). In the case of a perfect gas, the second makes no contribution. In order to find out how the internal energy varies with temperature when the pressure rather than the volume of the system is kept constant; it can be divided both sides of (dU = (U/V)T dV + (U/T)v dT) by dT and thus;

U / T p U / V T V / T p U / T v

(29)

It is usually sensible in thermodynamics to inspect the output of a manipulation like this to see if it contains any recognizable physical quantity. The partial derivatives on the right in this expression are the slope of the plot of volume against temperature at constant pressure, the slope of the plot of internal energy against volume at constant temperature and the slope of the plot of internal energy against temperature at constant volume, respectively. These properties are normally tabulated as the expansion coefficient, , of a substance, which is dened as =1/V (U/T) p, internal pressure, T, and constant volume heat capacity, C v, respectively. Thus;

U / T p

T V Cv

(30)

Equation (30) is entirely general for a closed system, which may be in solid, liquid, or gas states, with constant composition. It expresses the changing of internal energy with the temperature at constant pressure depends on two terms on the right in this expression The first term is related to the potential energy of particles and it comprises internal work made against internal pressure due to thermal expansion which can be considered for all substances in solid, liquid, or gas states, but weakness of inter-particles interactions in gas

A View from the Conservation of Energy to Chemical Thermodynamics 17

state requires to take account of an additional contribution to identify the real change in internal energy of any system in gas state heated at constant pressure. The fact that for a perfect gas, T = 0 and so (U/T)p = Cv ,supports to this remark. The second term also is interested in the kinetic energies of particles. That is, the energy at the constant-pressure of any substance must defined by an another thermodynamic property or function and this function must include external work made to external pressure due to volumetric expansion of any system in gas state. This thermodynamic function which takes account of external work is the enthalpy.
The enthalpy

The change in internal energy is not equal to the heat supplied when the system is free to change its volume. Under these circumstances some of the energy supplied as heat to the system is returned to the surroundings as expansion work, so U is less than q [1]. To determine E, it must be measured both heat and work which done by expanding of a gas. It can be found the quantity of pV work done by multiplying the external pressure (P) by the change in volume of the gas (V, or Vfinal - Vinitial). In an open flask (or a cylinder with a weightless, frictionless piston), a gas does work by pushing back the atmosphere (Figure 7) [18].
w pV

(31)

Figure 7. Pressure-volume work. When the volume (V) of a system increases by an amount of V against an external pressure (p), the system pushes back, and thus does pV work on the surroundings (w = -p V) [18].

For changes at constant pressure, a thermodynamic variable called the enthalpy, H, is mathematically defined as follows [1],
H U pV

(32)

where U is the internal energy of the system, p is the pressure of the system, and V is the volume of the system [3].

18 Thermodynamics Fundamentals and Its Application in Science

Since internal energy, pressure, and volume are all state functions, enthalpy is also a state function. But what exactly is enthalpy? To help answer this question, consider a process carried out at constant pressure and where the only work allowed is pressure-volume work (w= - pV). Under this conditions, the expression U qP w becomes (33)

U
or

qp pV

(34)

qp U pV

(35)

where qp, U and pV are the transferred energy as heat to the system heated at constant pressure, change in internal energy and change in pV, respectively. Since p is constant; the change in pV is due only to a change in volume. Thus

pV

p V

(36) (37)

H qp

Heat capacity in terms of derivative at constant pressure, i.e. changes in the energy of a system heated at constant pressure is also expressed as follows:

C p H / T p

(38)

The slope of a plot of internal energy against temperature at constant volume, for a perfect gas CV is also the slope at constant pressure. In order to obtain an easy way to derive the relation between Cp and CV for a perfect gas, both heat capacities can be used in terms of derivatives at constant pressure:

Cp Cv H / T p U / T v H / T p U / T p
Then, if (H = U + pV = U + nRT ) is introduced into the first term, which results in

(39)

Cp Cv U / T p nR U / T p

and C p Cv nR

(40)

This means that in the case of a perfect gas, R, universal gas constant may be considered as the work done to push back the atmosphere per unit increase in temperature. However, the general relation between the two heat capacities for any pure substance is demonstrated as follows; C p Cv 2TV / T (41)

A View from the Conservation of Energy to Chemical Thermodynamics 19

This formula is a thermodynamic expression, which means that it applies to any substance (that is, it is universally true). It reduces to previous equation for a perfect gas when it was set as = 1/T and T = 1/p Because thermal expansion coefficients, , of liquids and solids are small, it is tempting to deduce from last equation that for them CpCv. But this is not always so, because the compressibility T might also be small, so 2/T might be large. That is, although only a little work need be done to push back the atmosphere, a great deal of work may have to be done to pull atoms apart from one another as the solid expands. As an illustration, for water at 25 0C, Eqn (41) gives Cp = 75.3 J/Kmol compared with Cv = 74.8 J/Kmol. In some cases, the two heat capacities differ by as much as 30 per cent [21]. The constant-pressure heat capacity Cp differs from the constant-volume heat capacity Cv by the work needed to change the volume of the system to maintain constant pressure. This work arises in two ways. One is the work of driving back the atmosphere (external work); the other is the work of stretching the bonds in the material, including any weak intermolecular interactions (internal work). In the case of a perfect gas, the second makes no contribution. This suggests that the difference between two heat capacities is related to both internal work and external work done by the particles of a substance as an expended result of the conservation of energy. By considering the variation of H with temperature at constant volume, the validity of the enthalpy function can be differently verified. Firstly; for a closed system of constant composition, H is expressed in the total differential of T and p;

dH H / p T dp H / T p dT (
and then, divided this equation though by dT;

(42)

H / T v H / p T p / T v

Cp

(43)

The manipulation of this expression provides more involved equation which can be applied to any substance. Because all the quantities that appear in it can be measured in suitable experiments.

H / T v (1 / T ) C p
where the isothermal compressibility, , is defined as

(44)

T / V V / p T 1
and the Joule Thomson coefficient, , is defined as (T / p)H

(45)

(46)

This expression derived for the changing of the enthalpy with temperature at constant volume suggests that change in H with increased temperature at constant V is lower than that at constant p and the difference between them depend on some characteristic

20 Thermodynamics Fundamentals and Its Application in Science

properties of particles, such as external work.

and ,, indicating its relation with the absence of

The measurement of an enthalpy change An enthalpy change can be measured calorimetrically by monitoring the temperature change that accompanies a physical or chemical change occurring at constant pressure. A calorimeter for studying processes at constant pressure is called an isobaric calorimeter. A simple example is a thermally insulated vessel open to the atmosphere: the heat released in the reaction is monitored by measuring the change in temperature of the contents. For a combustion reaction an adiabatic flame calorimeter may be used to measure T when a given amount of substance burns in a supply of oxygen. Another route to H is to measure the internal energy change using a bomb calorimeter, and then to convert U to H. Because solids and liquids have small molar volumes, for them both pVm , external work and internal work is so small that the molar enthalpy and molar internal energy are almost identical (Hm = Um + pVm Um). Consequently, if a process involves only solids or liquids, the values of H and U are almost identical. Physically, such processes are accompanied by a very small change in volume; the system does negligible work on the surroundings when the process occurs, so the energy supplied as heat stays entirely within the system, as a expended result of the conversation of energy. Calorimeters The heat that is given out or taken in, when a chemical reaction occurs can be measured using a calorimeter. A simple, constant-pressure calorimeter (Coffee-cup calorimeter) for measuring heat for reactions in solution is shown in Fig. 8. This figure also shows a bomb calorimeter. The container is an expanded polystyrene cup with a lid. This material provides insulation which ensures that heat loss to, or gains from the surroundings is minimized; the outer cup in Fig. 8 provides additional insulation. As the reaction takes place, the thermometer records any change in temperature.

(a)

(b)

Figure 8. Calorimeter types; (a) Coffee-cup calorimeter [18] and (b) Bomb calorimeter [22].

A View from the Conservation of Energy to Chemical Thermodynamics 21

The relationship between the temperature change and the energy is given as follows;

Energy change in J

m g .C J / gK . T K

(47)

where C is the specific heat capacity of the solution. Since the reaction is carried out at constant pressure, the energy is equal to the enthalpy change. For dilute aqueous solutions, it is usually sufficient to assume that the specific heat capacity of the solution is the same as for water: Cwater 4.18 J/gK. It is assumed that no heat is used to change the temperature of the calorimeter itself. Where a calorimeter is made from expanded polystyrene cups, this is a reasonable assumption because the specific heat capacity of the calorimeter material is so small. However, the approximation is not valid for many types of calorimeter and such pieces of apparatus must be calibrated before use. Measurements made in the crude apparatus shown together with in Figure 8 are not accurate, and more specialized calorimeters, such as bomb calorimeter must be used if accurate results are required [18;19]. A bomb calorimeter is ideally suited for measuring the heat evolved in a combustion reaction. The system is everything within the double-walled outer jacket of the calorimeter. This includes the bomb and its contents, the water in which the bomb is immersed, the thermometer, the stirrer, and so on. Before using above equation, it must be emphasized that a rise in temperature of a system insulated with its surrounding does not occur by any heat transferred from the surroundings to the system because of the temperature difference between them. The difference in temperature observed during the measuring may be arisen from the change in the composition of system and considered as if the involved reaction occurs as exothermic or endothermic in diathermic condition. At constant pressure (where only pV work is allowed), the change in enthalpy H of the system is equal to the energy flow as heat. This means that for a reaction studied at constant pressure, the flow of heat is a measure of the change in enthalpy for the system. For this reason, the terms heat of reaction and change in enthalpy are used interchangeably for reactions studied at constant pressure. For a chemical reaction, the enthalpy change is given by the equation

H products Hreactants

(48)

In a case in which the products of a reaction have a greater enthalpy than the reactants, H will be positive. Thus heat will be absorbed by the system, and the reaction is endothermic. On the other hand, if the enthalpy of the products is less than that of the reactants, H will be negative. In this case the overall decrease in enthalpy is achieved by the generation of heat, and the reaction is exothermic [3]. Energy diagrams for exothermic and endothermic reactions are shown in Figure 9.
Standard enthalpy change

The standard enthalpy change of a reaction refers to the enthalpy change when all the reactants and products are in their standard states. The notation for this thermochemical quantity is rH0 (T) where the subscript r stands for reaction, the superscript o means standard state conditions, and (T) means at temperature T. This type of notation is found for other thermodynamic functions that we meet later on.

22 Thermodynamics Fundamentals and Its Application in Science

Figure 9. Energy diagrams for exothermic (a) and endothermic reactions (b) [20].

(a)

(b)

The standard state of a substance is its most thermodynamically stable state under a pressure of 1 bar (1.00 x 105 Pa) and at a specified temperature, T. Most commonly, T = 298.15 K, and the notation for the standard enthalpy change of a reaction at 298.15K is then rH0 (298.15 K). It is usually sufficient to write rH0 (298 K) [19]. Standard enthalpies of formation The standard enthalpy of formation (Hf0) of a compound is defined as the change in enthalpy that accompanies the formation of one mole of a compound from its elements with all substances in their reference states. The reference state of a element is its most thermodynamically stable state under a pressure of 1 bar (1.00 x 105 Pa) and at a specified temperature, T. A degree symbol on a thermodynamic function, for example, H, indicates that the corresponding process has been carried out under standard conditions. The standard state for a substance is a precisely defined reference state. Because thermodynamic functions often depend on the concentrations (or pressures) of the substances involved, it must be used a common reference state to properly compare the thermodynamic properties of two substances. This is especially important because, for most thermodynamic properties, it can be measured only changes in the property Enthalpy is a state function, so it can be chosen any convenient pathway from reactants to products and then sums the enthalpy changes along the chosen pathway. A convenient pathway, shown in Fig. 10, involves taking the reactants apart to the respective elements in their reference states in reactions (a) and (b) and then forming the products from these elements in reactions (c) and (d). This general pathway will work for any reaction, since atoms are conserved in a chemical reaction [3]. From Fig. 10, it can be seen that reaction (a), where methane is taken apart into its elements,

CH4 g C s 2 H 2 g
is just the reverse of the formation reaction for methane:

(49)

C s 2 H 2 g CH 4 g H 0 f 75 kJ / mol

(50)

A View from the Conservation of Energy to Chemical Thermodynamics 23

Since reversing a reaction means changing the sign of H, but keeping the magnitude the same, H for reaction (a) is H0f, or 75 kJ. Thus H0 (a) = 75 kJ. It can be secondarily considered reaction (b). Here oxygen is already an element in its reference state, so no change is needed. Thus H0 (b) = 0.

Figure 10. In this pathway for the combustion of methane, the reactants are first taken apart in reactions (a) and (b) to form the constituent elements in their reference states, which are then used to assemble the products in reactions (c) and (d) [3].

The next steps, reactions (c) and (d), use the elements formed in reactions (a) and (b) to form the products. That is, reaction (c) is simply the formation reaction for carbon dioxide:
C s O2 g CO2 g H 0 f 394 kJ / mol and H 0( c ) 0 f for CO2 g kJ / mol H 394 Reaction (d) is the formation reaction for water: H 2 g 1 / 2O2 g H 2O l H 0 f 286 kJ / mol (53) (52) (51)

However, since 2 moles of water are required in the balanced equation, it must be formed 2 moles of water from the elements:

2 H2 g O2 g 2 H2O
Thus H 0( d ) H 0 f for H 2O l 286 kJ / 572 kJ / mol 2x 2

(54)

(55)

It has now been completed the pathway from the reactants to the products. The change in enthalpy for the reaction is the sum of the H values (including their signs) for the steps:

24 Thermodynamics Fundamentals and Its Application in Science

H 0 reaction H 0( a) H 0 b H 0( c ) H 0( d )
H 0 for CH g 0 H 0 for CO g 2 x H 0 for H O l ] 4 2 2 f f f 75 kJ 0 394 kJ 572 kJ 891 kJ

(56)

(57)

This process is diagramed in Fig. 11. It can be seen that the reactants are taken apart and converted to elements [not necessary for O2 (g)] that are then used to form products. It can be seen that this is a very exothermic reaction because very little energy is required to convert the reactants to the respective elements but a great deal of energy is released when these elements form the products. This is why this reaction is so useful for producing heat to warm homes and offices. If it is examined carefully the pathway used in this example, it can be understood that first, the reactants were broken down into the elements in their reference states and then the products were then constructed from these elements. This involved formation reactions and thus enthalpies of formation. The entire process can be summarized as follows:

H 0 reaction p H 0 f products p H 0 f

( reactants )

(58)

where, is stoichiometric coefficients for both reactants and products. The enthalpy change for a given reaction can be calculated by subtracting the enthalpies of formation of the reactants from the enthalpies of formation of the products.

Figure 11. A schematic diagram of the energy changes for the reaction CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (l) [3].

Hesss law

Another way to calculate values of H for reactions involves manipulating equations for other reactions with known H values. When chemical equations are added to yield a different chemical equation, the corresponding H values are added to get the H for the desired equation. This principle is called Hesss law and it is an application of the first law of thermodynamic or the conservation of energy. For example, it can be calculated the H for the reaction of carbon with oxygen gas to yield carbon dioxide from the values for the reaction of carbon with oxygen to yield carbon monoxide and that of carbon monoxide plus oxygen to yield carbon dioxide [9].

A View from the Conservation of Energy to Chemical Thermodynamics 25

Desired

C s O2 g CO2 g
Given

(59)

C s 1 / 2 O2 g CO g CO g 1 / 2 O2 g CO2 g
Adding the two chemical equations given:

H 110 kJ H 283 kJ

(60) (61)

C( s) CO( g ) O2( g ) CO2( g ) CO( g )

Eliminating CO from both sides results in the desired equation:

(62)

C s O2 g CO2 g
Therefore, adding these two H values will give the H desired:

(63)

H 110 kJ 283 kJ 393 kJ

(64)

It must be noticed that enthalpies of formation have not been used explicitly in this process [9]. The Hesss law is shown schematically in Fig 12 [3].

Figure 12. A schematic diagram of Hesss law. The same change in enthalpy occurs when nitrogen and oxygen react to form nitrogen dioxide, regardless of whether the reaction occurs in one (red) or two (blue) steps [3].

The overall reaction can be written in one step, where the enthalpy change is represented by H1 [3].

N2 g 2O2 g 2 NO2 g H1 kJ 68

(65)

26 Thermodynamics Fundamentals and Its Application in Science

This reaction also can be carried out in two distinct steps, with enthalpy changes designated by H2 and H3:

N2 g O2 g 2 NO g 2 NO g O2 g 2 NO2 g
Net reaction:

H2 kJ 180 H3 112 kJ

(66) (67)

N2 g 2O2 g 2 NO2 g

H2 H3 68 kJ

(68)

The sum of the two steps gives the net, or overall, reaction and that H1 H 2 H 3 68 kJ
The temperature dependence of reaction enthalpies

(69)

The standard enthalpies of many important reactions have been measured at different temperatures. However, in the absence of this information, standard reaction enthalpies at different temperatures may be calculated from heat capacities and the reaction enthalpy at some other temperature (Fig. 13). In many cases heat capacity data are more accurate than reaction enthalpies. It follows from eqn (dH = CpdT at constant pressure) that, when a substance is heated from T1 to T2, its enthalpy changes from H (T1) to

H T2 H T1 CpdT
T1

T2

(70)

(It has been assumed that no phase transition takes place in the temperature range of interest.) Because this equation applies to each substance in the reaction, the Standard reaction enthalpy changes from H0r (T1) to Hr 0 T2 1 CpdT Hr 0 T
T1 T2

(71)

where Cp is the difference of the molar heat capacities of products and reactants under standard conditions weighted by the stoichiometric coefficients that appear in the chemical equation [12];
C p

C p( Products) C p Reactants

(72)

Equation 71 is known as Kirchhoffs law. It is normally a good approximation to assume that Cpr is independent of the temperature, at least over reasonably limited ranges. Although the individual heat capacities may vary, their difference varies less significantly. In some cases the temperature dependence of heat capacities is taken into account by using equation below.

A View from the Conservation of Energy to Chemical Thermodynamics 27

C p bT c / T 2 a

(73)

Figure 13. An illustration of the content of Kirchhoffs law. When the temperature is increased, the enthalpy of both the products and the reactants increases. In each case, the change in enthalpy depends on the heat capacities of the substances. The change in reaction enthalpy reflects the difference in the changes of the enthalpies [12].

Author details
Ahmet Grses Ataturk University, K.K. Education Faculty, Department of Chemistry, Erzurum, Turkey Mehtap Ejder-Korucu Kafkas University, Faculty of Science and Literature, Department of Chemistry, Kars, Turkey

5. References
[1] Atkins. P., and de Paula. J., Atkns Physical Chemistry. Oxford Universty Press. Seventh Edition. 2002. [2] Petrucci. R. H., Harwood. W. S., Genaral Chemistry Principles and Modern Applications. Sxth Edition. MacMillan Publishing Company. New York. 1993 [3] Zumdahl. S. S and Zumdahl S. A., Chemistry.Houghton Mifflin Company. Seventg Edition. 2007. [4] Svein Stolen and Tor Grande. Chemical Thermodynamics of Materials. 2004. John Wiley & Sons, Ltd ISBN 0 471 492320 2. [5] Levine. I. N., Physical Chemistry. McGRAW-HILL International Edition. Third Edition 1988. [6] McMURRAY. F., Chemistry. Fourth edition. [7] Gilbert. T. R., Kirss. R. V., Foster. N., and Davies. G., Chemistry the science in context. Second edition. 2009. W. W. Norton & Company, Inc.

28 Thermodynamics Fundamentals and Its Application in Science

[8] Lee. H-G., Chemical Thermodynamics for Metals and Materials. Imperial College Press. 1999. [9] Goldberg. D. E., Fundamentals of Chemistry. Fifth edition. The McGraw-Hill. 2007 [10] Powers. J. M., Lecture Notes on Thermodynamics. Notre Dame, Indiana; USA. 2012 [11] Tanaka. T., The Laws of Thermodynamics. Cambridge Universty Press. [12] Atkins. P., and de Paula. J., Atkns Physical Chemistry. Oxford Universty Press 2009. [13] Laider, Keith, J. (1993). The World of Physical Chemistry (http:/ / books. google. com) Oxford University Press. ISBN 0-19-855919-4. [14] International Union of Pure and Applied Chemistry, Physical Chemistry Division. "Quantities, Units and Symbols in Physical Chemistry" (http:/ / old. iupac. org/ publications/ books/ gbook/ gren book). Blackwell Sciences. p. 7. "The adjective specific before the name of an extensive quantity is often used to mean divided by mass." [15] International Bureau of Weights and Measures (2006), The International System of Units (SI) (http:/ / www. bipm. org) (8th ed.), ISBN 92-822-2213-6, [16] Gilbert. T. R., 7.chemistry-the science in context-second edition. 2008. [17] Minguez. J. M., The work-energy theorem and the first law of thermodynamics. International Journal of Mechanical engineering Education 33/1. [18] Silberg. M. S., Principles of General Chemistry. McGraw-Hill Higher Education. 2007. [19] Housecroft. C. E and Constable. E. C., Chemistry: An Introduction to Organic, Inorganic and Physical Chemistry. 3rd Edition. Pearson Prentice Hall. 2006. [20] Jones. A., Clement. M., Higton. A., and Golding. E., Access to Chemistry. Royal Society of Chemistry. 1999. [21] Atkins. P. W., Physical Chemistry. Oxford University Press. Sixth Edition. 1998. [22] Mortimer. R. G., Physical Chemistry. Third edition. Academic Press in an imprint of Elsevier.2008.

Chapter 2

Useful Work and Gibbs Energy

Nikolai Bazhin
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50119

1. Introduction
Devices for performing chemical reactions are widely used to produce heat and work. Heat, in turn, produces work, e.g., in the form of electric energy in the so-called heat engines. It is the well-known fact that the efficiency of heat engines is restricted by Carnot principle. Therefore, it is generally recognized that heat cannot be fully converted to work. The efficiency of electric energy production due to the burning of fossil fuel of various kinds varies from 30 to 50 %. On the other hand, there are galvanic and fuel cells whose efficiency can reach theoretically unity if it implies the ratio between the electric energy produced and the value of a change in Gibbs energy during chemical reactions occurring in a cell. These devices operate at constant temperature and pressure. It is concluded then that the devices, similar to a galvanic cell, cannot work at constant and uniform temperature according to the principle of heat engine. These devices assumed to operate only due to the direct transformation of chemical reaction energy, described by a change in the Gibbs energy, into work [1]. This viewpoint causes, however, numerous contradictions. The goal of this work is to analyze in detail the mechanism of useful work and heat production in chemical systems functioning at constant temperature and pressure.

2. Fundamental functions
In this Section, the fundamental functions of thermodynamics will be characterized, as the fundamental functions play the important role in the description of the process of the energy transformation. This notion includes four functions, i.e., internal energy, enthalpy, Helmholtz energy, and Gibbs energy. All of them are the state functions of energy dimension. It is generally believed that the value with energy dimension describes energy but this is by no means always the case. Below, the fundamental functions will elucidate whether these are energy values or not.
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30 Thermodynamics Fundamentals and Its Application in Science

2.1. Internal energy

According to IUPAC [2], "internal energy U is the quantity the change in which is equal to the sum of heat, q, brought to the system and work, w, performed on it, U q w ". Because of various transformations, the internal energy can be converted to other kinds of energy. However, the initial quantity of internal energy should be conserved due to the law of energy conservation. Conservation is the most important characteristic of energy. Hence U is energy.

2.2. Enthalpy
According to IUPAC, "enthalpy, H =U + pV is the internal energy of a system plus the product of pressure and volume. Its change in a system is equal to the heat, brought to the system at constant pressure [2]. It is worth noting that the change in the value describing energy always corresponds to the change in energy and not only in some special cases. Generally, a change in enthalpy may be inconsistent with the change in real physical values. Let us consider, e.g., the process of ideal gas heating at constant volume. The quantity of heat, taken in by ideal gas from the heat bath, q , equivalently changes only the internal gas q energy, U , and simultaneously causes changes in gas enthalpy, H U pV q . However, this change fails to reflect the changes in any physically significant values. Thus, the enthalpy is not energy but a function of state having the dimension of energy. It is easier and more correct to assume that the enthalpy is the part of a calculating means used to describe thermodynamic processes.

2.3. Helmholtz energy

According to IUPAC, "Helmholtz energy (function), A, is the internal energy minus the product of thermodynamic temperature and entropy: A = U - TS. It was formerly called free energy" [2]. Let us see why this quantity was called free energy. According to the first law [3]
U q w ,

(1)

where q is the heat, entering the system, and w is the total work performed on the system by the surroundings. Usually, the total work is given as the sum of two terms: expansion work ( pV ) and so-called useful work ( wuseful ) w pV wuseful . (2)

If the process occurs at constant volume, the expansion work is absent and w describes the useful work. In the case of reversible process [3]
q T S.

(3)

Thus, eq. (1) is of the form in the case of reversible process

Useful Work and Gibbs Energy 31

wuseful U T S (U TS) A ,

(4)

where A is the change in Helmholtz energy at constant temperature and volume. Since the term "energy" means the capacity of the system to perform work, from eq. (4) it is formally concluded that A is the energy (but in this case eq. (4) can have the second explanation A is the numerical characteristic of work and not the work itself). Further, from eq. (4) it was concluded that only the part of internal energy U minus TS can be used to produce work. Therefore, the TS quantity was called "bound energy" and (U - TS) "free energy". The meaning of these notions will be considered in more detail using the Gibbs energy as an example because it is more often used in chemical applications.

2.4. Gibbs energy

G According to IUPAC [2], "Gibbs energy (function), ( H TS) , is the enthalpy minus the product of thermodynamic temperature and entropy. It was formerly called free energy or free enthalpy". The reasons for the appearance of the term "Gibbs energy" are similar to those discussed when considering the Helmholtz energy except for the fact that the Gibbs energy describes the reversible useful work performed at constant temperature and pressure. This is readily observed by substituting eq. (3) and eq. (2) into eq. (1) with regard 0 to V p

wuseful H T S ( H TS) G ,

(5)

where G is the change in Gibbs energy at constant temperature and pressure in the reversible process. Unfortunately, the word "energy" as defined by IUPAC for a Gibbs energy (and also for a Helmholtz energy), causes great confusion. The Gibbs energy G = H TS consists of two terms, the enthalpy and the entropy one. The origin of both of the terms is quite different despite the same dimension. The enthalpy, considered above, is not energy. Consider now the problem of TS nature. In the case of the reversible process T S , but in q the case of the irreversible process T S q and additional contributions to T S can arise without change in energy. For example, it is well known the increase of the entropy in the process of ideal gas expansion in vacuum without heat consumption (q = 0). Let us consider another example. Let the ideal gas-phase system involves a spontaneous process of the monomolecular transformation of substance A into B. As suggested a change in enthalpy tends to zero in this reaction. Thus, the internal energy, temperature, pressure, and volume will not undergo changes in this process. However, the entropy will increase due to the entropy of the mixing, because the entropy is a function of state. The value of the TS product will increase accordingly. However, the energy and even the bound energy cannot arise from nothing, whereas the entropy, being a function of state, can increase thus reflecting a change in system state without any changes in the internal system energy. Therefore, the TS term is not the energy, which also implies the absence of the term "bound" energy.

32 Thermodynamics Fundamentals and Its Application in Science

Since neither enthalpy nor TS are the energy quantities, the difference between them cannot represent energy. Thus, G cannot represent energy precisely in terms of this notion. Note that in the irreversible process, occurring at constant temperature and pressure, the Gibbs energy decreases and thus, is not conserved. This is readily demonstrated by e.g., the aforementioned example of a monomolecular transformation of substance A into B. Thus, conservation, as the most important criterion for energy quantity, fails for the Gibbs energy. It is concluded then that the Gibbs energy is not energy [4] but a function of state. In this regard, the Gibbs energy does not differ from heat capacity. The notions of the non-existing in reality quantities of free energy" and "bound energy" cause only confusion and are, at present, obsolete [5]. Nevertheless, the notions that the Gibbs energy is the energy and thus, obeys conservation laws, prove to be long-lived, which causes erroneous interpretation of a number of processes some of which are of paramount importance. Let us consider now the reaction of adenosine triphosphate (ATP) hydrolysis in water solution which is of great concern in biochemistry ATP + H2O = ADP + Pi. Under the standard conditions [6] rG o 7, r H o 4 kcalmol-1. According to D. Haynie [6, p. 143], "measurement of the enthalpy change of ATP hydrolysis shows that H o 4 kcalmol-1. That is, the hydrolysis of one mole of ATP at 25 results in about 4 kcalmol-1 being transferred to a solution in the form of heat and about 3 kcalmol-1 remaining with ATP and Pi in the form of increased random motion." The heat of 4 kcalmol-1 is actually released into solution due to hydrolysis. Unfortunately, it is then assumed that the Gibbs energy is conserved which makes his difference in r H o and rG o of 3 calmol-1 be located on the degrees of freedom of product molecules. However, in this connection, the product molecules could appear in the non-equilibrium excited states and transfer this energy to solvent molecules which would result in the emission of 7 kcalmol-1 rather than 4 kcalmol-1 which contradicts the experiment. There are no additional 3 calmol-1 on the degrees of freedom of A and Pi because the Gibbs energy is not conserved.

2.5. Conclusions
Thus, among the four quantities, that claims to be called energy quantity, only the internal energy deserves this name. The other functions, i.e., enthalpy , Helmholtz energy A, and Gibbs energy G are the parts of a mathematical apparatus for calculating various quantities, such as useful work, equilibrium constants, etc. This also means that the useful work is only calculated by using functions A and G, but cannot arise from the change in either the Helmholtz or the Gibbs energy. The physical nature of the work performed should be considered separately. Since the Helmholtz energy and the Gibbs energy are not energies, then, to avoid misunderstanding, it is better to exclude the word energy from the name of corresponding functions and to use the second variant of the name of these functions according to IUPAC: a Helmholtz function and a Gibbs function [7].

Useful Work and Gibbs Energy 33

3. Direct conversion of chemical reaction energy to useful work

This Section is devoted to the discussion of the generally accepted theory of the direct conversion of energy [1, 8] produced by chemical reaction to useful work. For simplicity, hereafter exergonic ( rG 0) and exothermic ( r H 0) reactions will be considered. The useful work of the chemical reaction occurring at constant temperature and pressure in the reversible conditions can be calculated through the change in the Gibbs function (5). When the interest is the useful work performed by the system in the environment ( wuseful ) , then wuseful r H T rS rG. (6)

From eq. (6) it follows formally that the useful work of the reversible system in the environment is the sum of the enthalpy member ( r H ) and the entropy member T rS . In this connection it is interesting to discuss the various situations which arise in dependence on the relation between ( r H ) and T rS . From eq. (6) it follows, that for rS 0 the useful work in the environment exceeds ( r H ) : wuseful r H . Therefore, the system must drag the thermal energy from the environment in the volume T rS to perform useful work. What is the physical reason for thermal energy consumption? Why does the system consume thermal energy of volume T rS neither more or less? How can two different contributions produce the same useful work? The second case of rS 0 is also of interest. In this case wuseful r H and the system must evolve the part of reaction heat to the environment. Why cannot the system use the total reaction heat for useful work production if this energy is at its disposal? Why can the system transfer energy of volume T rS and neither more or less to the environment? The third case is r H 0 . Here the system can use only the thermal energy of the environment to produce useful work. In the fourth case rS 0 and the system performs work formally due to the reaction heat ( r H ) without exchanging thermal energy with the environment. But it is not the case. As mentioned in the Introduction, at present, it is generally accepted that the high efficiency of reversible devices is inconsistent with the notions that heat can be used to produce work and that such devices realize the direct conversion of chemical system energy into work. But below it will be shown that in all the cases, the useful work results from the heat of volume rG dragged from the environment.

4. A mechanism of useful work production - A Vant Hoff Equilibrium Box

In this Section, it will demonstrate the mechanism of producing useful reversible work which involves no notions of the direct conversion of reaction energy into useful work. To this end, let us consider a Vant Hoff equilibrium box (VHEB) [9 11]. A thermodynamic

34 Thermodynamics Fundamentals and Its Application in Science

system must provide realization of the reversible process. This means that all changes in the system are infinitely slow at infinitely minor deviation from equilibrium. It is assumed that in the system the following reaction occurs

i Ai j Bj ,
i j

(7)

where A i are the reagents and B j are the products. The reaction takes place in the reactor (Fig. 1) where the reagents and products are in equilibrium. The chemical process is afforded by reservoirs with reagents and products contained in the system. For simplicity, the reagents and products are assumed to be in standard states. The system should have instruments to transport both the reagents from standard vessels to reactor and the products from reactor to standard vessels. In addition, the system should have tools to perform work, because the reversible process must be followed by reversible work production. The instruments and tools for performing work can be used together. The reactor, transporting instruments, and tools for performing work can be placed either separately or together. To provide constant and uniform temperature, it is necessary to locate the system, including reactor, standard vessels, transporting instruments, and tools in a thermostat, which can also imply the environment of constant temperature.

Figure 1. Production of useful work and heat in a closed reversible system. Ast (Bst) indicate the reagents Ai (products Bj) in the standard states; Aeq (Beq) indicate the reagents Ai (products Bj) in the equilibrium states, which correspond to the equilibrium at the reactor; the green figures in circles indicate the step numbers (see text)

Useful Work and Gibbs Energy 35

Let us consider reversible chemical process in a closed system (Fig. 1). The realization of the reversible chemical process consists in reversible transformation of the reagents to products via chemical reaction. Let us consider the closed system.

4.1. Closed system

The process of reversible work production includes six stages. Step 1. A small amount of substance Ai is removed from the vessel with reagent Ai in the standard state upon reversible process. Gaseous substances can be removed from a standard vessel and put into a portable cylinder with pistons [11]; solid or liquid substances are placed in lock chambers. Then, the change in the Gibbs function and the work are zero ( G1i 0, w1i 0) because a minor portion of substance Ai is in the same standard state as the residual reagent. Step 2. Reagent Ai is transformed reversibly from the standard into the equilibrium state in the reactor. For example, for ideal gas, the gas pressure will vary from a standard value to the equilibrium partial value in the reactor. In this stage, the reversible work w2 i is produced and G2 i 0 . The work w2 i can be done only due to thermostat heat because there are no other energy sources in the system (reaction is in the equilibrium). This work depends on the difference in the physical states of reagent Ai in the initial and equilibrium states. All reagents Ai participate in all stages in quantities proportional to i . For ideal gas, the useful work is
w2 i i RT ln( pi ,eq / pi ,st ),

(8)

where pi ,eq is the equilibrium pressure of i-th gas in the reactor, and pi ,st is the pressure of i-th gas in a standard vessel. For gaseous components, e.g., the process of reversible gas expansion (compression) in a portable cylinder for producing the maximum useful work, must proceed to the value pi ,eq . If expansion (compression) stops at pi pi ,eq , then the inlet of gas into the reactor causes irreversible gas expansion and thus, the useful work will be less than the maximum one. When due to expansion (compression) the final pressure is less than pi ,eq , then the inlet of gas into the reactor causes the irreversible inlet of the i-th gas from an equilibrium mixture in the reactor to the portable cylinder, which also leads to a decrease in useful work. The solid and liquid substances can be transported by lock chambers. The pressure above either solid or liquid substances is varied from 1 bar to the value of the total equilibrium pressure in the reactor. The pressure is created using a minor portion of equilibrium reaction mixture.

w2 i . The thermostat enthalpy varies as follows: H 2 i ,thermostat

Step 3. Reagent Ai is reversibly introduced into the reactor. Gaseous components are introduced into the reactor through semipermeable membranes using portable cylinders G3i [11]; the solid or liquid ones by means of lock chambers. Hence, 0, w3i 0 .

36 Thermodynamics Fundamentals and Its Application in Science

The useful work production and the change in thermostat enthalpy ( H 2,thermostat ) take place only at step 2:

w2 H 2,thermostat ,

(9)

where w2 w2i and H 2,thermostat ,thermostat . H2i

i i

The same procedure is used to bring products from the standard vessels to reactor.
Step 4. An equivalent amount of product BJ is reversibly removed from the reactor. After this step is G4 0, w4 0 . j j Step 5. Product BJ, removed from the reactor, is reversibly transformed from the equilibrium state into the standard one to perform work w5 j . The change in the Gibbs function is not zero, G5 j 0 . The change in the thermostat enthalpy is H 5 j ,thermostat w5 j . Step 6. Product BJ, removed from the reactor, is reversibly introduced into the standard vessel. In this case is G6 j 0 and w6 j 0 .

The change in the thermostat enthalpy upon thermal energy conversion into useful work at step 5 is
w5 H 5,thermostat ,

(10)

where and w5 w5 j , H 5,thermostat ,thermostat H5 j

j j

The change in the thermostat enthalpy at the second and fifth steps obeys the equation
H 2,thermostat H 5,thermostat Qdragged ,

(11)

where Qdragged is the heat dragged by tools. For the reversible process, the maximal useful work is numerically equal to rG , eq. (5) and, hence, the heat dragged by tools from thermostat in the volume
wuseful w2 w5 rG r H T rS Qdragged .

(12)

The process has resulted in the useful work of the reaction, rG , but the reaction did not occur yet. To put it otherwise, reaction work was performed without reaction. Only the thermal energy of the thermostat (environment) may be the source of work. This means that the process of useful work production and the reaction itself may be temporally and spatially separated. Thus, eq. (6) numerically connects reaction parameters and the magnitude of the work. However, no reaction energy is needed to produce the work. There is no need to subdivide energy sources into reaction source ( r H ) and thermal T rS , because there is only one energy source: the thermal energy of thermostat (environment).

Useful Work and Gibbs Energy 37

For ( rS 0) , the thermal energy dragged by the tools exceeds r H , (Qdragged r H ) ; in the case of ( rS 0) , the dragged thermal energy is less than r H (Qdragged r H ) ; in 0) the case of ( rS the energy extracted is equal to r H (Qdragged r H ) and for ( r H the dragged thermal energy is of volume T rS (Qdragged T rS) . The volume of 0) extracted thermal energy is controlled by chemical equilibrium via rG . Thus, the mixture in the reactor is moved off balance to be restored later. As a result, the reaction heat is emitted into the thermostat. Indeed, because of the elementary chemical act in the reactor, the energy released concentrates at the degrees of freedom of the product molecules. As the reactor temperature is constant, this energy is dissipated in the reactor and transferred to the thermostat which causes a r H change in thermostat enthalpy. The total change in thermostat enthalpy is
H thermostat w2 w5 r H .

(13)

The cycle is over. Equations (12, 13) can be used to calculate the total change in thermostat enthalpy
H thermostat rG r H T rS.

(14)

The change in thermostat enthalpy is controlled only by reaction entropy [11].

4.2. The main principles of reversible device functioning in useful work production
This consideration demonstrates the main characteristics of the reversible process of useful work production at constant temperature and pressure in closed systems: 1. 2. 3. 4. 5. The useful work arises from the stage of the reversible transport of reagents from reservoir to reactor and from the stage of the reversible transport of products from the reactor. The only energy source of useful work is the thermal energy of thermostat (or environment). The heat released by chemical reactions is dissipated to the thermostat; the reaction heat is infinitely small in comparison with the volume of the thermostat thermal energy; therefore no reaction heat is really needed to produce work. Although the useful work is produced by the cooling of one body (thermostat), the second law of thermodynamics is not violated, because the process is followed by a change in the amount of reagents and products. The useful work is produced by heat exchange with thermostat (environment) according to the scheme reaction heat thermal thermostat energy useful work 6. 7. (scheme I)

The maximal useful work is equal the heat dragged by tools from thermostat. Useful work depends on the difference in the concentrations of standard and equilibrium states of reagents and products. Therefore, the amount of extracted energy can be calculated via the change in the Gibbs function.

38 Thermodynamics Fundamentals and Its Application in Science

8.

There is no direct conversion of the Gibbs energy into useful work. Gibbs energy is equal numerically the thermal energy dragged by systems from the environment for doing work.

4.3. The energy limit of chemical reactions - Open systems

Usually, the total energy which can be produced by chemical system, is r H . However, this holds for closed systems only. For open systems, the case is quite different [11]. The open system is depicted in Fig. 2. As compared with the closed one (Fig. 1), the open system consists of two thermostats: the first one contains a reactor and the second one contains standard vessels with substances A and B and tools. The second thermostat can be replaced by the environment. In the process, steps 1, 2, 5, and 6 occur in the second thermostat (environment); steps 3 and 4 take place in the first one. Thus, the heat is released in the first thermostat only and the work is performed by thermal energy of the second thermostat (environment). The processes of heat and work production are spatially separated! The energy potential of the open system obeys the equation
q wuseful r H rG

(15)

Figure 2. Production of useful work and heat in the open reversible system. The designations see in the subscription to Fig. 1

In the case of coal burning, it is possible to obtain the double total energy [11]. Thus, understanding the mechanism of useful work production in the reversible process allows us to predict an increase in the energy potential of chemical reactions in the open system.

Useful Work and Gibbs Energy 39

It is worth noting that the open system under study is not a heat pump. The heat pump consumes energy to transfer heat from a cold body to the warm one. The open system studied does not consume external energy and produces heat due to chemical reactions in one thermostat and performs work by extraction of thermal energy from the second one.

4.4. Conclusions
The chemical reaction heat is always released in the reversible chemical processes and passes to the environment independent of the fact whether the system produces work or not, whether it is closed or open. The discussed mechanism of useful work production in the reversible systems did not use such notions as "free energy", "bound energy", "direct Gibbs energy conversion". The useful work arises only due to the heat exchange with a thermal basin in the process, described by the scheme I. The total energy of chemical system can be high and equal to r H rG .

5. The mechanism of electric work production in a galvanic cell

The current theory of galvanic cells [1, 3, 8] is based on a direct transformation of the energy ( rG ) of oxidation-reduction reactions into electric work. However, using VHEB as an example, It is clear that the energy of chemical reactions is first converted into the thermal energy of thermostat (environment) and then the thermal energy is extracted from the thermostat and transformed into work by means of special devices. It is assumed then that in galvanic cells, useful work is produced via the mechanism similar to the VHEB one [12, 13]. The rG value is used to calculate electric work which does not, however, mean that the electric work is performed at the expense of the Gibbs energy, all the more it was shown that the Gibbs energy is not energy. The electric work of a galvanic cell results from the electrodes discharged. Electric charging of electrodes is caused by chemical reactions in electrodes. The mechanism of electric energy production in galvanic cells will be solved by analyzing the behavior of one ion. But it does not denote that thermodynamics will be applied to a real single ion: thermodynamic parameters of one ion imply the averaged parameters of many ions.

5.1. A galvanic cell

For simplicity a Daniell cell will be considered, consisting of zinc (1) and copper (2) electrodes (Fig. 3). The activity of salts in solutions is denoted by 1 and 2 , respectively. Let the cell with an open, external circuit be in equilibrium. Close now the external circuit for the moment and two electrons will transfer from the zinc to the copper electrode. The balance of the cell is distorted. Consider now the establishment of equilibrium on the zinc electrode (Fig 3). To this end, the zinc ion must leave a metallic plate and escape into the bulk. The dissolving of zinc ions is described by the change in a Gibbs function
rG1 1 RT ln a1 , rG o

(16)

40 Thermodynamics Fundamentals and Its Application in Science

o where rG1 is a standard change in the Gibbs function upon dissolving. The ion penetrates further into solution with execution of the work ( w1g ) in the electric field

w1 nF sol 1 , g Met1

(17)

where n is the number of electrons, participating in the reactions, F is the Faraday constant, and sol 1 is the difference in potentials of solution and metal. The work described in Met1 equation (17), is the electric work spent to charge an electrode. It is performed at the extraction of the thermal energy of solution due to the absence of other energy sources in the system. Since in equilibrium, the chemical potential of ions in solution equals the chemical potential of metal, it is possible to derive the equation for electrochemical equilibrium
o rG1 RT ln a1 nF sol 1 0, Met1

(18)

which readily gives the expression for both the work performed on the first electrode and its galvanic potential [3]
o w1g nF sol 1 rG1 RT ln a1 , Met1

(19)
(20)

G o RT ln a1 sol 1 1 r . Met1 nF nF

The latter is the potential for a half-cell. Thus, the approach, based on the consideration of the behavior of one ion, provides a common expression for electrode potential.

Figure 3. Establishment of equilibrium on the electrodes

Useful Work and Gibbs Energy 41

The change in electrode enthalpy involves dissolution enthalpy and thermal energy consumption upon ion transport into solution. The equation for dissolution enthalpy is readily obtained from eq. (16)
r H1 1 RT 2 r H o ln a1 , T

(21)

o where r H1 is a standard change in enthalpy during ion dissolving. The total change in the enthalpy of the first electrode ( H1,thermostat ) is the sum of the expressions r H1 and wg1 o H1,thermostat r H1 wg1 T rS1 RT ln a1 RT 2

ln a1 T rS1 , T

(22)

o where rS1 is a standard change in entropy upon ion dissolving and rS1 is the change in entropy upon ion dissolving on the first electrode which amounts to

rS1 S1 R ln a1 RT r o

ln a1 . T

(23)

As follows from eq. (22), the change in enthalpy, related to the first electrode, is independent of the processes, occurring on the second one. Therefore, studying either release or absorption of heat on a separate electrode, one may calculate the change in entropy due to the escape of the ions of the same type into the bulk. A corresponding expression for the second electrode is of the same form but index "1" should be substituted by index "2":
rG2 2 RT ln a2 , rG o
sol o w2 g nF Met22 rG2 RT ln a2

(24)

(25) (26)

G o RT ln a2 sol 2 2 r . Met2 nF nF
r H 2 2 RT 2 r H o ln a2 , T

(27)

rS2 S2 R ln a2 RT r o

ln a2 , T
ln a2 T rS2 . T

(28) (29)

o H 2,thermostat r H 2 w2 g T rS2 RT ln a2 RT 2

In the operation of the galvanic cell, the processes on the second electrode are oppositely directed which should be taken into account in consideration of the thermodynamic cell parameters.

42 Thermodynamics Fundamentals and Its Application in Science

Equations (20) and (26) allow to get the Nernst equation for the potential of the cell [3]
sol E sol 2 Met11 Met2 o o where E the cell potential, rG o rG1 rG2 .

rG o RT a1 ln , nF nF a2

(30)

The electric work of the galvanic cell ( wel ) results from the transformation of the potential energy of the charged electrodes into electric energy. The potential energy arises from the thermal energy of both of the electrodes upon ions transport into solution and equals

wel w1g w2 g rG o RT ln The change in thermostat enthalpy is of the form

a1 wuseful . a2

(31)

H thermostat H1,thermostat H 2,thermostat T rS ,

(32)

which is in fair agreement with similar expression, described by eq. (14), for the VHEB. The detailed equation for H thermostat can be get after substitution corresponding expressions (22) and (29) into (32)
o o H thermostat T ( rS1 rS2 ) RT ln( a2 / a1 ) RT 2 (

ln a2 ln a1 ). T T

(33)

The sum of eqs. (31) and (33) gives the total energy (electric work + heat), produced by the galvanic cell

wel Hthermostat r H o RT 2 (

ln a2 ln a1 ). T T

(34)

From eq.(34) it follows that the total energy produced by the galvanic cell is equal to the heat emitted by oxidation-reduction reaction. Thus, the approach, based on the analysis of the behavior of one ion gives the same results as the present-day theory. However, it uses not a mysterious, direct transformation of the chemical energy ( rG ) into electric work, but the concept of chemical energy conversion into the thermal one, and then, the thermal energy of thermostat (environment) is converted into the potential energy of charged electrodes [12, 13]. The electric energy of the galvanic cell arises according to the scheme: reaction heat thermal thermostat energy potential energy of charged electrodes electric energy. Thus, in various systems with uniform temperature, useful work is produced by the same mechanism through the exchange of thermal energy with thermostat (environment). No direct conversion of chemical energy into useful work is observed. Unfortunately, in the

Useful Work and Gibbs Energy 43

galvanic cell, the processes of heat release and useful work production cannot be spatially separated, because both of them occur in a double layer. Therefore, galvanic cells are unpromising in production of a double amount of energy.

5.2. A concentration cell

Consider now a concentration cell, consisting of two electrodes, e.g., the zinc ones of different solution activity. Standard changes in the Gibbs function, enthalpy, and entropy for the concentration cell tend to zero due to the same chemical nature of both of the electrodes. By definition, it has been considered that a2 a1 . From eq. (31) it follows wel RT ln( a2 / a1 ) wuseful , (35)

which is a usual expression for the electric energy of the concentration cell. From eq. (34) it follows

wel Hthermostat RT 2 (

ln a2 ln a1 ). T T

(36)

For the system in which the activities are temperature-independent, the electric energy arises from the thermal thermostat energy (environment)
wel H thermostat wuseful ,

(37)

which is in fair agreement with conventional concepts.

6. Useful work of the systems with concentration gradient

An ideal system with concentration gradient has no potential energy because the mixing does not result in heat release and H 0 . Nevertheless, the system with concentration gradient can be used, as any non-equilibrium system, to produce useful work if this system is supplied with special tools for extracting heat from the environment with a simultaneous transformation of the extracted thermal energy into work upon the system approaches to the equilibrium. The volume of useful work is equal to the volume of the heat extracted from the environment
wuseful H thermostat

(38)

The useful work of the system with a concentration gradient wuseful obeys expressions (35) and (38). The concentration cell is a good example of such a system.

7. General conclusions
Any non-equilibrium state can serve as an energy source. The thermostat (environment) is an active participant of the process of reversible useful work production in devices operating at constant temperature. The heat released by chemical reactions, always

44 Thermodynamics Fundamentals and Its Application in Science

dissipates in the thermostat (environment). The useful work is produced by special tools that provide the extraction of the thermal energy of the thermostat (environment) and the transformation of thermal energy into work at the process of the restoration of the chemical equilibrium. The volume of the useful work is equal, in reversible conditions, to the change in Gibbs function. A spatial separation of reactor and tools can lead to a substantial increase in the energy produced. The direct conversion of the Gibbs energy into useful work does not exist. The concepts of free and bound energy become unnecessary.

Author details
Nikolai Bazhin Institute of Chemical Kinetics and Combustion, Novosibirsk State University, Institutskaya 3, Novosibirsk, Russia

8. References
[1] Denbigh K (1971) The Principles of Chemical Equilibrium, 3rd ed., The University Press: Cambridge, 494 p. [2] IUPAC Green Book (1996) Quantities, Units and Symbols in Physical Chemistry 48 p. [3] Atkins P (2001) The Elements of Physical Chemistry, 3rd ed., Oxford University Press, Oxford,.549 p. [4] Lower S. (2010) Chemistry. Available http://www.chem1.com/acad/webtext/ virtualtextbook.html [5] Gokcen NA, Reddy RG (1996) Thermodynamics, Second edition, Springer, 416 p. [6] Haynie DN (2008), Biological Thermodynamics, 2nd ed., Cambridge University Press, 422 p. [7] Haywood RW (1980) Equilibrium Thermodynamics for Engineers and Scientists, J. Wiley, N.Y., 456 p. [8] Adam NK (1956) Physical Chemistry, Oxford, Clarendon Press, 658 p. [9] Physical Chemistry (1980) Gerasimov YaI, Ed., Chimiya, oscow (in Russian), 1279 p. [10] Steiner LE (1948) Introduction to Chemical Thermodynamic, 2nd ed.; McGraw-Hill Book Company, New York, 516 p. [11] Bazhin NM, Parmon VN (2007) Conversion of the Chemical Reaction Energy into Useful Work in the Vant Hoff Equilibrium Box. J. Chem. Ed. 84: 1053 1055 [12] Bazhin NM, Parmon VN (2007) Ways of Energy Conversion in Electrochemical Cells. Doklady Physical Chemistry 417: 335-336 [13] Bazhin NM (2011) Mechanism of electric energy production in galvanic and concentration cells. J. Eng. Thermophysics 20: 302-307

Section 2

Statistical Thermodynamics

Chapter 3 Chapter 0

Gibbs Free Energy Formula for Protein Folding

Yi Fang
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/52410

1. Introduction
Proteins are lifes working horses and natures robots. They participate in every life process. They form supporting structures of cell, bre, tissue, and organs; they are catalysts, speed up various life critical chemical reactions; they transfer signals so that we can see, hear, and smell; they protect us against intruders such as bacteria and virus; they regulate life cycles to keep that everything is in order; etc., just mention only a few of their functions. The rst thing drawing our attention of proteins are their size. Proteins are macromolecules, that is, large molecules. Non-organic molecules usually are small, consisting of from a couple of atoms to a couple of dozen atoms. A small protein will have thousands of atoms, large ones have over ten thousand atoms. With their huge number of atoms, one can imaging that how complicated should be of a protein molecule. Fortunately, there are some regularities in these huge molecules, i.e., proteins are polymers building up by monomers or smaller building blocks. The monomers of proteins are amino acids, life employs 20 different amino acids to form proteins. In cell, a series of amino acids joined one by one into amino acids sequences. The order and length of this amino acid sequence is translated from DNA sequences by the universal genetic code. The bond joining one amino acid to the next one in sequence is peptide bond (a covalent bond) with quite regular specic geometric pattern. Thus amino acids sequences are also called peptide chains. But the easy translation and geometric regularities stop here. The peptide chain has everything required to a molecule, all covalent bonds are correctly formed. But to perform a proteins biological function, the peptide chain has to form a specic shape, called the proteins native structure. Only in this native structure a protein performs its biological function. Proteins fall to wrong shapes not only will not perform its function, but also will cause disasters. Many disease are known to be caused by some proteins taking wrong structure. How the peptide chain take its native structure? Is there another genetic code to guide the process of taking to the native structure? In fact, at this stage, lifes most remarkable drama
2012 Fang, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

48 2 Thermodynamics Fundamentals and Its Application in Science

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takes stage. Once synthesized, the peptide chain of a protein spontaneously (some need the help of other proteins and molecules) fold to its native structure. This process is called protein folding. At this stage, everything is governed by simple but fundamental physical laws. The protein folding problem then can be roughly divided into three aspects: 1. folding process: such that how fast a peptide chain folds, what are the intermediate structures between the initial shape and the native structure. 2. the mechanics of the folding, such as what is the deriving force. 3. the most direct application to biological study is the prediction of the native structure of a protein from its peptide chain. All three parts of the protein folding problem can have a unied treatment: writing down the Gibbs free energy formula G (X) for any conformation X = (x1 , , xi , , x M ) R3M of protein, where xi R3 is the atom ai s atomic center. The fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure of the protein has the minimum Gibbs free energy among all possible conformations as stated in Annsen (1973). Let X be a conformation of a protein, is there a natural Gibbs free energy function G (X)? The answer must be positive, as G. N. Lewis said in 1933: There can be no doubt but that in quantum mechanics one has the complete solution to the problems of chemistry." (quoted from Bader (1990), page 130.) Protein folding is a problem in biochemistry, why such a formula G (X) has not been found and what is the formula? This chapter is trying to give the answers. First, the Gibbs free energy formula is given, it has two versions, the chemical balance version (1) and the geometric version (2).

1.1. The formula

Atoms in a protein are classied into classes Hi , 1 i H, according to their levels of hydrophobicity. The formula has two versions, the chemical balance version is: G (X) = e Ne (X) + i Ni (X),
i =1 H

(1)

where Ne (X) is the mean number of electrons in the space included by the rst hydration shell of X, e is its chemical potential. Ni (X) is the mean number of water molecules in the rst hydration layer that directly contact to the atoms in Hi , i is the chemical potential. Let MX (see F IGURE 3) be the molecular surface for the conformation X, dening MX i MX as the set of points in MX that are closer to atoms in Hi than to any atoms in Hj , j = i. Then the geometric version of G (X) is: G (X) = e e V (X ) + dw e e A( MX ) + i i A( MXi ),
i =1 H

e , i > 0,

(2)

where V (X ) is the volume of the domain X enclosed by MX , dw the diameter of a water molecule, and A( MX ) and A( MXi ) the areas of MX and MXi , e [V (X ) + dw A( MX )] = Ne , i A( MXi ) = Ni (X), 1 i H. The e and i are independent of X, they are the average numbers of particles per unit volume and area.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 49 3

Before the actual derivation is given, some basic facts should be stated, such as hydrophobicity, protein structures, and the environment in which the protein folds. Brief description of the methods in the experimental measurements and theoretical derivation of the Gibbs free energy of the protein folding is introduced to give the motivation and idea of the derivation. By making critics on the previous derivation, the necessary concepts would be claried, what are important in the derivation would be identied, and would set the thermodynamic system that most t the reality currently known about the protein folding process. Then both classical and quantum statistical derivations were given, the only difference is that in the classical statistically derived formula, the volume and the whole surface area terms in formula (2) are missing. Thus it is that only quantum statistical method gives us the volume and whole surface terms in formula (2). After the derivations, some remarks are made. A direct application of the Gibbs free energy formula (2) is the ab initio prediction of proteins natives structures. Gradient formulas of G (X) are given to be able to apply the Newtons fastest descending method. Finally, it should be emphasized that the gradient G (X) not only can be used to predict the native structure, it is actually the force that forces the proteins to fold as stated in Ben-Naim (2012). In Appendix, integrated gradient formulas of G (X) on the molecular surface are given.

2. Proteins
2.1. Amino acids
There are 20 different amino acids that appear in natural proteins. All amino acids have a common part, or the back bone consisting of 9 atoms in F IGURE 1 (except the R). NH2 is the amino group and COOH is the carboxyl group of the back bone. Single amino acid is in polar state, so the amino group gains one more hydrogen from the carboxyl group, or perhaps the amino group losses one electron to the carboxyl group. Geometrically it is irrelevant since after forming peptide bonds the amino group will loss one H to become NH and the carboxyl group will loss one OH to become CO. Thus an amino acid in the sequence is also called a residue. H H \ | N C / | H R
Figure 1. An generic amino acid.

O || C | O H

The group R in F IGURE 1 is called side chain, it distinguishes the 20 different amino acids. A side chain can be as small as a single hydrogen atom as in Glycine, or as large as consisting of 18 atoms including two rings as in Tryptophan. 15 amino acids have side chains that contain more than 7 atoms, i.e., more atoms than that of the back bone in an amino acid sequence. Except Glycine, a C carbon in a side chain forms a covalent bond with the central carbon C of the back bone.

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2.2. Hydrogen bonds

A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom (the accepter), like nitrogen, oxygen or uorine (thus the name hydrogen bond", which must not be confused with a covalent bond to hydrogen). The hydrogen must be covalently bonded to another electronegative atom (forming a donor group) to create the hydrogen bond. These bonds can occur between molecules (intermolecular), or within different parts of a single molecule (intramolecular). The hydrogen bond is stronger than the van der Waals interaction, but weaker than covalent or ionic bond. Hydrogen bond occurs in both inorganic molecules such as water and organic molecules such as DNA, RNA, and proteins. Some amino acids side chains contain hydrogen bond donors or acceptors that can form hydrogen bond with either other side chains in the same protein (intramolecular hydrogen bond) or with surrounding water molecules (inter-molecular hydrogen bond). Those amino acids whose side chains do not contain either donors or acceptors of hydrogen bond are classied as hydrophobic.

2.3. Hydrophobicity levels

Every atom in a protein belongs to a moiety or atom group, according to the moietys level of ability to form hydrogen bond, the atom is assigned a hydrophobicity level. All the hydrophobicity scales are tested or theorized in some aspects of individual amino acid, either as a independent molecule or as a residue in a protein, in various environments such as solvent, PH value, temperature, pressure, etc. That is just like taking a snap shot of an object with complicated shape. All snap shots are different if taking from different angles of view. Therefore, there are many different classications of hydrophobicity, for example, in Eisenberg and McLachlan (1986) there are ve classes, C, O/N, O , N+ , S. Let a protein have M atoms {a1 , , ai , , a M }. One can assume that there are H hydrophobic classes, such that {a1 , , ai , , a M } = iH 1 Hi . =

2.4. Protein structures

Let a molecule have M atoms, listed as (a1 , , ai , , a M ). A presentation of a structure X of this molecule is a series atomic centers (nuclear centers) of the atoms ai , xi R3 . Hence it can be written as a point in R3M , X = (x1 , , xi , , x M ). The space R3M then is called the control space. The real shape of the structure X is realized in R3 , called the behavior space as dened in Bader (1990), it is a bunch of overlapping balls (spheres), PX = iM 1 B(xi , ri ), where ri is the = van der Waals radius of the atom ai and B(x, r ) is the closed ball {y : |y x| r } R3 , of center x and radius r. Protein native structures are complicated. Unlike the famous double-helix structure of DNA structure, the only general pattern for protein structure is no pattern at all. To study the native structures of proteins people divide the structures in different levels and make structure classications. The amino acid sequence of a protein is called its primary structure. Regular patterns of local (along the sequences) structures such as helix, strand, and turn are called the secondary structure which contain many intramolecular hydrogen bonds in regular patterns. The global

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 51 5

assembly of these secondary structures, connected by turns and irregular loops, is called the tertiary structure. For proteins having multiple amino acid sequences or structurally associated with other molecules there are also quaternary structures, see Branden and Tooze (1999) and Finkelstein and Ptitsyn (2002). The secondary structures are local structures, they are usually in helix, strand, and turn. A common feature of them is that they have regular geometric arrangement of their main chain atoms, such that there are good opportunities to form hydrogen bonds between different residues. Several strands may form sheet, stabilized by regular pattern of hydrogen bonds. Turns and loops are necessary for the extended long chain to transfer to a sphere like shape. Turns are short, 3 or 4 residues long. Loops involves many residues, but without any regular pattern of hydrogen bonds. Loops often form the working place of the protein, therefore appear on the out surface of the native structure.

Figure 2. PX is a bunch of overlapping balls, called the space-lling model, or CPK model.

3. Some functions in thermodynamics

A thermodynamic system consists of particles in a region R3 and a bath or environment surrounding it. A wall, usually the boundary separating the system with its surrounding.

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If no energy and matter can be exchanged through the wall, the system is an isolated system. If only energy can be exchanged, the system is a closed system. If both energy and matter can be exchanged with the surrounding, the system is an open system. For an open system of variable particles contacting with surrounding thermal and particle bath, let U, T, S, P, V, and N be the inner energy, temperature, entropy, pressure, volume, chemical potential, and the number of particles of the system respectively, then dU = TdS PdV + dN, By Legendre transformations various extensive quantities can be derived, F = U TS, G = U TS + PV, = F N = U TS N (4) (3)

where F, G, and are Helmholtz, Gibbs free energies, and thermodynamic potential respectively. Then dF = SdT PdV + dN, dG = SdT + VdP + dN, d = SdT PdV Nd. (5)

Which shows that U = U (S, V, N ), F = F ( T, V, N ), G = G ( T, P, N ), = ( T, V, ). All extensive quantities satisfy a linear homogeneous relation, i.e., consider a scaling transformation which enlarges the actual amount of matter by a factor , then all extensive quantities are multiplied by a factor . U, S, V, N, F, G, are extensive, while T, P, are intensive. Thus U = U (S, V, N ), F = F ( T, V, N ),

G = G ( T, P, N ),

( T, V, ) = ( T, V, ). (6)

From equations in (5) ( V ) T, = P. By equations in (6) = and Equation (8) is true for any open thermodynamics system. ( T, V, ) = PV. (8) d() =V d V
T,

= PV

(7)

4. Statistical mechanics
Thermodynamics is a phenomenological theory of macroscopic phenomena that neglects the individual properties of particles in a system. Statistical mechanics is the bridge between the macroscopic and microscopic behavior. In statistical mechanics, the particles in a system obey either classical or quantum dynamic laws, and the macroscopic quantities are statistical averages of the corresponding microscopic quantities. If the particles obey classical dynamical law, it is the classical statistical mechanics. If the particles obey quantum dynamical law, it is the quantum statistical mechanics. But the averaging to get macroscopic quantities from microscopic ones are in the same principle and formality.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 53 7

Protein folding studies the structure of the protein molecule, what is the native structure and why and how the protein folds to it. All these aspects are specic properties of a particle, the protein molecule. To get the Gibbs free energy formula G (X) for each conformation X, statistical mechanics is needed with careful specication of the thermodynamic system.

4.1. The canonic ensemble

Statistical mechanics uses ensembles of all microscopic states under the same macroscopic character, for example, all microscopic states corresponding to the same energy E. The probability of this ensemble then is proportional to p E exp( E), (9)

where = 1/kT, k the Boltzmann constant and T the temperature. If there are only a series energy levels E1 , E2 , , then the probability distribution for canonic ensemble is pi = exp( Ei ) . 1 exp( En ) n= (10)

Various of thermodynamic quantities, such as the inner energy of the system, can be put as the means: Ei exp( Ei ) U = Ei = i=1 . (11) 1 exp( En ) n= If only the Halminltonian H (q, p) is known, where q = (q1 , , qi , , q N ) N is the position of the N particles in the thermodynamic system R3 under study, and p = (p1 , , pi , , p N ) momentums of these particles, the canonical phase-space density of the system then is pc (q, p) = exp[ H (q, p)]
1 N!h3N N

dq N

R3N

exp[ H (q, p)]dp N

exp[ H (q, p)] . Z( T, V, N )

(12)

where N! is the Gibbs corrector because that the particles in the system is indistinguishable. Z( T, V, N ) is called the canonic partition function, it depends on the systems temperature T, volume V, and particle number N. Note that under the assumption of the canonic ensemble, they are all xed for the xed thermodynamical system . Especially, V = V () = dq implicitly set that R3 has a volume. Then the entropy S is k N!h3N

S = S() = k ln pc =

1 [ H + kT ln Z( T, V, N )] . T

dq N

R3N

[ H (q, p) + ln Z( T, V, N )] pc (q, p)dp N

(13)

From which the Helmholtz free energy F = F () and the Gibbs free energy G = G () are obtained, F = U TS = kT ln Z( T, V, N ), G = PV + F = PV kT ln Z( T, V, N ). (14)

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Therefore, to obtain the Gibbs free energy one has to really calculate ln Z( T, V, N ), a task that often cannot be done.

4.2. The grand canonic ensemble

The grand canonic ensemble or macroscopic ensemble deals with an open thermodynamic system , i.e., not only energy can be exchanged, matter particles can also be exchanged between and environment. Therefore, the particle number N in is variable. In classical mechanics, suppose that the phase space is (q, p) N R3N . Let H be the Hamiltonian, the grand canonic phase-space density is exp[ ( H N )] , Z( T, V, ) (15) where V = V () is the volume of the system. By denition the entropy is p gc (q, p, N ) = =0 N
1 N!h3N N

dq N

exp[ ( H N )]
R3N

exp[ ( H (q, p) N ]dp N

S() = k ln p gc = k

N N =0

dq N

R3N

{ [ H (q, p) N ] + ln Z } p gc (q, p)dp N

(16)

1 [ H N + kT ln Z] . T

Here H = U is the inner energy of the system , N = N () is the mean number of particles in . More importantly, the function kT ln Z( T, V, ) is nothing but the grand canonic potential , from equation (8) it is just PV. Thus G = U + PV TS = N . (17)

5. Experimental measuring and theoretical derivation of the Gibbs free energy of protein folding
The newly synthesized peptide chain of a protein automatically folds to its native structure in the physiological environment. Change of environment will make a protein denatured, i.e., the protein no longer performs its biological function. The facts that denaturation does not change the protein molecule, that the only thing changed is its structure, was rst theorized by Hisen Wu based on his own extensive experiments, Hisen Wu (1931). It was found that after removing the agents that caused the change of environment, some protein can automatically retake its native structure, this is called renaturation or refolding. After many experiments in denaturation and renaturation, Annsen summarized the Thermodynamic Principle as the fundamental law of the protein folding, Annsen (1973). Annsens work actually show that protein refolds spontaneously after removing denaturation agents. Therefore, in the physiological or similar environment, the native structure has the minimum Gibbs free energy; and in a changed environment, the denatured structure(s) will have the smaller Gibbs free energy. The Thermodynamic Principle of protein folding then is the general thermodynamics law, if a change happens spontaneously, then the end state will have smaller Gibbs free energy than the initial state.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 55 9

To apply the Thermodynamic Principle in the research of protein folding, it is necessary to know the Gibbs free energy formula G (X) for each conformation X. Until now, theoretical derivation of G (X) is unsuccessful and rarely being tried. Most knowledge of the Gibbs free energy of protein folding comes from experiment observations.

The basic principle of experimentally measuring G, the difference in Gibbs free energy between the native and the denatured structures of a protein is as follows. For protein molecules in a solution, the criterion of the protein is in the native structure is that it performes its biological function, otherwise the protein is denatured or not in the native structure. The level of biological function indicates the degree of the denaturation. Let B be the native structure, denote its molar concentration as [ B]. Denote A as an non-native structure of the same protein in the solution and [ A] its molar concentration. Three things to be borne in mind: 1. the environment is the physiological environment or similar one such that the protein can spontaneously fold; 2: individual molecule cannot be directly measured, so the measuring is in per mole term, R = NA k instead of k should be used, where NA is the Avogadros number; 3: the environment in reality has constant pressure P, hence the enthalpy H = U + PV can replace the inner energy U, where V is the volume of the system (it is a subset of the whole R3 ). As expressed in (9), the probabilities of the protein takes the conformations A and B are p A WA exp HA RT , PB WB exp HB RT , (18)

5.1. Experimental measuring of G

where H A = U A + PV and HB = UB + PV are the enthalpy per mole for A and B, WA (WB ) is the number of ways of the enthalpy H A (HB ) can be achieved by microscopic states. The quantities [ A] and [ B] are assumed to be measurable in experiment. Therefore their ration K = [ A]/[ B] is also measurable. Then

G o = RT ln K.

(19)

To see that equation (19) is true, note that the ratio K is equal to the ratio p A /p B and the entropies per mole are S A = R ln WA , SB = R ln WB , therefore

RT ln K = RT ln

pA = RT pB

HB H A RT RT

RT (ln WA ln WB )

= H A HB T ( R ln WA R ln WB ) = H A HB T (S A SB ) = H A TS A ( HB TSB ) = G A GB = G o .
(20) But in reality, the ratio K is measurable in experiment is only theoretical, since in physiological environment K 0, i.e., almost all protein molecules take the native structure B. = There is no way to change the native structure B to A while keeping the environment unchanged. In experiments, one has to change the environment to get the protein denatured,

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that is, to change its shape from the native structure B to another conformation A. Heating the solution is a simple way to change the environment, during the heating, the system absorbs an amount of heat H, the systems temperature increased from T0 to T1 . Then G ( A, T1 ) G ( B, T0 ) = f ( H ), (21)

where f ( H ) is a function depending on H and its value is obtained from experiment. What really needed is G = G ( A, T0 ) G ( B, T0 ). (22) To get G, interpolation to equation (21) is used to estimate the value in T0 . Other methods of changing environment face the same problem, i.e., interpolation has neither theoretical nor observation basis.

Equation (19) may give the reason why G is used whenever referring the Gibbs free energy. For experiment, only G can be got. In theoretical derivation, this rule no longer to be followed and moreover, without a base structure to compare to, the notation G will look strange. More importantly, it should be emphasized again, that the Thermodynamic Principle really says that in the physiological environment the native structure has the minimum Gibbs free energy; and in other environment, the native structure no longer has the minimum Gibbs free energy. Summarizing, it is G ( B, T0 ) < G ( A, T0 ), G ( A, T1 ) < G ( B, T1 ). (23)

It should always keep in mind that before comparison, rst clarify the environment. When deriving the Gibbs free energy formula, the rst thing is also to make clear what is the environment. Another reality that should be borne in mind is that during the protein folding process, the environment does not change. Remember that after removing the denaturation agent some proteins will spontaneously refold to their native structure, this is called the refolding or renaturation. Distinguish the original protein folding problem and protein refolding problem is another important issue. Only in the refolding case, a theoretical derivation can make the environment change, for example, lower the temperature to the room temperature (around 300K). Some discussions on protein folding are really talking about refolding, because they start from changing the environment from nonphysological to physiological. While experiment has no way to change the native structure without disturbing the environment, theory can play a role instead. Formulas (1) and (2) give us the chance to compare G, as long as the accurate chemical potentials values are known.

5.2. Theoretical consideration of the protein folding problem

Protein folding is a highly practical eld. Very few attention was paid to its theoretical part. For example, almost nobody has seriously considered the Gibbs free energy formula. Instead, all kinds of empirical models are tried in computer simulation, without any justication in fundamental principle.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 57 11

One attempt to theoretically get the Gibbs free energy formula from canonic ensemble is summarized by Lazaridis and Karplus (2003), the theoretical part of it is reported below and why it is not successful will be briey pointed out. Their notations such as R = X as conformation, A = F as the Helmholtz free energy, Q = Z as the partition function, = h, etc., will be kept in this section. Treating the protein folding system as the set of all conformations plus surrounding water molecules with a phase point (R, r), where r are coordinates of N water molecules plus their orientations. The Hamiltonian H can be decomposed as H = Hmm + Hmw + Hww , (24)

where mm means interactions inside the protein, mw between protein and water molecules, and ww water to water, all in the atomic level. Triplet interactions mmm, mmw, etc., can also be considered, but for simplicity only take the pairwise atomic interactions. Applying the canonic ensemble, the canonic partition function is Q= exp( H )dr N dR M Z = , N!3M 3N N!3M 3N

and the Helmholtz free energy is given by A = kT ln Q = kT ln exp( H )dr N dR M + kT ln( N!3M 3N ). (25)

To separate the contributions made by water molecules and the conformations, the effective energy W is dened, exp( W ) = exp( Hmm ) Dene exp( Hmw Hww )dr N = exp( Hmm ) exp( X ), (26) exp( Hww )dr N exp( Hmw ) exp( Hww )dr N . exp( Hww )dr N

exp( Hmw )o =
The effective energy W (R) is:

(27)

W (R) = Hmm (R) + X (R) = Hmm (R) kT lnexp( Hmw )o Hmm (R) + Gslv (R). (28) The term Gslv (R) is called the solvation free energy while Hmm is the intra-macromolecular energy. After changing R to interior coordinates q, it is stated that Z = V8 2 exp( Hww )dr N exp( W )dq, (29)

because the interior coordinates has only 3M 6 dimension, the integration of the remaining 6 dimension over the system getting the value V8 2 , implying that each xi in R can be any point in the system that has volume V. As usual, the probability of nding the system at the

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conguration (q) is: p(q) = Consequently, p(q) ln p(q)dq = ln Z + ln From equation (25), A = kT exp( Hww )dr N + kT ln 3M V8 2

exp[ W (q)] . exp[ W (q)]dq

(30)

exp( Hww )dr N + ln(V8 2 )

p(q)W (q)dq, (31)

3M V8 2

p(q)W (q)dq + kT

p(q) ln p(q)dq (32)

= Ao + kT ln

+ W TSconf ,

where Ao = kT exp( Hww )dr N is the pure Helmholtz free energy of pure solvent; the term TSconf = kT p(q) ln p(q)dq is the contribution of the congurational entropy of the macromolecule to the free energy. The Gibbs free energy is G = A + PV. Since the volume is thought negligible under ambient conditions so Gibbs and Helmholtz free energies are considered identical. Now for any subset of A , integrals restricted on A gives the Helmholtz energy A A , i.e., A A = Ao + kT ln 3M V8 2

+ W A TSconf . A

(33)

Thus for two different subsets A and B, the difference in the Helmholtz free energy is

A = A B A A = W B W A T (Sconf Sconf ) B A = Hmm + Gslv T Sconf .

(34)

Especially, If A is the denatured state and B the native state, both of which have to be dened in some way and both of which include many congurations, Eq. (34) gives the free energy of folding."

5.3. Critics of the derivation in Lazaridis and Karplus (2003)

Protein folding is considered a very practical research eld, dominating activities are computer simulations with empirical models. There are very few theoretical discussions about protein folding. This derivation in Lazaridis and Karplus (2003) is a rare example deserving an analysis to see why for decades there has been no theoretic progress in this eld. Many lessons can be learned from this example. One important lesson from the derivation Lazaridis and Karplus (2003) is that when dealing with thermodynamics and statistical mechanics, the thermodynamic system must be clearly dened. The system will occupy a space in R3 , what is it? How to delimit it?

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 59 13

More importantly, it is not just one conformation R, but all conformations of a single protein are considered in the derivation. As a single point R R3M , no structural features of the conformation R are considered, i.e., this particle is structureless. Remember that the research object is the conformation of the protein, we cannot treat them as structureless particles. Yes, classical derivations such as the ideal gas system are dened this way, that is because that the interest is not in the individual particles structure but the macroscopic properties of the idea gas. The lesson then is that instead of considering all conformations together in a system, specic thermodynamic system has to be tailored for each individual conformation R. And such a system contains only one conformation R, with its structure geometry, and other particles such as water molecules, thus the Gibbs free energy of such a system will be indexed by R, G = G (R). Perhaps the biggest lesson to be learned is that when solving a problem, one should concentrate on the specic features of the problem to design the ways to attack it, not just imitate successful classical examples. The derivation of Lazaridis and Karplus (2003) gives the effective energy W (R) as some substitute of the Gibbs free energy without theoretic basis for its relation to the Thermodynamic Principle. Moreover, the formula W (R) tells us nothing of how to calculate it, all are buried in multiple-integrations without clear delimitation. Being the only function for individual conformation R, it was pointed out in Lazaridis and Karplus (2003) that The function W denes a hyper-surface in the conformation space of the macromolecule in the presence of equilibrated solvent and, therefore, includes the solvation entropy. This hyper-surface is now often called an energy landscape. It determines the thermodynamics and kinetics of macromolecular conformational transitions." From this comment it can be seen that the authors are not against individual quantities such as W (R) and think they are important to the study of protein folding. Changing the effective energy" W (R) to the Gibbs free energy G (R), the comment really makes sense. The lesson should be learned is that never invent theoretical concepts without rm theoretical basis. Another one is that always keep in mind that useful Gibbs free energy formula should be calculable. From now on, the notation X = R will be used to represent a conformation. To put the Thermodynamic Principle in practice, not merely as a talking show, what really needed is G (X), the Gibbs free energy of each individual conformation X, not the effective energy W (R). One hopes that the formula G (X) should be calculable, not buried in multiple integrations. To get such a formula, the grand canonic ensemble and eventually the quantum statistics have to be applied.

6. Necessary preparations for the derivation of the Gibbs free energy formula
Summarizing what have learned from the critics of the derivation in Lazaridis and Karplus (2003), in any attempt of derivation of the Gibbs free energy formula one has to: 1. clearly state all assumptions used in the derivation; and 2. for each conformation X, set a thermodynamic system TX associated with X; 3. use the grand canonic ensemble.

60 14 Thermodynamics Fundamentals and Its Application in Science

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6.1. The assumptions

All assumptions here are based on well-known facts of consensus among protein folding students. Let U be a protein with M atoms (a1 , , ai , , a M ). A structure (conformation) of U is a point X = (x1 , , xi , , x M ) R3M , xi R3 is the atomic center (nuclear) position of ai . Alternatively, the conformation X corresponds to a subset in R3 , PX = iM 1 B(xi , ri ) R3 = where ri s are van der Waals radii. 1. The proteins discussed here are monomeric, single domain, self folding globular proteins. 2. Therefore, in the case of our selected proteins, the environment of the protein folding, the physiological environment, is pure water, there are no other elements in the environment, no chaperonins, no co-factors, etc. This is a rational simplication, at least when one considers the environment as only the rst hydration shell of a conformation, as in our derivation of the G (X). 3. During the folding, the environment does not change. 4. Annsen (1973) showed that before folding, the polypeptide chain already has its main chains and each residues covalent bonds correctly formed. Hence, our conformations should satisfy the following steric conditions set in Fang (2005) and Fang and Jing (2010): there are ij > 0, 1 i < j M such that for any two atoms ai and a j in PX = M k =1 B ( x k , r k ),
ij | xi x j |, dij ij |xi x j | dij + ij ,

no covalent bond between ai and a j ; dij is the standard bond length between ai and a j .

(35)

5. A water molecule is treated as a single particle centered at the oxygen nuclear position w R3 , and the covalent bonds in it are xed. In the Born-Oppenheimer approximation, only the conformation X is xed, all particles, water molecules or electrons in the rst hydration shell of PX , are moving. 6. As in section 2.3, there are H hydrophobic levels Hi , i = 1, , H, such that iH 1 Hi = = ( a1 , , a i , , a M ).

All conformations satisfying the steric conditions (35) will be denoted as X and in this chapter only X X will be considered.

6.2. The thermodynamic system TX

Let dw be the diameter of a water molecule and MX be the molecular surface of PX as dened in Richards (1977) with the probe radius dw /2, see F IGURE 3. Dene

RX = {x R3 : dist(x, MX ) dw } \ PX

(36)

as the rst hydration shell surrounding PX , where dist(x, S) = infyS |x y|. Then TX = PX RX will be our thermodynamic system of protein folding at the conformation X.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 61 15

Figure 3. Two dimensional presenting of molecular surface Richards (1977) and solvent accessible surface Lee and Richards (1971). This gure was originally in Fang and Jing (2010).

Let Ii {1, 2, , M} be the subset such that a j Hi if and only if j Ii . Dene PX i = j Ii B(x j , r j ) PX and as shown in F IGURE 4,

RX i = {x RX : dist(x, PXi ) dist(x, PX \ PX i )},

Let V () be the volume of R3 , then

1 i H.

(37)

RX = iH 1 RX i , =

V (RX ) =

i =1

V (RX i ), and for i = j,

V (RX i RX j ) = 0.

(38)

Since MX is a closed surface, it divides R3 into two regions X and such that X = X = MX and R3 = X MX . Note that PX X and all nuclear centers of atoms in X X the water molecules in RX are contained in . Moreover, X is bounded, therefore, has X a volume V (X ). For S R3 , denote S as the closure of S. Dene the hydrophobicity subsurface MX i , 1 i H, as (39) MX i = MX R X i . Let A(S) be the area of a surface S R3 , then MX = iH 1 MX i , = A ( MX ) =
i =1

A( MX i ), and if i = j, then A( MX i MX j ) = 0.

(40)

Although the shape of each atom in a molecule is well dened by the theory of atoms in molecules as in Bader (1990) and Popelier (2000), what concerning us here is the overall

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RX i

PX MX

RX m

RX i Water
Figure 4. Note that RXi generally are not connected, i.e., having more than one block.

shape of the structure PX . The cutoff of electron density 0.001au in Bader (1990) and Popelier (2000) gives the overall shape of a molecular structure that is just like PX , a bunch of overlapping balls. Moreover, the boundary of the 0.001au cutoff is very similar to the molecular surface MX which was dened by Richards (1977) and was shown has more physical meaning as the boundary surface of the conformation PX in Tun et. al. (1992) and Jackson and Sternberg (1993).

7. Gibbs free energy formula: Classical statistical mechanics derivation

The grand canonic ensemble or macroscopic ensemble will be applied to derive the desired Gibbs free energy formula G (X). In addition to let the number of water molecules vary, the assumptions is that the chemical potential will be different for water molecules contacting to different hydrophobicity levels Hi (or falling in RX i ). Counting the numbers Ni of water molecules that contact to atoms in Hi , the N and in equation (15) should be modied M to N = ( N1 , , Ni , , NH ), = (1 , , i , , H ). Let (q, p) RX R3M be the H water molecules phase space for a xed N, where M = i=1 Ni . Let HX = HX (q, p) be the Hamiltonian. The grand canonic phase density function will be

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 63 17

pX (q, p, N ) =

1 =0 M!h3M M

Ni = M iH 1 R Ni dq Ni = Xi

exp{ [ HX (q, p) iH 1 i Ni ]} =
R3M

exp{ [ HX iH 1 i Ni ]}dp3M = (41)

exp{ [ HX (q, p) iH 1 i Ni ]} = . Z( T, V, )
H

The entropy S(X) = S(TX ) is S = k ln pX = k

i M=0 N1 ++ NH = M i =1 RX i

dq Ni

R3M

ln pX pX dp M

= k = =

M=0 N1 ++ NH = M i =1

N RX ii

dq Ni i Ni HX (q, p) ln Z pX dp M
i =1

(42)

H 1 H i Ni + kT ln Z( T, V, ) T i =1 H 1 U (TX ) i Ni (TX ) + kT ln Z( T, V, ) T i =1

(43)

where U (X) = U (TX ) = H is the inner energy, Ni (X) = Ni the mean number of water molecules in RX i . By equation (8), kT ln Z( T, V, ) = ( T, V, ) = PV (TX ). Therefore, from G = U + PV TS, G (X) = G (TX ) = U (X) + PV (TX ) TS(TX ) =
i =1

Ni (X).

(44)

The Gibbs free energy given in formula (44) does not involve any integration at all, just counting the number of water molecules contacting atoms in Hi . Furthermore, against the effective energy, potential function Hmm plays no role at all, a surprise indeed. But formula (44) also is not easy to calculate, counting the number of water molecules actually need more knowledge of the conformations boundary, the molecular surface MX . Formula (44) can be directly transfered into a geometric version.

7.1. Converting formula (44) to a geometric version

Since every water molecule in RX i has contact with the surface MX i , Ni (X) is proportional to the area A( MX i ). Therefore, there are i > 0, such that i A( MX i ) = Ni (X), Substitute in (44), G (X) = G (TX ) =
H

1 i H.

(45)

i =1

i i A( MX i ).

(46)

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For each conformation X, the molecular surface MX is calculable, see Connolly (1983). The areas A( MX ) and A( MX i ) are also calculable. Therefore, unlike the formula given in (34), this formula is calculable. Moreover, our derivation theoretically justied the surface area models that will be discussed later, only difference is that the molecular surface area is used here instead of the solvent accessible surface area. But still something is missing. That is, the volume V (TX ), an important thermodynamic quantity, does not show here at all. It seems that no way to put the V (TX ) here in the classical statistical mechanics. To resolve this, the quantum statistical mechanics is necessary.

8. A quantum statistical theory of protein folding

In 1929 Dirac wrote: The underlying physical laws necessary for the mathematical theory of ... the whole of chemistry are thus completely known, and the difculty is only that the exact application of these laws leads to equations much too complicated to be soluble." (quoted from Bader (1990), page 132). Yes, the multidimensional Shrdinger equation for protein folding is beyond our ability to solve, no matter how fast and how powerful our computers are. But mathematical theory guarantees that there is a complete set of eigenvalues (energy levels) and eigenfunctions to the Shrdinger equation in the Born-Oppenheimer approximation. Then consider that in the statistical mechanics, ensembles collect all (energy) states of the same system. Although one cannot have exact solutions to the Shrdinger equation, the eigenvalues of it are theoretically known. Thus one can apply the grand canonical ensemble to obtain the desired Gibbs free energy formula G (X). This is the main idea of the derivation.

8.1. The Shrdinger equation

For any conformation X X, let W = (w1 , , wi , , w N ) R3N be the nuclear centers of water molecules in RX and E = (e1 , , ei , , e L ) R3L be electronic positions of all electrons in TX . Then the Hamiltonian for the system TX is
M h2 h2 N 2 h2 L H = T+V = 2 i 2me 2 + V (X, W, E), i i 2mi 2mw i=1 i =1 i =1

(47)

where mi is the nuclear mass of atom ai , mw and me are the masses of water molecule and electron; 2 is Laplacian in corresponding R3 ; and V the potential. i

8.2. The rst step of the Born-Oppenheimer approximation

Depending on the shape of PX , for each i, 1 i H, the maximum numbers NX i of water molecules contained in RX i vary. Theoretically all cases are considered, i.e., there are 0 Ni NX i water molecules in RX i , 1 i H. Let M0 = 0 and Mi = ji Nj and
N iH 1 RX ii denote the nuclear positions of water molecules in RX . As well, there will be all = possible numbers 0 Ne < of electrons in TX . Let E = (e1 , e2 , , e Ne ) R3Ne denote their nuclear positions. For each xed X X and N = ( N1 , , NH , Ne ), the Born-Oppenheimer N Wi = (w Mi1 +1 , , w Mi1 + j , , w Mi ) RX ii , 1 i H, and W = (W1 , W2 , , W MH )

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 65 19

N N The eigenfunctions iX,N (W, E) L2 (iH 1 RX ii TX e ) = HX,N , 1 i < , comprise an = 0 i orthonormal basis of HX,N . Denote their eigenvalues (energy levels) as EX,N , then HX iX,N = i EX,N iX,N .

approximation has the Hamiltonian h2 1 M H 2 1 Ne 2 HX = + + V (X, W, E). 2 mw j j m e =1 =1

(48)

8.3. Grand partition function and grand canonic density operator

Since the numbers Ni and Ne vary, the grand canonic ensemble should be adopted. Let i be the chemical potentials, that is, the Gibbs free energy per water molecule in RX i . Let e be electron chemical potential. The grand canonic density operator is like in equation (15), or see Greiner et. al. (1994) and Dai (2007) H X i Ni e Ne (X) . (49) X = exp H
i =1

where (X) is the grand canonic potential in equation (8) with the index X and the grand partition function is H X i Ni e Ne exp[ (X)] = Trace exp H
i =1

i,N

i exp EX,N i Ni e Ne i =1

(50)

8.4. The Gibbs free energy G (X)

As in equation (16), under the grand canonic ensemble the entropy S(X) = S(TX ) of the system TX is H S(X) = kTrace(X ln X ) = k ln X = k HX (X) i Ni e Ne
i =1

H 1 HX (X) i Ni e Ne T i =1

(51)

H 1 U (X) (X) i Ni (X) e Ne (X) . T i =1

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Denote Ni = Ni (X) as the mean number of water molecules in RX i , 1 i H, and Ne = Ne (X) the mean number of electrons in TX . The inner energy HX of the system TX is denoted as U (X) = U (TX ). By equation (8) and the remark after it (X)( T, V, 1 , , H , e ) = PV (X), where V (X) = V (TX ) is the volume of the thermodynamic system TX . Thus by equation (51) the Gibbs free energy G (X) = G (TX ) in formula (1) is obtained: G (X) = G (TX ) = PV (X) + U (X) TS(X) =

i =1

i Ni (X) + e Ne (X).

(52)

8.5. Converting formula (1) to geometric form (2)

As in the classical statistical mechanics case, i A( MX i ) = Ni (X), 1 i H. (53)

Similarly, there will be a e > 0 such that e V (TX ) = Ne (X). By the denition of TX and X , it is roughly V (TX \ X ) = dw A( MX ). Thus Ne (X) = e V (TX ) = e [V (X ) + V (TX \ X )] = e V (X ) + dw e A( MX ). Substitute equations (45) and (54) into formula (1), formula (2) is obtained. (54)

9. Some remarks
The question to applying fundamental physical laws directly to the protein folding problem is, can it be done? It should be checked that how rigorous is the derivation and be asked that are there any fundamental errors? Possible ways to modify the formula or the derivation will also be discussed. By applying quantum statistics the protein folding problem is theoretically treated. A theory is useful only if it can make explanations to the observed facts and if it can simplify and improve research methods as well as clarify concepts. It will be shown that G (X) can do exactly these. If the same theoretical result can be derived from two different disciplines, it is often not just by chance. An early phenomenological mathematical model Fang (2005), starting from purely geometric reasoning, has achieved formula (2), with just two hydrophobic levels, hydrophobic and hydrophilic. A theory also has to be falsiable, that is making a prediction to be checked. The fundamental prediction is that minimizing formula (1) or (2) the native structures will be obtained for the amino acid sequences of proteins considered in the assumptions of the formulas. That can only be done after the actual values of the chemical potentials appear in the formulas, for the physiological environment, are determined.

9.1. How rigorous is the derivation?

Two common tools in physics, the rst step of the Born-Oppenheimer approximation in quantum mechanics and the grand canonic ensemble in statistical physics, are applied to obtain formula (1).

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 67 21

9.1.1. The Born-Oppenheimer approximation The Born-Oppenheimer approximation treats the electrons as if they are moving in the eld of xed nuclei. This is a good approximation because, loosely speaking, electrons move much faster than nuclei and will almost instantly adjust themselves to a change in nuclear position." Popelier (2000). Since the mass of a water molecule is much less than the mass of a protein, this approximation can be extended to the case of when X changes the other particles, electrons and water molecules, will quickly adjust themselves to the change as well. 9.1.2. The statistical physics in general and the grand canonic ensemble in particular Up to now there is no evidence to show that statistical physics itself is responsible for any mistakes," the Preface of Dai (2007). Via the ensemble theory of statistical mechanics only one protein molecule and particles in its immediate environment are considered, it is justied since as pointed out in Dai (2007) page 10, When the duration of measurement is short, or the number of particles is not large enough, the concept of ensemble theory is still valid." And among different ensembles, Generally speaking, the grand canonic ensemble, with the least restrictions, is the most convenient in the mathematical treatment." Dai (2007) page 16. In fact, the canonic ensemble has been tried and ended with a result that the eigenvalues of the quantum mechanics system have to be really calculated, to do it accurately is impossible. The derivations in this chapter only puts together the two very common and sound practices: the Born-Oppenheimer approximation (only the rst step) and the grand canonic ensemble, and apply them to the protein folding problem. As long as protein folding obeys the fundamental physical laws, there should not be any serious error with the derivation.

9.2. Equilibrium and quasi-equilibrium

A proteins structure will never be in equilibrium, in fact, even the native structure is only a snapshot of the constant vibration state of the structure. The best description of conformation X is given in Chapter 3 of Bader (1990). Simply speaking, a conformation X actually is any point Y such that all yi are contained in a union of tiny balls centered at xi , i = 1, , M. In this sense, it can only be anticipated that a quasi-equilibrium description (such as the heat engine, Bailyn (1994) page 94) of the thermodynamic states of the protein folding. This has been built-in in the Thermodynamical Principle of Protein Folding. So the quantities such as S(X), (X), and G (X) can only be understood in this sense. That is, observing a concrete folding process one will see a series of conformations Xi , i = 1, 2, 3, . The Thermodynamic Principle then says that measuring the Gibbs free energy G (Xi ) one will observe that eventually G (Xi ) will converge to a minimum value and the Xi will eventually approach to the native structure. While all the time, no conformation Xi and thermodynamic system TXi are really in equilibrium state.

9.3. Potential energy plays no role in protein folding

Formulas (1) and (2) theoretically show that hydrophobic effect is the driving force of protein folding, it is not just solvent free energy besides the pairwise interactions such as the Coulombs, etc., as all force elds assumed. Only in the physiological environment the

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hydrophobic effect works towards to native structure, otherwise it will push denaturation as discussed in explanation of folding and unfolding. Formulas (1) and (2) show that the Gibbs free energy is actually independent of the potential energy, against ones intuition and a bit of surprising. The explanation is that during the folding process, all covalent bonds in the main chain and each side chain are kept invariant, the potential energy has already played its role in the synthesis process of forming the peptide chain, which of course can also be described by quantum mechanics. According to Annsen (1973), protein folding is after the synthesis of the whole peptide chain, so the synthesis process can be skipped and the concentration can be focused on the folding process. The steric conditions (35) will just keep this early synthesis result, not any X = (x1 , , xi , , x M ) is eligible to be a conformation, it has to satisfy the steric conditions (35). The steric conditions not only pay respect to the bond length, it also reect a lot of physic-chemical properties of a conformation: They are dened via the allowed minimal atomic distances, such that for non-bonding atoms, the allowed minimal distances are: shorter between differently charged or polarized atoms; a little longer between non-polar ones; and much longer (generally greater than the sum of their radii) between the same charged ones, etc. For example, minimal distance between sulfur atoms in Cysteine residues to form disulde bonds is allowed. And for any newly found intramolecular covalent bond between side chains, such as the isopeptide bonds in Kang and Baker (2011), the steric conditions can be easily modied to allow the newly found phenomenon. The drawback of the steric conditions is that the minimization in equation (57) becomes a constrained minimization.

9.4. Unied explanation of folding and denaturation

Protein denaturation is easy to happen, even if the environment is slightly changed, as described by Hsien Wu (1931). (Hsien Wu (1931) is the 13th article that theorizes the results of a series experiments, and a preliminary report was read before the Xlllth International Congress of Physiology at Boston, August 19-24, 1929, and published in the Am. J. Physiol. for October 1929. In which Hsien Wu rst suggested that the denatured protein is still the same molecule, only structure has been changed.) Annsen in various experiments showed that after denaturation by changed environment, if removing the denature agent, certain globular proteins can spontaneously refold to its native structure, Annsen (1973). The spontaneous renaturation suggests that protein folding does not need outside help, at least to the class of proteins in this chapter. Therefore, the fundamental law of thermodynamics asserts that in the environments in which a protein can fold, the native structure must have the minimum Gibbs free energy. The same is true for denaturation, under the denatured environment, the native structure no longer has the minimum Gibbs free energy, some other structure(s), will have the minimum Gibbs free energy. Thus let En present environment, any formula of Gibbs free energy should be stated as G (X, En) instead of just G (X), unless the environment is specied like in this chapter. Let En N be the physiological environment and EnU be some denatured environment, X N be the native structure and XU be one of the denatured stable structure in EnU , then the thermodynamic principle for both of protein folding and unfolding should be that G (X N , En N ) < G (XU , En N ), G (X N , EnU ) > G (XU , EnU ). (55)

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 69 23

To check this, an experiment should be designed that can suddenly put proteins in a different environment. Formulas (1) and (2) should be written as G (X, En N ). Indeed, the chemical potentials e and i s are Gibbs free energies per corresponding particles, = u + Pv Ts. Two environment parameters, temperature T and pressure P, explicitly appear in , the inner energy u and entropy s may also implicitly depend on the environment. According to formulas (1) and (2), if i < 0, then make more Hi atoms to expose to water (make larger A( MX i )) will reduce the Gibbs free energy. If i > 0, then the reverse will happen. Increase or reduce the Hi atoms exposure to water (A( MX i )), the conformation has to change. The conformation changes to adjust until a conformation X N is obtained, such that the net effect of any change of the conformation will either increase some Hi atoms exposure to water while i > 0 or reduce Hi atoms exposure to water while i < 0. In other words, the G (X, En N ) achieves its minimum at G (X N , En N ). Protein folding, at least for the proteins considered in the assumptions, is explained very well by formulas (1) and (2). In changed environment, the chemical potentials e and i s in formulas (1) and (2) changed their values. With the changed chemical potentials, G (X, EnU ) has the same form as G (X, En N ) but different chemical potentials. Therefore, the structure XU will be stable, according to the second inequality in (55), the process is exactly the same as described for the protein folding if the changing environment method does not include introducing new kinds (non-water) of particles, for example, if only temperature or pressure is changed. Even in the new environment including new kinds of particles, formulas (1) and (2) can still partially explain the denaturation, only that more obstructs prevent the protein to denature to XU , but any way it will end in some structure other than the X N , the protein is denatured. Actually, this is a hint of how to modify the current formulas to extend to general proteins.

9.5. Explain hydrophobic effect and the role played by hydrogen bonding
In 1959, by reviewing the literature Kauzmann concluded that the hydrophobic effect is the main driving force in protein folding, Kauzmann (1959). Empirical correlation between hydrophobic free energy and aqueous cavity surface area was noted as early as by Reynolds et.al. (1974), giving justication of the hydrophobic effect. Various justications of hydrophobic effect were published, based on empirical models of protein folding, for example, Dill (1990). But the debate continues to present, some still insist that it is the hydrogen bond instead of hydrophobic effect plays the main role of driving force in protein folding, for example, Rose et. al (2006). The theoretically derived formulas (1) and (2) can explain why the hydrophobic effect is indeed the driving force. A simulation of reducing hydrophobic area alone by Fang and Jing (2010) shows that the result is the appearance of regularly patterned intramolecular hydrogen bonds associated to the secondary structures. In fact, according to formulas (1) and (2), if i < 0, then make more Hi atoms to appear in the boundary of PX will reduce the Gibbs free energy. If i > 0, then the reverse will happen, reducing the exposure of Hi atoms to water will reduce the Gibbs free energy. This gives a theoretical explanation of the hydrophobic effect. The kinetic formulas Fi = xi G (X) (will be discussed later) is the force that push the conformation to change to the native structure. The mechanics stated above works through the chemical potentials i for various levels of hydrophobicity. In physiological environment, all hydrophobic Hi s will have positive i , all

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hydrophilic Hi s will have negative i . Thus changing conformation PX such that the most hydrophilic Hi (i = min(1 , , H )) gets the rst priority to appear on the boundary, and the most hydrophobic Hi (i = max(1 , , H )) gets the rst priority to hide in the hydrophobic core to avoid contacting with water molecules, etc. One should keep in mind that all the time, the steric conditions (35) have to be obeyed. But the hydrophobic effect is actually partially working through hydrogen bond formation. This is well presented in the chemical potentials in formulas (1) and (2). In fact, the values of the chemical potentials reect the ability of the atoms or atom groups to form hydrogen bond, either with another atom group in the protein or with water molecules. This gives a way to theoretically or experimentally determine the values of hydrophilic chemical potentials: checking the actual energy value of the hydrogen bond. According to Fikelstein and Ptitsyn (2002), energies of hydrogen bonds appearing in protein (intermolecular or intramolecular) are (the positive sign means that to break it energy is needed) and their energies are: OH : : : O (21 kJ mol1 or 5.0 kcal mol1 ); OH : : : N (29 kJ mol1 or 6.9 kcal mol1 ); NH : : : N (13 kJ mol1 or 3.1 kcal mol1 ); NH : : : O (8 kJ mol1 or 1.9 kcal mol1 ). For hydrophobic ones, it will be more complicated, common sense is that it reduces the entropy that certainly comes from the inability of forming hydrogen bonds with water molecules. Hence although hydrophobic effect is the driving force of protein folding, it works through the atoms ability or inability to form hydrogen bonds with water molecules. How to explain the intramolecular hydrogen bonds? It seems that formulas (1) and (2) do not address this issue. The possible theory is that the amino acid sequence of a protein is highly selectable in evolution, in fact only a tiny number of amino acid sequences can really become a protein. Indeed, suppose in average each species (or kind" of prokaryote) has 105 proteins (Homo sapiens has around 3 105 ), and assume that per protein has 100 variants (versions with tiny difference in the peptide sequence of the protein), then there are at most 1047 peptide sequences that can really produce a natural protein. Now further suppose that only one in 1013 theoretically protein producing peptide sequences on the earth get a chance to be realized, then there will be at most 1060 possible protein producing peptide sequence. A huge number! The number of peptide sequences of length less than or equal to n is N (n) =

i =1

20i =

20n+1 20 20 = (20n 1) 20n+0.0171 101.301(n+0.0171) . = = 19 19

(56)

The longest amino acid sequence in the record of ExPASy Proteomics Server has 35,213 residues. Then N (35, 213) > 101.335,213 > 1045060 and the ratio of the number of potentially protein producing peptide sequences to the number of all possible sequence of length up to 35,213 is less than 1060 /1045060 = 1045000 , so tiny a number that it is undistinguishable from zero. Even assuming that the longest peptide sequence is only 400, the ratio is still less than 10460 . How small a chance that a random peptide sequence happens to be a proteins peptide sequence!

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 71 25

With these highly specially selected peptide sequences, one can assume that while shrinking the various hydrophobic surfaces to form a hydrophobic core, residues are put in positions to form secondary structures and their associated hydrogen bonds. This sounds a little bit too arbitrary. But the huge number of candidate peptide sequences makes the evolutional selection not only possible but also probable. Moreover, a simulation of shrinking hydrophobic surface area alone indeed produced secondary structures and hydrogen bonds. The simulation was reported by Fang and Jing (2010). Without calculating any dihedral angles or electronic charges, without any arbitrary parameter, paying no attention to any particular atoms position, by just reducing hydrophobic surface area (there it was assumed that there are only two kinds of atoms, hydrophobic and hydrophilic), secondary structures and hydrogen bonds duly appeared. The proteins used in the simulation are 2i9c, 2hng, and 2ib0, with 123, 127, and 162 residues. No simulation of any kind of empirical or theoretical models had achieved such a success. More than anything, this simulation should prove that hydrophobic effect alone will give more chance of forming intramolecular hydrogen bonds. Indeed, pushing hydrophilic atoms to make hydrogen bonds with water molecules will give other non-boundary hydrophilic groups more chance to form intramolecular hydrogen bonds. Again formula (2) can partly explain the success of this simulation, when there are only two hydrophobic classes in formula (2), the hydrophobic area presents the main positive part of the Gibbs free energy, reducing it is reducing the Gibbs free energy, no matter what is the chemical potentials real value.

9.6. Explanation of the successes of surface area models

In 1995, Wang et al (1995) compared 8 empirical energy models by testing their ability to distinguish native structures and their close neighboring compact non-native structures. Their models WZS are accessible surface area models with 14 hydrophobicity classes of atoms, 14 1 i Ai . Each two combination of three targeting proteins were used to train WZS to get i= i , hence there are three models WZS1, WZS2, and WZS3. Among the 8 models, all WZSs performed the best, distinguishing all 6 targeting proteins. The worst performer is the force eld AMBER 4.0, it failed in distinguishing any of the 6 targets. These testing and the successes of various surface area models such as Eisenberg and MacLachlan (1986), showed that instead of watching numerous pairwise atomic interactions, the surface area models, though looking too simple, have surprising powers. Now the formula (2) gives them a theoretic justication. On the other hand, the successes of these models also reenforce the theoretical results. There is a gap between the accessible surface area model in Eisenberg and Maclanchlan (1986) and the experiment results (surface tension), as pointed out in Tun et. al. (1992). The gap disappeared when one uses the molecular surface area to replace the accessible surface area, in Tun et. al. (1992) it was shown that molecular surface area assigned of 72-73 cal/mol/2 perfectly ts with the macroscopic experiment data. Later it was asserted that the molecular surface is the real boundary of protein in its native structure by Jackson and Sternberg (1993). By the denition of X , as shown in F IGURE 3 and F IGURE 4, water molecules contact to PX must be outside the molecular surface MX . Since the assessable surface is in the middle of the rst hydration shell, it is better to use the molecular surface MX as the boundary of

72 26 Thermodynamics Fundamentals and Its Application in Science

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the conformation PX . Moreover, the conversion of the mean numbers Ni (X) to surface area, Ni (X) = i A( MX .i ), only works for the molecular surface, not for the accessible surface. This can explain the conclusions that molecular surface is a much better boundary than accessible surface as stated in Tun et. al. (1992) and Jackson and Sternberg (1993). In fact, the advantage of the solvent accessible surface is that by denition of it one knows exactly each atom occupies which part of the surface, therefore, one can calculate its share in surface area. This fact may partly account why there are so many models based on the solvent accessible surface, even people knew the afore mentioned gap. For other surfaces, one has to dene the part of surface that belongs to a specic hydrophobicity class. This was resolved in Fang (2005) via the distance function denition as is used here. All surface area models neglected one element, the volume of the structure. As early as in the 1970s, Richards and his colleagues already pointed out that the native structure of globular proteins is very dense, or compact, (density = 0.75, Richards (1977)). To make a conformation denser, obviously we should shrink the volume V (X ). The model in Fang (2005) introduced volume term but kept the oversimplication of all atoms are either hydrophobic or hydrophilic. The derivation of formulas (1) and (2) shows that volume term should be counted, but it may be that e e is very small, in that case, volume maybe really is irrelevant.

9.7. Coincidence with phenomenological mathematical model

If a theoretical result can be derived from two different disciplines, its possibility of correctness will be dramatically increased. Indeed, from a pure geometric consideration, a phenomenological mathematical model, G (X) = aV (X ) + bA( MX ) + cA( MX 1 ), a, b, c > 0 (it was assumed that there are only two hydrophobicity levels, hydrophobic and hydrophilic, the hydrophilic surface area A( MX 2 ) is absorbed in A( MX ) by A( MX 2 ) = A( MX ) A( MX 1 )), was created in Fang (2005). It was based on the well-known global geometric characteristics of the native structure of globular proteins: 1. high density; 2. smaller surface area; 3. hydrophobic core, as demonstrated and summarized in Richards (1977) and Novotny et.al (1984). So that to obtain the native structure, one should shrink the volume (increasing the density) and surface area, and form better hydrophobic core (reducing the hydrophobic surface area A( MX 1 )) simultaneously and cohesively. The coincidence of formula (2) and the phenomenological mathematical model of Fang (2005) cannot be just a coincidence. Most likely, it is the same natural law reected in different disciplines. The advantage of formula (2) is that everything there has its physical meaning.

10. Applications
After the derivation it is suitable to point out some immediate applications of the formula G ( X ).

10.1. Energy surface or landscape

An obvious application is the construction of Gibbs free energy surface or landscape. Empirical estimate is no longer needed, the Gibbs free energy formula G : X R gives

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 73 27

a graph (X, G (X)) over the space X (all eligible conformations for a given protein), and this is nothing but the Gibbs free energy surface. Mathematically it is a 3M dimensional hyper-surface. Its characteristics concerned by students of energy surface theory, such as how rugged it is? how many local minimums are there? is there a funnel? etc., can be answered by simple calculations of the formula. Since the function G is actually dened on the whole R3M (on an domain of R3M containing all X is enough), mathematical tools can be explored to study its graph, and compare the results with the restricted conformations. One important question is: Does the absolute minimum structure belongs to X?

10.2. Structure prediction

Prediction of protein structures is the most important method to reveal proteins functions and working mechanics, it becomes a bottle neck in the rapidly developing life science. With more and more powerful computers, this problem is attacked in full front. Various models, homologous or ab initio, full atom model or coarse grained, with numerous parameters of which many are quite arbitrary, are used to achieve the goal. Although our computer power growths exponentially, prediction power does not follow that way. At this moment, one should take a deep breath and remind what the great physicist Fermi said: There are two ways of doing calculations in theoretical physics. One way, and this is the way I prefer, is to have a clear physical picture of the process that you are calculating. The other way is to have a precise and self consistent mathematical formalism." And I remember my friend Johnny von Neumann used to say, with four parameters I can t an elephant, and with ve I can make him wiggle his trunk." Quoted from Dyson (2004). These remarks should also apply to any scientic calculation, not just theoretical physics. Look at the current situation, all ab initio prediction models are actually just empirical with many parameters to ensure some success. Fermis comments remind us that a theory should be based on fundamental physical laws, and contain no arbitrary parameters. Look at formulas (1) and (2), one sees immediately that they are neat, precise and self consistent mathematical formulas. Furthermore, they including no arbitrary parameter, all terms in them have clear physical meanings. Chemical potentials e and i s, geometric constants e and i s, can be evalued by theory or experiments, they are not arbitrary at all. But a theory has to be developed, tested, until justied or falsied. For interested researchers, the tasks are to determine the correct values of the chemical potentials in formula (1) and the geometric ratios e and i in formula (2). There are many estimates to them, but they are either for the solvent accessible surface area such as in Eisenberg and MaLachlan (1986) hence not suit to the experiment data as pointed out in Tun et. al., or do not distinguish different hydrophobicity levels as in Tun et. al. (1992). To get the correct values of the chemical potentials and geometric constants, commonly used method of training with data can be employed, in which one can also test the formulas ability of discriminating native and nearby compact non-native structures. After that, a direct test is to predict the native structure from the amino acid sequence of a protein by minimizing the following: G (X N ) = inf G (X).
X X

(57)

74 28 Thermodynamics Fundamentals and Its Application in Science

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This is the rst time that a theoretically derived formula of the Gibbs free energy is available. Before this, all ab intitio predictions are not really ab initio. A combined (theoretical and experimental) search for the values of chemical potentials will be the key for the success of the ab initio prediction of protein structure.

10.3. Gradient
With formula (2) as the Gibbs free energy, the minimization in equation (57) can be pursued by Newtons fastest descending method. To state the result, some denitions are necessary. 10.3.1. Molecular graphs Given a molecule U, let V be the set of atoms in U and N = |V | be the number of atoms and label the atoms as a1 , a2 , , a N . For 1 i, j N, dene Bij = n if atoms i and j are connected by a bond with valency n (one can imagine that n is not necessarily a whole number), if i and j do not form a bond, then Bij = 0. The molecule formula of U in chemistry can be seen as a graph G (U ) = (V, E), where V acts as the vertex set of G (U ) and E is the edge set of G (U ). An edge in E is denoted by {i, j}, If two atoms ai and a j are connected by a covalent bond, i.e., Bij = n 1, then {i, j} E is an edge. Call G (U ) the molecular graph of U. F IGURE 1 is a molecular graph if the side chain R consisting of only one atom, such as in the amino acid Glycine. A graph G is connected if from any vertex v one can follow the edges in the graph to arrive any other vertex. If a graph is not connected, then it has several connected components, each is itself a connected graph. All molecular graphs are connected. 10.3.2. Rotatable bonds Let b = a a be a covalent bond in the molecule U connecting two atoms a and a . The bond b is rotatable if and only if: 1. the valency of b is not greater than 1; 2. in the molecular graph G (U ), if one deletes {, }, the remaining graph G (U )\{, } = (V, E\{, }) has exactly two connected components and neither component has rotational symmetry around the bond b. 10.3.3. Derivatives of G (X) Let xi = ( xi , yi , zi ), write F = xi G (X) = ( Gxi , Gyi , Gzi )(X). The calculation of Gxi (X), for example, is via Lie vector eld induced by moving the atomic position xi . In fact, any innitesimal change of structure X will induce a Lie vector eld L : X R3 . For example, moving xi from xi to xi + (xi , 0, 0) while keep other nuclear center xed, will induce L xi : X R3 , such that L xi (xi ) = (1, 0, 0) and L xi (x j ) = (0, 0, 0) for j = i. Similarly Lyi and Lzi can be described as well. Then write Gxi = GL , etc. and
xi

xi G (X) = ( GLx , GLy , GLz )(X),

i i i

(58)

Rotating around a covalent bond bij also induce a Lie vector eld Lbij : X R3 . In fact if ai a j form the covalent bond bij , then the bond axis is

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 75 29

bij =

If bij is rotatable, denoting all nuclear centers in one component by Rbij and others in Fbij . One can rotate all centers in Rbij around bij for certain angle while keep all centers in Fbij xed. The induced Lie vector eld Lbij will be Lbij (xk ) = (xk xi ) bij , if xk Rbij ; Lbij (xk ) = 0, if xk Fbij . (60) (61)

x j xi . | x j xi |

(59)

Any such a Lie vector eld L will generate a family of conformations Xt = (x1 t , , xi t , , x M t ), where xk t = xk + t L(xk ), k = 1, , M. Moreover, the Lie vector eld L can be generated to the molecular surface MX , as shown in Appendix A. The derivative GL (X) is given by GL (X) = e e VL (X ) + dw e e A L ( MX ) + i i A L ( MX i ),
i =1 H

(62)

with VL (X ) =
MX

L NdH2 ,

A L ( MX ) = 2

MX

H ( L N )dH 2 ,

(63)

where N is the outer unit normal of MX , H the mean curvature of MX , and H2 the Hausdorff measure. Dene f t,i : R3 R as f t i (x) = dist(x, MXt i ) dist(x, MXt \ MXt i ), and dene on MX d f 0,i f MX f 0,i = f 0,i ( f 0,i N ) N, f 0,i = t i , = L f 0,i + f 0,i , (64) t t=0 dt then let be the unit outward conormal vector of MX i (normal to MX i but tangent to MX ), A L ( MX i ) = 2 H ( L N )dH 2 + L
d f 0,i dt

MX i

MX i

| MX f 0,i |

dH 1 .

(65)

The Xt is all the information needed in calculating the molecular surface MXt , see Connolly (1983). To calculate, the above formulas have to be translated into formulas on the molecular surface MX . These translations are given in Appendix A, they are calculable (all integrals are integrable, i.e., can be expressed by analytic formulas with variables X) and were calculated piecewise on MX . 10.3.4. The gradient Let a protein U have L rotatable bonds (b1 , , bi , , b L ). Let i denote the dihedral angle around the rotatable bond bi . A conformation X of U can be expressed in terms of these rotatable dihedral angles = (1 , , i , , L ), then G ( X ) = G ( ), (66)

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and the gradient of G can be written as

G () =

G G G , , , , 1 i L

() = ( G , , G , , G )(X). L L L
b1 bi bL bi

(67)

as Mi , new conformation Ys = ML ML1 . . . M1 will be obtained, where s > 0 is a suitable step length. That is to say, the dihedral angles of Ys are

If the rotation around bi with rotating angle sG (X) on Rbi and x atoms in Fbi be denoted L

[1 sG (X), , i sG (X), , L sG (X)]. L L L

b1 bi bL

The order of rotations in fact is irrelevant, i.e., by any order, the same conformation Ys will always be obtained, as proved in Fang and Jing (2008) and Appendix A. This way one can fast change the structure by simultaneous rotate around all rotatable bonds. This actually is the Newtons fastest descending method, it reduces the Gibbs free energy G (X) most efciently. Afore mentioned simulations of Fang and Jing (2010) used this method.

10.4. Kinetics
There are evidence that some proteins native structure is not the global minimum of the Gibbs free energy, but only a local minimum. If the native structure of a protein achieves the global minimal value of the Gibbs free energy, the folding process is thermodynamic; if it is only a local minimum, the folding process is kinetic, Lazaridis and Karplus (2003). With the formula (2) and the gradient just obtained, one actually has the kinetic in hand. In fact, for any atomic position xi , the kinetic force is Fi (X) = xi G (X), Dai (2007). With formula (2) these quantities are readily calculable as mentioned above. The resulting Newtons fastest descending method will help us nd the native structure, either in the thermodynamic case or in the kinetic case, here the thermodynamic and kinetic cases are combined by the Gibbs free energy formula (2) and its derivatives. The moving along G method was used in the simulation in Fang and Jing (2010).

11. Conclusion
A quantum statistical theory of protein folding for monomeric, single domain, self folding globular proteins is suggested. The assumptions of the theory t all observed realities of protein folding. The resulting formulas (1) and (2) do not have any arbitrary parameters and all terms in them have clear physical meaning. Potential energies involving pairwise interactions between atoms do not appear in them. Formulas (1) and (2) have explanation powers. They give unied explanation to folding and denaturation, to the hydrophobic effect in protein folding and its relation with the hydrogen bonding. The formulas also explain the relative successes of surface area protein folding models. Relation between kinetic and thermodynamic of protein folding is discussed, driving force formula comes from the Gibbs free energy formula (2) are also given. Energy surface theory will be much easier to handle. The concept of G is claried.

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 77 31

Appendix A. Calculations on the molecular surface

A.1. Rotation order
Let PX = iN 1 B(xi , ri ) and x0 and x1 be bonded by b , the rotation line of b is x0 + = x x t |x1 x0 | = x0 + tb . Each b divides {x1 , , x M } into two groups F and R , balls in 0 1 R will be rotated while balls in F will be xed. Note that these partitions are independent of PX , they only depend on the molecular graph of the protein molecule. Let M be this rotation-xation, it will be shown that M M (X) = M M (X), X (x1 , x2 , , x M ), 1 , L. (1)

The formula of rotating a point X around a line L : y = x + tb (|b| = 1) by an angle is R( X ) = x + A( )( X x). Let I be the identity matrix, B = bb T and Zb the matrix such that the outer product b X = Zb X, then the orthonormal matrix A( ) = (1 cos ) B + cos I + sin Zb . The topology of a protein molecule guarantees that if two bonds b and b such that R R , then {x0 , x1 } R . Let b1 and b2 be two bonds and L1 : x = x1 + tb1 and L2 : x = x2 + tb2 be the two rotating lines and X (x1 , x2 , , x N ). To prove equation (1), there are only two cases to consider: R1 R2 and R1 R2 = . In any case, if X F1 F2 , then M1 M2 ( X ) = M2 M1 ( X ) = X. If X R1 R2 , then M2 M1 ( X ) = x2 + A2 (2 )(x1 x2 )+ A2 (2 )A1 (1 )( X x1 ). (2)

On the other hand b1 and hence L1 itself will be rotated by M2 , L3 = M2 ( L1 ) = x3 + tb3 , where x3 = x2 + A2 (2 )(x1 x2 ), b3 = A2 (2 )b1 . Since X R1 R2 and M2 ( X ) R1 (in the new conformation M2 ( P) where rotation around b1 is rotation around L3 ), M1 M2 ( X ) will be the rotation R3 around L3 of M2 ( X ) by angle 1 , thus M1 M2 ( X ) = x2 + A2 (2 )(x1 x2 ) + A3 (1 )A2 (2 )( X x1 ). (3)

For any orthonormal matrix O, (Ob1 )(Ov) = b1 v, O(b1 v) = (Ob1 )(Ov). Then by b 3 = A 2 ( 2 ) b 1 , A3 A2 v = (1 cos 1 )[b3 (A2 v)]b3 + cos 1 (A2 v) + sin 1 b3 (A2 v)

Let v R3 be an arbitrary vector, writing A1 (1 ) = A1 , A2 (2 ) = A2 , and A3 (1 ) = A3 , then A2 A1v=(1 cos 1 )(b1 v)A2 b1 + cos 1 A2 v + sin 1 A2 (b1 v). (4)

= (1 cos 1 )(b1 v)A2 b1 + cos 1 A2 v + sin 1 A2 (b1 v).

(5)

Since v was arbitrary, equations (2) to (5) show equation (1) is true. If R1 R2 = and X R2 , then X and M2 ( X ) F1 hence M1 M2 ( X ) = M2 ( X ) = M2 M1 ( X ).

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The molecular surface is consisted of faces. Thus all integrals can be integrated piecewise on faces. There are three kinds of faces, convex, concave, and saddle, Connolly (1983). The formulas on each kind of face are given below. The notation x means L(x) with L the corresponding Lie vector eld. All van der Waals radii ri , as well as the probe radius r p , are constants.

A.2. Convex face

A convex face is a piece of spherical surface lying on some Si = B(xi , ri ) and bounded by circular arcs , = 1, , n F , let v0 and v1 be s vertices and c and r the center and radius of s circle, r the arc length of , e3 = (z1 , z2 , z3 ) be the unit vector in the direction
of (v0 c )(v1 c ), d = e3 (c xi ), e1 = r ij = ( x1 , x2 , x3 ), e2 = e3 e1 = (y1 , y2 , y3 ), 1 n F . A point x on F has the form x = xi ri N and X (x) = x ri N, by N N 0 and the general divergence formula on sphere, v0 c

ri where X =

( X N ) H dH 2 =

X N dH 2 =

M 1 xi ( X , Y , Z ), ri =1

(6)

r2 { z1 + sin [cos ( x2 y3 + x3 y2 ) + sin (y2 y3 x2 x3 )} 2 +r d z2 [y3 sin x3 (1 cos )] , r2 { z2 + sin [cos ( x3 y1 + x1 y3 ) + sin (y1 y3 x1 x3 )]} 2 +r d z3 [y1 sin x1 (1 cos )] , r2 { z3 + sin [cos ( x1 y2 + x2 y1 ) + sin (y1 y2 x1 x2 )]} 2 +r d z1 [y2 sin x2 (1 cos )] .

(7)

Y =

(8)

Z =

(9)

A.3. Concave face

A concave face F is a spherical polygon on the probe sphere S when S is simultaneously tangent to 3 balls B(xi , ri ), 1 i 3. F is expressed by parameters ti 0, i = 1, 2, 3, x = p + rN = p + r t1 x1 + t2 x2 + t3 x3 p , | t1 x1 + t2 x2 + t3 x3 p | t1 + t2 + t3 = 1. (10) (11)

t (x) = p(t) + rN (t) = p(t) + r

t1 x1 ( t ) + t2 x2 ( t ) + t3 x3 ( t ) p ( t ) , |t1 x1 (t) + t2 x2 (t) + t3 x3 (t) p(t)|

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 79 33

= p + r N. Using |p(t) xi (t)| = ri + r = constant, let bi = (xi p) xi , x1 p b = (b1 , b2 , b3 ) T , A = x2 p , then det A = 0, p = A1 b. By X N = p N, x3 p

t =0

dt (x) X (x) = dt

r ( X N ) H dH 2 =
F

3 1 X N dH2 = p ( Xi , Yi , Zi ). r i =1 F

(12)

Here the Xi , Yi , and Zi are the same as in equations (7) to (9). Assume that x1 has different water association with x2 and x3 , let Ri = ri + r, dij = |xi x j |, yij = ( R2 R2 )/2dij . Then f P (x) = (x p) nk , where nk = (xk x1 )/d1k is the directed i j

unit normal of the dividing plane Pk (passing through p and t1k = 1 (x1 + xk ) + y1k nk and 2 perpendicular to it), k = 2, 3. The projection of W F on the x1 x2 x3 plane is in the form of one or two curves k , ({ j, k} = {2, 3}) tk = Ak t j + Bk , 0 t j z j , Ak = where cos =
(x2 x1 )(x3 x1 ) . d12 d13

d1j cos

d1k

, Bk =

d1k + 2y1k , 2d1k

(13)

some k as above, so

Let Ak = x j x1 + Ak (xk x1 ), Bk = Bk (xk x1 ) + (x1 p), Ck = Bk Ak . Treating Ak and Bk as constants and setting Hk = p Ck , Jk = Ak Ck , and Kk = Bk Ck . Let ak t2 + bk t j + ck = j
2 |Ak t j + Bk |2 > 0, then k = 4ak ck bk > 0. By = Ntj N/| Ntj | and dH1 = r | Ntj |dt j ,

F W is a spherical polygon with arcs , 1 n, including ( X N ) HdH2 has the similar form as that in equation (12). W F

(W F )k

2ak z j + bk 2rH b X dH1 k arctan = arctan k k k k 2J bk z j + 2ck 2r k + 2 ck k a z2 + b z + c 2ak z j + bk 2r2 Kk bk + . k ck a z2 + b z + c

k j k j k k j k j k

(14)

where the sign is determined by orientation.

Let Uk = (Ak nk ), Vk = (Bk nk ), Wk = |Ck nk | > 0, then d fP 2r2 (2ak z j + bk )Vk bk V dt dH 1 = k 2+b z +c Wk ck k | M P f P | ak z j k j k (bk z j + 2ck )Uk , + 2 ck Uk a k z 2 + bk z j + c k j

(15)

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A.4. Saddle face

A saddle face F is generated when the probe S simultaneously tangents to two balls B(x1 , r1 ) and B(x2 , r2 ), and rolls around the axis e2 = x2dx1 . The starting and stopping positions of 12

the probe center is p and q. Let y = [(r1 + r )2 (r2 + r )2 ]/2d12 and t = 1 (x1 + x2 ) + ye2 , 2 R = |p t|, e1 = (p t)/R, e3 = e1 e2 , then F is parametrized by 0 s , 1 2 , x(, ) = t + ( R r cos )(cos e1 + sin e3 ) + r sin e2 , (16)

where let s = arccos[(p t) (q t)/R2 ], then s = s or 2 s . 1 = arctan[(d12 + 2y)/2R], 2 = arctan[(d12 2y)/2R]. These data are uniquely determined by the conformation P, see Connolly (1983). Let k (t) and s (t) be similarly dened for
s 2 1 the conformation Pt , one can dene t () = s , t ( ) = U () = cos e1 + sin e3 , then for the same 0 s and 1 2 ,

(t)

(t)( )+2 (t)( 2 ) , 2 1

and (17)

t (x) = t(t) + [ R r cos t ( )]U (t ()) + r sin t ( )e2 (t). Let U = cos e1 + sin e3 , U = sin e1 + cos e3 , then X (x) = t + ( R + r sin )U + ( R r cos )(U + U ) cos e2 + r sin e2 . +r

(18)

2r cos On F, N = cos U () + sin e2 , dH2 = r ( R r cos )dd, 2H = rRRr cos ) . Let J = ( s J (s ) = 0 U ()d, then

X NdH2 = 4rR(s t e2 RJ e2 )(cos 1 cos 2 )

+ 4rR(s R + t J )(sin 1 sin 2 ) 2 e2 RJ e2 )(cos 21 cos 22 ) r (s t + r2 (s R + t J )[2(1 2 ) + sin 21 sin 22 ],

(19)

( X N ) H H2 = 2R(s t e2 R e2 )(cos 1 cos 2 ) d r (s t e2 RJ e2 )(cos 21 cos 22 ) + t J )[2(1 2 ) + sin 21 sin 22 ]. + r (s R + 2R(s R + t J )(sin 1 sin 2 ) (20)

Assume that x1 is hydrophobic and x2 is not, then the dividing plane P passing through p and t and is perpendicular to e2 . The curve W F is given by x() = t + ( R r )U (), 0 s , on which dH1 = ( R r )d. The hydrophobic surface integral on F then is the same as in d (t) equation (20), except 1 = 0. Since on W F, = N N = e2 , |t=0 = 0 = 1 2 2 1 , by equation (18),
dt 2 1

W F

X dH1 = ( R r )s (r 0 + t e2 ) ( R r )2 e2 J,

(21)

Gibbs Free Energy Formula for Protein Folding

Gibbs Free Energy Formula for Protein Folding 81 35

d f Pt (t ( X )) | t =0 dt

Let n j = e2 , then f Pt (t (x)) = [t (x) t(t)] n j (t), | MP f P | = n j = 1, and [t ( X ) t(t)] e2 + [( R r )U ] e2 = r 0 .

WP F

| MP f P |

d fP dt

dH1 = ( R r )s r 0 .

(22)

Author details
Yi Fang Department of Mathematics, Nanchang University, 999 Xuefu Road, Honggutan New District, Nanchang, 330031, China

12. References
[1] Annsen, C. B. (1973) Principles that govern the folding of protein chains. Science 181, 223-230. [2] Bader, R. F. W. (1990) Atoms in Molecules: A Quantum Theory. (Clarendon Press Oxford). [3] Bailyn, M. (1994) A Survey of Thermodynamics. American Institute of Physics New York. [4] Ben-Naim, A. (2012) Levinthals question revisited, and answered. Journal of Biomolecular Structure and Dynamics 30(1), 113-124 (2012). [5] Branden, C. and J. Tooze, J. (1999) Introduction to Protein Structure. (Second Edition, Garland). [6] Connolly, M. L. (1983) Analytical molecular surface calculation. J. Appl. Cryst., 16:548-558. [7] Dai, X. (2007) Advanced Statistical Physics. (Fudan University Press, Shanghai). [8] Dill, K. A. (1990) Dominant forces in protein folding. Biochemistry, 29 7133-7155. [9] Dyson, F. (2004) A meeting with Enrico Fermi: How an intuitive physicist rescued a team from fruitless research. Nature 427, 297. [10] Eisenberg, D and McLachlan, A. D. Solvation energy in protein folding and binding. Nature 319, 199-203. [11] ExPASy Proteomics Server. http://au.expasy.org/sprot/relnotes/relstat.html [12] Fang, Y. (2005) Mathematical protein folding problem. In: D. Hoffman, Ed, Global Theory of Minimal Surfaces. ( Proceedings of the Clay Mathematical Proceedings, 2 2005) pp. 611-622. [13] Fang, Y. and Jing, J. (2008) Implementation of a mathematical protein folding model. International Journal of Pure and Applied Mathematics, 42(4), 481-488. [14] Fang, Y. and Jing, J. (2010) Geometry, thermodynamics, and protein. Journal of Theoretical Biology, 262, 382-390. [15] Finkelstein, A. V. and Ptitsyn, O. B. (2002) Protein Physics: A Course of Lectures. Academic Press, An imprint of Elsevier Science, Amsterdam ... . [16] Greiner, W., Neise, L., and Stker, H. (1994) Thermodynamics and Statistical Mechanics. (Spriger-Verlag, New York, Berlin, ... ). [17] Jackson, R. M., and Sternberg, M. J. E. (1993) Protein surface area dened. Nature 366, 638. [18] Kang, H. J. and Baker, E. N. (2011) Intramolecular isopeptide bonds: protein crosslinks built for stress? TIBS, 36(4), 229-237.

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[19] Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63 (1959). [20] Lazaridis, T., and Karplus, M. (2003) Thermodynamics of protein folding: a microscopic view. Biophysical Chemistry, 100, 367-395. [21] Lee, B., and Richards, F. M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400. [22] Novotny, J., Bruccoleri, R., and Karplus, M. (1984) An analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol. 177, 787-818. [23] Popelier, P. (2000) Atoms in Molecules: An Introduction. (Prentice Hall). [24] Reynolds, J. A., Gilbert, D. B., and Tanford, C. (1974) Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. USA 71(8), 2925-2927. [25] Richards, F. M. (1977) Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6, 151-176. [26] Rose, G. D., Fleming, P. J., Banavar, J. R., and Maritan, A. (2006) A backbone based theory of protein folding. PNAS 103(45), 16623-16633. [27] Tun, I., Silla, E., and Pascual-Ahuir, J. L. (1992) Molecular surface area and hydrophobic effect. Protien Engineering 5(8), 715-716. [28] Wang, Y., Zhang, H., Li, W., and Scott, R. A. (1995) Discriminating compact nonnative structures from the native structure of globular proteins. PNAS, 92, 709-713. [29] Wu, H. (1931) Studies on denaturation of proteins XIII. A theory of denaturation. Chinese Journal nof Physiology 4, 321-344 (1931). A preliminary report was read before the XIIIth International Congress of Physiology at Boston, Aug. 19-24, 1929 and published in the Am. J Physiol. for Oct. 1929. Reprinted in Advances in Protein Chemicsty 46, 6-26 (1995).

Chapter 4 Chapter 0

Information Capacity of Quantum Transfer Channels and Thermodynamic Analogies

Bohdan Hejna
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50466

1. Introduction
We will begin with a simple type of stationary stochastic1 systems of quantum physics using them within a frame of the Shannon Information Theory and Thermodynamics but starting with their algebraic representation. Based on this algebraic description a model of information transmission in those systems by dening the Shannon information will be stated in terms of variable about the system state. Measuring on these system is then dened as a spectral decomposition of measured quantities - operators. The information capacity formulas, now of the narrow-band nature, are derived consequently, for the simple system governed by the BoseEinstein (BE) Law [bosonic (photonic) channel] and that one governed by the Fermi-Dirac (FD) Law [fermionic (electron) channel]. The not-zero value for the average input energy needed for information transmission existence in FD systems is stated [11, 12]. Further the wideband information capacity formulas for BE and FD case are stated. Also the original thermodynamic capacity derivation for the wideband photonic channel as it was stated by LebedevLevitin in 1966 is revised. This revision is motivated by apparent relationship between the BE (photonic) wideband information capacity and the heat efciency for a certain heat cycle, being further considered as the demonstrating model for processes of information transfer in the original wideband photonic channel. The information characteristics of a model reverse heat cycle and, by this model are analyzed, the information arrangement of which is set up to be most analogous to the structure of the photonic channel considered, we see the necessity of returning the transfer medium (the channel itself) to its initial state as a condition for a sustain, repeatable transfer. It is not regarded in [12, 30] where a single information transfer act only is considered. Or the return is
1

We deal with such a system which is taking on at time t = 0, 1, . . . states t from a state space . If for any t0 the relative frequencies IB of events B is valid that 1 T
t0 + T t = t0 +1

IB (t ) tends for T to probabilities pt0 ( B) we speak

about a stochastic system. If these probabilities do not depend on the beginning t0 , a stationary stochastic system is spoken about.

2012 Hejna, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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regarded, but by opening the whole transfer chain for covering these return energy needs from its environment not counting them in - not within the transfer chain only as we do now. The result is the corrected capacity formula for wideband photonic (BE) channels being used for an information transfer organized cyclicaly.

2. Information transfer channel

An information, transfer channel K is dened as an arranged tripartite structure [5]
Def Def Def

K = [ X, , Y ] where X = [ A, p X ()] , Y = [ B, pY ()] and

- X is an input stochastic quantity, a source of input messages a A+ = X , a transceiver,

(1)

- Y is an output stochastic quantity, a source of output messages b B+ = Y , a receiver, - output messages b Y are stochastic dependent on input messages a X and they are received by the receiver of messages, Y, - is the maximal probability of an error in the transfer of any symbol x A in an input message a X [the maximal probability of erroneously receiving y B (inappropriate for x) in an output message b Y ], - A denotes a nite alphabet of elements x of the source of input messages, - B denotes a nite alphabet of elements y of the source of output messages, - p X () is the probability distribution of evidence of any symbol x A in an input message, - pY () is the probability distribution of evidence of any symbol y B in an output message. The structure ( X, K, Y ) or (X , K, Y ) is termed a transfer (Shannon) chain. The symbols H ( X ) and H (Y ) respectively denote the input information (Shannon) entropy and the output information (Shannon) entropy of channel K, discrete for this while, H(X) =
Def x A

p X ( x ) ln p X ( x ), H (Y ) =

Def

y B

pY (y) ln pY (y)

(2)

The symbol H ( X |Y ) denotes the loss entropy and the symbol H (Y | X ) denotes the noise entropy of channel K. These entropies are dened as follows, H ( X |Y ) = p X,Y ( x, y) ln p X |Y ( x |y), H (Y | X ) = p X,Y ( x, y) ln pY | X (y| x ) (3)
A B A B Def Def

where the symbol p| (|) denotes the condition and the symbol p, (, ) denotes the simultaneous probabilities. For mutual (transferred) usable information, transinformation T ( X; Y ) or T (Y; X ) is valid that T ( X; Y ) = H ( X ) H ( X |Y ) and T (Y; X ) = H (Y ) H (Y | X ) (4)

From (2) and (3), together with the denitions of p| (|) and p, (, ), is provable prove that the transinformation is symmetric. Then the equation of entropy (information) conservation is valid H ( X ) H ( X |Y ) = H (Y ) H (Y | X ) (5)

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 85 3

The information capacity of the channel K (both discrete an continuous) is dened by the equation C = sup I ( X; Y )
Def

(6)

over all possible probability distributions q(), p().It is the maximum (supremum) of the medium value of the usable amount of information about the input message x within the output message y. Remark: For continuous distributions (densities) p[] (), p[|] (|) on intervals X , Y R, x X , y Y is H (X) = H (Y ) = H ( X |Y ) = H (Y | X ) =
X Y X X

p X ( x ) ln p X dx, pY (y) ln pY (y) dy

Y Y

(7) (8)

p X,Y ( x, y) ln p X |Y ( x |y) dxdy, p X,Y ( x, y) ln p(y| x ) dxdy

Equations (4), (5 are valid for both the quantities H () and H (|), as well as for their respective changes H ()[= H ()] and H (|)[= H (|)].

3. Representation of physical transfer channels

The most simple way of description of stationary physical systems is an eucleidian space of their states expressed as linear operators.2 This way enables the mathematical formulation of the term (physical) state and, generally, the term (physical) quantity. Physical quantities , associated with a physical system represented by the Eucleidian space are expressed by symmetric operators from the linear space L() of operators on , A L() [7]. The supposition is that any physical quantity can achieve only those real values which are the eigenvalues of the associated symmetric operator (symmetric matrix [i,j ]n,n , n = dim ). They are elements of the spectrum S() of the operator . The eigenvalues S() R of the quantity being measured on the system depend on the (inner) states of = this system . The pure states of the system = are represented by eigenvectors . It is valid that the scalar project (, ) = 1; in quantum physics they are called normalized wave functions. The mixed states are nonnegative quantities A; their trace [of an square matrix (operator) ] is dened Tr() =
Def i =1

i,i

and, for is valid that Tr() = 1.

(9)

The symmetric projector {} = [({})] (orthogonal) on the onedimensional subspace ({}) of the space is nonnegative quantity for which Tr( {}) = 1 is valid. The projector {} represents [on the set of quantities A L()] the pure state of the system . Thus, an arbitrary state of the system can be dened as a nonnegative quantity A for which Tr() = 1 is valid. For the pure state is then valid that 2 = and the state space of the system is dened as the set of all states of the system .
2

The motivation is the axiomatic theory of algebraic representation of physical systems [7].

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3.1. Probabilities and information on physical systems

3.1.0.1. Theorem: For any state the pure states i = {i } and numbers q(i |) 0 exists, that q(i |) 0, = 3.1.0.2. Proof: Let D () = { D : S()} is a disjoint decomposition of the set {1, 2, ..., n} of indexes of the base {1 , 2 , ..., n } of . The set {i : i D } is an orthogonal basis of the eigenspace ( |) of the operator [for its eigenvalue S()]. Then card D = dim ( |) 1 and [( |)] =
i D i =1

q(i|) i

where

i =1

q(i|) = 1

(10)

{i }, S()

(11)

Let q(i |) = is taken for all i D , S(). By the spectral decomposition theorem [9], =
S()

= Tr() =

S() n i =1

[( |)] =

S() n i =1

i D

{i } =

i =1

q(i|) {i }

(12)

q(i|) Tr( {i }) = q(i|) = 1

The symbol q(|) denotes the probability distribution into pure, canonic components i of is called: canonic distribution (q-distribution) of the state .3 Further the two distribution dened on spectras of A and A will be dealt: dimensional distribution (d-distribution) of the state 4 d( |) =
Def

dim ( |) dim ( |) = , dim n

S()

(13)

distribution of measuring (p-distribution) of the quantity A in the state , p(||) = Tr( ),

Def

S()

(14)

where { : S()} is the spectral decomposition of the unit operator 1. Due the nonnegativity of is p(||) = Tr( ) 0. By spectral decomposition of 1 and by denition of the trace Tr() is
S()

Thus the relation (14) denes the probability distribution on the spectrum of the operator S ( ).
3 4

p(||) = Tr

S()

= Tr(1) = 1

(15)

Or, the system spectral distribution SSD [11]. Or, the system distribution of the system spectral dimension SDSD [11].

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 87 5

The special case of the p-distribution is that for measuring values of , , p( ||) = Tr( ) = dim ( |), S() (16) It is the case of measuring the itself. Thus, by the equation (14), the term measuring means just the spectral decomposition of the unit operator 1 within the spectral relation with [4, 20]. The act of measuring of the quantity A in (the system) state gives the value from the spectrum S() with the probability p(||) = Tr( ) given by the p-distribution,
S()

p(||) =

S()

Tr( ) = 1

(17)

The measured quantity in the state is a stochastic quantity with its values [occuring with probabilities p(||)] from its spectrum S(). For its mathematical expectation, medium value is valid E() = Nevertheless, in the pure state = {} the values i = S() are measured, Tr(i ) = (i , i ) = ii . Let is an arbitrary stationary physical system and A is its arbitrary state. The physical entropy H() of the system in the state is dened by the equality
S()

Tr( ) = Tr

S()

= Tr() = (, )

(18)

H() = Tr( ln )

Def

(19)

When { : S()} is the decomposition of 1 spectral equivalent with , then it is valid that ln = ln and H() = ln dim ( |) (20)
S() S()

3.1.0.3. Theorem: For a physical system in any state is valid that

n

H() = q(i|) ln q(i|) = H [q(|)] = ln n

i =1

= ln n I [ p(||) d(|)]

S()

p( ||) ln

p( ||) d( |) (21)

where H () is the Shannon entropy, I () is the information divergence, p(||) is the p-distribution for the state , q(|) is the q-distribution for the state and d(|) is the d-distribution for the state , n = dim . 3.1.0.4. Proof: The relations in (21) follows from (20) and from denition (10) of the distribution q(|). From denitions (13) and (16) of the other two distributions follows that [12, 38] I [ p(||) d(|)] =

S() S()

dim ( |) ln

n dim ( |) dim ( |) (22)

dim ( |) ln n H() = ln n H()

88 6 Thermodynamics Fundamentals and Its Application in Science

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description denoted as follows, X = , Y = or Y = (), ( X |Y ) = (|), (Y | X ) = (|). The laws of information transfer are writable in this way too: C = sup I (; ), I (||) T (; )
,

Due to the quantities X, Y, X |Y, Y | X describing the information transfer are in our algebraic

(23)

H (, ) = H (, ) = H() + H (|) = H () + H (|)

I (; ) = I (; ) = H() H (|) = H () H (|) = H() + H () H (, )

(24)

4. Narrow-band quantum transfer channels

Let the symmetric operator of energy of quantum particle is considered, the spectrum of which eigenvalues i is S(). Now the equidistant energy levels are supposed. In a pure state i of the measured (observed) system the eigenvalue i = i , > 0. Further, the output quantity of the observed system is supposed (the system is cell of the phase space BE or FD) with the spectrum of eigenvalues S() = {0 , 1 , ..., } being measured with probability distribution Pr() = { p(0), p(1), p(2), ...} p(k ||i ) = 0 p(k i ) pro k i k<i (25)

Such a situation arises when a particle with energy i is excited by an impact from the output environment. The jump of energy level of the impacted particle is from i up to i+ j , i + j = k. The output i+ j for the excited particle is measured (it is the value on the output of the channel K . This transition j occurs with the probability distribution = Pr( j), j {0, 1, 2, ...} (26) Let be considered the narrowband systems (with one constant level of a particle energy) of BE or FD type [27] (denoted further by BE, , FD, ). Pr( j) = (1 p) p j , pj , 1+ p j {0, 1, ...}, p (0, 1), p k

In the BE system, bosonic, e.g. the photonic gas the BE distribution is valid

(27)

In the FD system, fermionic, e.g. electron gas the FD distribution is valid Pr( j) = j {0, 1}, p (0, 1), p k

(28)

where parameter p is variable with absolute temperature > 0; k is the Boltzman constant. Also a collision with a bundle of j particles with constant energies of each and absorbing the energy j of the bundle is considerable. E.g., by (e.g. BE, is the photonic gas) the monochromatic impulses with amplitudes i S are transferred, nevertheless generated from the environment of the same type but at the temperature TW , TW > T0 where T0 is the temperature of the transfer system K (the noise temperature). = It is supposed that both pure states i in the place where the input message is being coded - on the input of the channel K and, also, the measurable values of the quantity being =

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 89 7

The pure states with energy level i = i are achievable by sending i particles with energy of each. When the environment, through which these particles are going, generates a bundle of j particles with probability Pr( j) then, with the same probability the energy i+ j = k is decoded on the output. It is supposed, also, the innite number of states i , innite spectrum S() of the measured The narrowband, memory-less (quantum) channel, additive (with additive noise) operating on the energy level S() is dened by the tripartite structure (1), quantity , then S() = {0, 1, 2, ...}, S() = D (); [S() = S, k = ].

observed on the place where the output message is decoded - on the output of the channel K = are arrangable in such a way that in a given i-th pure state i of the system K only = the values k S(), k = i + j are measurable and, that the probability of measuring the k-th value is Pr( j) = Pr (k i ). This probability distribution describes the additive noise in the given channel K. Just it is this noise which creates observed values from the output spectrum = S() = {i , i+1 , ...} being the selecting space of the stochastic quantity .

K = {[S , q(i|)], p(||i ), [S , p(||)]}.

(29)

4.1. Capacity of BoseEinstein narrowband channel

Let now i i, i = 0, 1, ... are pure states of a system BE, K and let is output quantity = taking on in the state i values S with probabilities p(||i ) = (1 p) pi (30) Thus the distribution p(||i ) is determined by the forced (innerinput) state i = {i } representing the coded input energy at the value i = i S(), = const. For the medium value W of the input i is valid

W=

i =0

i q(i|) = E(),

W = W

(31)

The quantity W is the medium value of the energy coding the input signal i. For the medium value of the number of particles j = i 0 with BE statistics is valid
j =0

j (1 p) p j = (1 p) p j p j1 = (1 p) p dp
j =0

1 p = 1 p 1 p (32)

The quantity E() is the medium value of the output quantity and E() =
S()

p(||)

where p(||) is the probability of measuring the eigenvalue = k of the output variable . n This probability is dened by the state = q(i |) i of the system BE, K =
i =0

p(||) =

i =0

q(i|) p(||i ) = (1 p) q(i|) pi

i =0

[= Tr( )]

(33)

90 8 Thermodynamics Fundamentals and Its Application in Science

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From the differential equation with the condition for = 0 p(||) = p( 1||) p + (1 p) q(|), 1; p(0||) = (1 p) q(0|) follows, for the medium value E() of the output stochastic variable , that E() =
1 1

(34)

p( 1||) p + (1 p) q(|)
1 1

(35)

p( 1||) p + W (1 p) = p E() + p p( 1||) + W (1 p)

W = E() > 0,
0 (36)

p E() (1 p) = p + W (1 p) E() = + W, 1+ p

The quantity H (i ) is the p-entropy of measuring for the input i S being represented by the pure state i of the system BE,

H (i ) =

= (1 p) ln(1 p) p j (1 p) p ln p j p j1
j j

jS

(1 p) p j ln[(1 p) p j ]

(37)

= ln(1 p) (1 p) p ln p

1 d h( p) , i S = dp 1 p 1 p

The quantity H (|) is the conditional Shannon entropy of the stochastic quantity in the state of the system BE, , not depending on the (the noise entropy) H (|) =
i =0

where h( p) = (1 p) ln(1 p) p ln p is the Shannon entropy of Bernoulli distribution { p, 1 p}.

q(i|) H (i ) = q(i|) 1 p
i =0

h( p)

h( p) 1 p

(38)

For capacity CBE of the channel K BE is, following the capacity denition, valid = h( p) CBE = sup H () H (|) = sup H () 1 p 0 0 (39)

where the set 0 = { , E() = W 0} represents the coding procedure of the input i S. The quantity H () = H ( p(||)) is the p-entropy of the output quantity . Its supremum is determined by the Lagrange multipliers method: H () =

S()

p(||) ln p(||) =

S()

p ln p , p = p(||)

(40)

The conditions for determinating of the bound extreme are

S()

p = 1,

S()

p = E() = const.

(41)

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 91 9

The Lagrange function L = p ln p 1 p + 1 2 p + 2 E()

(42)

which gives the condition for the extreme,

L = ln p 1 1 2 = 0, yielding in p

p = e11 e2 = p(||) and further, in

p =

e 1 1 e 1 1 = =1 2 e 1 e 2 2

(43)

Then for the medium value E() the following result is obtained E ( ) = p = e 1 1 e 2 = e 1 1

e
2

(44)

= e 1 1

1 1 e 2

e 1 1 e 2 e 2 = 2 )2 (1 e 1 e 2

By (35), (36) and for the parametr p=e k = const. ( = const. = const.) E() is a function is e2 = p(W ) and E() is the medium value for with the of W only. For 2 = kTW geometric probability distribution p() = p(||) = [1 p(W )] p(W ) , S() (45)

depending only on valid that

or, on the absolute temperature TW respectively. Thus for E() is kTW E() = p(W ) , p(W ) = e kTW 1 p(W )

(46)

From (35) and (46) is visible that p(W ) or TW respectively is the only one root of the equation e kTW p e kT0 p(W ) + W , resp. = +W = kT 1 p(W ) 1 p 1 e kT0 1e W

(47)

From (34) and (45) follows that for state 0 or, for the q-distribution q(|) respectively, in which the value H () is maximal [that state in which achieves the distribution q(|) = p()], is valid that q(|) = 1 p(W ) 1 p(W ) [ p(W ) p] p(W )1 , > 0 , = 0 and q(|) = 1 p 1 p (48)

For the effective temperatutre TW of coding input messages the distribution (45) supremizes (maximizes) the p-entropy H () of and, by using (37) with p(W ), is gained that h[ p(W )] sup H () = 1 p(W ) 0 h[ p(W )] h( p) 1 p(W ) 1 p (49)

From (39) and (49) follows [12, 37] the capacity CBE, of the narrowband channel K BE = CBE, = (50)

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By (35), (36) and (46) the medium value W of the input message i S is derived,

W=

p(W ) p 1 p(W ) 1 p

(51)

By (31) the condition for the minimal average energy WKrit needed for coding the input message is

W 0 resp. W = W 0, W WKrit , WKrit = 0

The relations (35), (36), (46) and (52), (53) yield in E() =

S()

(52) (53)

p(W ) p and, then p(W ) p, 1 p(W ) 1 p 1 p(W ) 1 p

(54)

From (47) and (54) follows that for the dened direction of the signal (messaage) transmission at the temperature TW of its sending and decoding is valid that p(W ) p , p(W ) > p, W > 0 > 1 p(W ) 1 p
kT W

(55) (56)

p(W ) = e

kT 0

= p and thus TW T0

4.2. Capacity of FermiDirac narrowband channel

Let is now considered, in the same way as it was in the BE system, the pure states i i of the system which are coding the input messages i = 0, 1, ... and the output stochastic quantity having its selecting space S. On the spectrum S probabilities of realizations S are dened, p i p(||i ) = , p (0, 1), i = 0, 1, ... (57) 1+ p expressing the additive stochastic transformation of an input i into the output for wich is valid = i or = i + 1.5 The uniform energy level = const. of particles is considered. The quantity W is the mathematical expectation of the energy coding the input signal W = W, W =
iS

i q(i|) = E()

(58)

The medium value of a stochastic quantity with the FD statistic is given by

j{0,1}

pj p = 1+ p 1+ p

(59)

The quantity E() is the medium value of the output quantity , E() =
5

S()

p(||)

(60)

In accordance with Pauli excluding principle (valid for fermions) and a given energetic level S().

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 93 11

where p(||) is probability of realization of S in the state of the system FD, , =K =

iS

q(i|) i ,

p(||) =

i =0

q(i|) p(||i ) = 1 + p q(i|) pi

i =0

(61)

From the differential equation p(||) = with the condition for = 0, p(0||) = q( 1|) p + q(|) , 1+ p 1 (62)

1 q(0|) 1+ p

follows that for the medium value E() of the output stochastic variable is valid that E() = p 1 q( 1|) + q(|) 1 + p 1 1 + p 1 p p 1 = ( 1) q( 1|) + q( 1|) + W 1 + p 1 1 + p 1 1+ p p p 1 W + + W 1+ p 1+ p 1+ p (63)

E() =

p + W , W = E(), 0 1+ p

The quantity H (i ) is the p-entropy of measuring for the input i S being represented by the pure state i of the system FD, H (i ) = pj 1 p pj 1 p ln = ln ln 1+ p 1+ p 1+ p 1+ p 1+ p 1+ p j =0 p 1+ p
1

(64) , i S

= 1

ln 1

p 1+ p

p p ln =h 1+ p 1+ p

p 1+ p

The quantity H (|) is the conditional (the noise) Shannon entropy of the stochastic quantity in the system state , but, independent on this , H (|) =

i =0

q(i|) H (i ) = q(i|) h
i

p 1+ p

=h

p 1+ p

(65)

For capacity CFD, of the channel K FD, is, by the capacity denition in (23)-(24), valid = that p CFD = sup H () H (|) = sup H () h (66) 1+ p
0 0

The quantity H () = H ( p(||)) is the p-entropy of the stochastic quantity in the state of the system FD, . Its supremum is determined by the Lagrange multipliers method in the same way as in BE case and with the same results for the probility distribution p(||) (geometric) and the medium value E()

where the set 0 = { : E() = W > 0} represents the coding procedure.

94 12 Thermodynamics Fundamentals and Its Application in Science

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p() = p(||) = [1 p(W )] p(W ) , S() p(W ) , p(W ) = e kTW E() = 1 p(W )

(67)

For the q-distribution q(|) = p() of states 0 , for which the relation (62) and (67) is gained, follows that q( 1|) p + q(|) = [1 p(W )] p(W ) , 1+ p
1 i =0

, or on absolute temperature TW respectively, only. By kTW using E() in (63) it is seen that p(W ) or TW respectively is the only one root of the equation [12, 30] p(W ) e kTW p e kT0 + W , resp. = +W (68) = 1 p(W ) 1+ p 1 + e kT0 1 e kTW Again , the value E() depends on

S with conditions

(69)

q(0|) = (1 + p) [1 p(W )] and q(1|) = (1 + p) [1 p(W )] [ p(W ) p]; q(|) = (1 + p) [1 p(W )]

(1)i p(W )i pi

+ (1) p , > 1

For the effective temperatutre TW of coding the input messages the distribution (67) supremises (maximizes) the p-entropy H () of is valid, in the same way as in (49), that h[ p(W )] sup H () = 1 p(W ) 0 h[ p(W )] h 1 p(W ) (70)

By using (70) in (66) the formula for the CFD, capacity [12, 37] is gained CFD, = p 1+ p (71)

The medium value W of the input i = 0, 1, 2, ... is limited by a minimal not-zero and positive bottom value WKrit . From (58), (63) and (68) follows E() = p(W ) p , p(W ) = e kTW e kT0 = p and thus TW T0 1 p(W ) 1 p (72)

W=

For the average coding energy W, when the channel CFD, acts on a uniform energetic level , is 2p2 W WKrit = (74) 1 p2 For the FD channel is then possible speak about the effect of the not-zero capacity when the difference between the coding temperatures TW and the noise temperature T0 is zero.6 This phennomenon is, by necessity, given by properties of cells of the FD phase space.
6

p(W ) p 2p2 2e 0, W = WKrit , resp. W = W (73) 2 1 p(W ) 1 + p 1 p2 1 e kT0

2 kT 0

Not not-zero capacity for zero input power as was stated in [37]. The (74) also repares small missprint in [11].

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 95 13

5. Wideband quantum transfer channels

Till now the narrowband variant of an information transfer channel K , S(), card S() = 1 has been dealt. Let is now considered the symmetric operator of energy of a particle, having the spectrum of eigenavalues S() = 0, h 2h nh , , ..., , ...

rh

r =0, 1, ..., n

, card S() = n + 1

(75)

where > 0 denotes the time length of the input signal and h denotes Planck constant. The multiband physical transfer channel K, memory-less, with additive noise is defend by the (arranged) set of narrowband, independent components K , S(), K= i= =
S()

K = ) S(
i =
S()

i , p( | |,i ), = i, p(||i ), i S = {0, 1, 2, ...} S = {0, 1 , 2, ...}

(76)

S()

[S, q (i | )],

Due the independency of narrowband components K the vector quantities i , , , j are independent stochastic quantities too. The simultaneous q-distribution of the input vector of i and the simultaneous p-distribution of measuring the output vector of values (of the individual narrowband components K ) are

S( S() = ) [S, p( | | )],

S() S()

q (i | ) = q(i |),

= =

S() S()

, ,

i S (i ) S()

(77) (78)

p( | | ) = p(||),

The system of quantities (the set of states of the narrowband components K ) is the state of the multiband channel K in which the (canonic) q-distribution of the system K is dened. Values i , j , = j + i ; =
S()

, j =

(79) are the numbers of the input, output and additive (noise) particles of the multiband channel K. In this channel the stochastic transformation of the input i into the output is performed, being determined by additive stochastic transformations of the input i into the output in individual narrowband components K . Realizations of the stochastic systems i, , , j are the vectors (sequences) i, , , j i = (i )S() , = ( )S() , = ( )S() , j = ( j )S() ; i, , j =
i S

S()

j , i =

S()

i ; j = i 0, S(), cardS > 1

i , , j S, S( ),

,i ,

S()

S, (80)

S()

96 14 Thermodynamics Fundamentals and Its Application in Science

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For the probability of the additive stochastic transformation (77), (78) of input i into the output is valid
S()

p( | |,i ) = p(||i ), = j + i, i S(i ), j S( j), S()

(81)

The symbol ,i denotes the pure state coding the input i S of a narrowband component K and the state i = S() ,i codes the input i for which q(i |) = q =
S()

q ( )

(82)

For the multiband channel K the following quantities are dened:7 the p-entropy of the output H () =
S()

H ( ) = sup H ( )

S() S

p( | | ) ln p( | | )

(83)

S()

for which, following the output narrowband BE and FD components K K, is valid that h[ p (W )] sup H () = sup H ( ) = sup H ( ) = 1 p (W ) S() S() 0 0 S() the conditional noise entropy (entropy of the multiband BE | FD noise) H (|) =
S()

(84)

H ( | ) =
kT
0W

S() iS

q(i|,i ) H ( ,i ) =
kT
0

h( p ) h 1 p S()

p 1 + p

(85)

where p (W ) = e p ).

, p = e

, TW T0 > 0 and h( p) = p ln p (1 p) ln(1

the transinformation T (; ) and the information capacity C (K), C (K ) = sup T (; ) = sup H () H (|) 0 0 p h( p ) h[ p (W )] = h 1 p (W ) ) 1 p 1 + p S() S( The set 0 =
S()

(86)

of the K into i , [by transforming each input i into pure state ,i , S()].
7

{ ; E( ) = W 0} represents a coding procedure of the input i

Using the chain rule for simultaneous probabilities it is found that for information entropy of an independent stochastic system X = ( X1 , X2 , ..., Xn ) is valid that H ( X ) = H ( Xi | X1 , ...Xi1 ) = H ( Xi ). Thus the physical entropy H() of independent stochastic system, = { } , is the sum of H [q(| )] over S too.
i i

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 97 15

5.1. Transfer channels with continuous energy spectrum

Let a spectrum of energy with the nite cardinality n + 1 and a nite time interval > 0 are considered S() = { r }r=0, 1, ..., n = card S() = rh
r =0, 1, ..., n

h rh , r = = r ,

(87)

n h h = n + 1, n = n = n , = = const. n n

For a transfer channel with the continuous spectrum of energies of particles and with the n bandwidth equal to card S() = , is valid that h

lim r = lim

rh 1 d = lim r = r d resp. lim = , h

S() = 0, n )

(88)

But the innite wideband and innite number of particles ( , n ) will be dealt with. Then S() = { r }r=0, 1, ... = rh
r =0, 1, ...

= lim r = lim

rh = lim r = r d 0

(89)

and thus the wideband spectrum S() of energies is

lim

1 d = , h

S() = 0, )

(90)

With the denotation = , i = i , j = j , i , j S, S, S() For the p-entropy of the output of the wideband transfer channel KBE|FD is valid that H () = lim

1 1 H ( ) = lim p( | | ) ln p( | | )(91) ) S( S() S

0 S

1 h

p(| | ) ln p(| | ) d
0

sup H () = lim

1 1 sup H ( ) = h S()

h[ p (W )] d 1 p (W )

For conditional entropy of the wideband transfer channel KBE|FD [entropy of the wideband noise independent on the system (KBE|FD ) state ] and for its information capacity is valid, by (85) and (86) H (|) = lim

1 h

1 1 H ( | ) = lim q(i|,i ) H ( ,i ) ) S( S() iS H ( | ) d =

0

(92)

1 h

C ( KBE|FD ) = =

1 h

h[ p (W )] 1 d 1 p (W ) h

h( p ) h 1 p

p 1 + p

d d (93)

h( p ) h 1 p

p 1 + p

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By (52) and (74) the average number of particles on the input of a narrowband component K is

W =

iS

i q(i| )

2p2 1 p2

(94)

and then for the whole average number of input particles W of the wideband transfer channel K is obtained 1 1 W = W d, W = W d (95) h 0 h 0 where W is whole input energy and TW is the effective coding temperature being supposingly at the value TW , TW = TW , S().

5.2. BoseEinstein wideband channel capacity

By derivations (86) and (92), (93) is valid that [12] C ( KBE ) = 1 h
0

For the rst or, for the second integral respectively, obviously is valid 1 h
0

h[ p (W )] 1 d 1 p (W ) h

h( p ) d 1 p

(96)

Then, for the capacity of the wideband BE transfer channel KBE is valid C ( KBE ) =

1 h[ p (W )] 2 kTW d = resp. 1 p (W ) 3h h

h( p ) 2 kT0 d = 1 p 3h

(97)

2 k 2 kTW TW T0 2 kTW ( TW T0 ) = = max , TW T0 3h 3h TW 3h

2 k2 TW p (W ) d = 1 p (W ) h

(98)

and for the whole average output energy is valid p (W ) 1 1 1 p (W ) = h S() lim
0

1 0

2 2 k2 TW ln(1 t) dt = t 6h

For the whole average energy of the BE noise must be valid

(99)

lim

p 1 1 = ) 1 p h S(

p 2 k2 T0 2 d = 1 p 6h

(100)

From the relations (79) among the energies of the output , of the noise j and the input i ,
2 2 k2 TW 2 k2 T0 2 = +W 6h 6h

(101) 1+ 6hW . Using it in (98) 2 k2 T0 2 (102)

the effective coding temperature TW is derivable, TW = T0 gives C ( KBE ) = 2 kT0 3h 1+ 6hW 2 k2 T0 2

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 99 17

For T0 0 the quantum aproximation of C (KBE ), independent on the heat noise energy (deminishes whith tempertures aiming to absolute 0 K) 2 4 2 2 k T0 + 2 2W kT0 = 2W (103) lim C (KBE ) = lim 3h 3h 3h 9h2 T0 0 T0 0

The classical approximation of C (KBE ) is gaind for temperatures T0 0 (T0 respectively). It is near to value W , the Shannon capacity of the wideband Gaussian kT0 channel with the whole noise energy kT0 and with the whole average input energy W. For T0 from (101), great enough, is gained that8 3hW W . 2 kT0 C ( KBE ) = = (104) 3h kT0 2 k2 T0 2

5.3. FermiDirac wideband channel capacity

By derivations (86) and (92), (93) is valid that [12] p p 1 h[ p (W )] 1 2 kTW 1 d = d d h h C ( KFD ) = h 0 1 p (W ) h 0 1 + p 3h h 0 1 + p (105) For the second integral obviously is valid p 1 2 kT0 h (106) d = h 0 1 + p 6h By guring (105) the capacity of the wideband FD channel KFD is gained, 2 k T C ( KFD ) = TW 0 3h 2 and for TW > T0 is writable C (KFD ) = C (KBE )

0

(107)

For the whole average output energy is valid the same as for the BE case, 1 h
2 2 k2 TW p (W ) d = 1 p (W ) 6h

2TW T0 2TW 2T0

(108)

(109)

For the whole average FD wideband noise energy is being derived p 1 1 lim 1 + p = h S()

0

kT

1+e
0

kT 0

d = dt =

k2 T0 2 h

e x dx 1 + e x

(110)

=
8

k2 T0 2 h

1 ln t

t+1

2 k2 T0 2 12h

For | x | < 1,

1+x = 1+

1 2x

1 2 8x

. + . . . = 1 + 1 x where x = 2

6hW < 1. 2 k2 T0 2

100 18 Thermodynamics Fundamentals and Its Application in Science

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From the relation (79) among the whole output, input, and noise energy,
2 2 k2 TW 2 k2 T0 2 = +W (111) 6h 12h 1 6hW + . Using it in (107) the follows the effective coding temperature TW = T0 2 2 k2 T0 2 result is [24] 2 kT0 1 6hW 1 (112) C ( KFD ) = + 3h 2 2 k2 T0 2 2

By (74) the condition for the medium value of the input particles of a narrowband component 2p2 , from which the condition for K , S(), of the channel KFD is valid, W 1 p2 the whole input energy of the wideband channel KFD follows. By (95) it is gaind, for TW T0 > 0, that10 W lim 2p2 . 2 1 1 W lim 1 p2 = h S() S()
2 kT 0 e

The classical approximation of the capacity C (KFD ) is gained for T0 09 2 kT0 1 12hW 1 . 2 kT0 1 6hW 1 1+ C ( KFD ) = 1+ = (114) 3h 2 3h 2 2 k2 T0 2 2 k2 T0 2 2 2 W 2 kT0 2 kT0 = 21 + 2 2 1 , W = const. Wcrit T0 6h 6h kT0

For T0 0 the quantum approximation capacity C (KFD ), independent on heat noise energy kT0 is gaind (the same as in the BE case (103), 4 k2 T0 2 1 2W 2 kT0 1 2W + 2 = (113) lim C (KFD ) = lim 2 3h 3h 2 3h 9h2 T0 0 T0 0

1 e

2 kT

d=

2 k2 T0 2 = Wcrit>0 (115) 12h

6. Physical information transfer and thermodynamics

Whether the considered information transfers are narrowband or wideband, their algebraic-information description remains the same. So let be considered an arbitrary stationary physical system of these two bandtypes as usable for information transfer. Let a system state =
i =1

q(i| ) {i }
n i =1

of the system is the successor (follower, is written. The

equivocant) of the system state =

9 10

q(i|) {i } ,

. 1 + x = 1 + 1 x when | x | < 1; x = 12hW 2 . 2 2 k2 T0 If, in the special case of FD channel, it is considered that the value W given by the number of electrons as the average energy of the modulating current entering into a wire, over a time unit, then it is the average power on the electric resistor R = 1 too. For

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 101 19

distribution q(i | ) =

n n of the transformation matrix [ui,j ] of a base of the space = {}i=1 into the base { }i=1 .11

j =1

p(i| j) q( j|),

p(i | j) = (i , j )2 = u2 and , ensures existence ji

From the relation also is visible that it is reexive and transitive relation between states and, thus, it denes (a partial) arrangment on the set space . The terminal, maximal state for this arrangement is the equilibrial state + of the system : it is the successor of an arbitrary system state, including itself. The statistic, Shannon, information) entropy H () is a generalization of the physical entropyH(). The quantity I-divergence I () is, by (21), a generalization of the physical quantity I ( pd) = H(+ ) H() where the state + = 1 n for i = {i }, n i i =1 i = 1, 2, ..., n (116)

Information divergence I ( pd) 0 expresses the distance of the two probability distributions q(|) and q(|+ ) of states (stochastic quantities) = [S, q(|)] and + = [S, q(|+ )] (118)

is the equlibrial state of the system . The probability distribution into the canonic components i of + is uniform and thus H(+ ) = ln n = ln dim () (117)

Let for states , of the system is valid that . Then

6.0.0.5. H-Theorem, I I. Second Principle of Thermodynamics:

In the physical sense the divergence I ( pd) is a measure of a not-equilibriality of the state of the physical (let say a thermodynamic) system . Is maximized in the initial (starting), not-equilibrium state of the (time) evolution of the . It is clear that I ( pd) T (; )

H( ) H()
and the equality arises for = only [12, 38]. 6.0.0.6. Proof: (a) For a strictly convex function f (u) = u ln u the Jensen inequality is valid [23]

(119)

i =1 n

=
11

j =1

f [q( j|)] = q( j|) ln q( j|) = H [q(|)] = H()

j =1

f p(i| j) q( j|) p(i| j) f [q( j|)]

j =1 i =1 j =1 n

f p(i | j) q( j|)
j =1 n

j =1 n

p(i| j) f [q( j|)],

n

i = 1, 2 , ..., n

(120)

due to

i =1

p (i | j ) = 1

It is the matrix of the unitary operator u(t) expressing the time evolution of the system .

102 20 Thermodynamics Fundamentals and Its Application in Science

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and for distributions q(i | ) is valid H( ) H():

n n n i =1 j =1 i =1

(b) The equality in (119) arises if and only if the index permutation [i (1), i (2), ..., i (n)] exists that p(i | j) = [i |i ( j)], j = 1, 2, ..., n; then q[i ( j)| ] = q( j|), j = 1, 2, .... Let a xed j is given. Then, when 0 = p(i | j) = (i , j )2 , i = i ( j), the orthogonality is valid (j | j )

f p(i| j) q( j|) = q(i| ) ln q(i| ) = H( )

[ H()]

i =i ( j )

and, consequently, j [i( j) |i( j) ], p[i ( j)| j] = (i( j) , j )2 = 1. It results in j = i( j) . This ) = H( ) implies the equality q( j| ) { } = q [i ( j )| ] { } prooves that the equality H( j i( j)

(i |i ) ,

j = { j } = j ,

i = {i } = i

(121)

and = .

reppresents the information-theoretical expressing of the Brillouin (maximal) entropy defect H (the Brillouin negentropic information principle [2, 30]). For the state + is valid that + , . It is also called the terminal state or the (atractor of the time evolution) of the system .12 6.0.0.7. Gibbs Theorem: For all , of the system is valid

H-theorem says, that a reversible transition is not possible between any two different states = . From the inequality (119) also follows that any state of the system is the successor of itself, and, that any reversibility of the relation (the transition ) is not possible within the system only, it is not possible without openning this system . The difference H(+ ) H() = max H( ) H() = H q(|+ ) H [q(|)] (122)

and the equality arises only for = [38]. 6.0.0.8. Proof:

n

H() Tr( ln )

(123)

Let for , is valid that = q(i |) {i }, = q(i |) {i } and let the operators
i =1 i =1

, are commuting = , D () = { D : S()}, D () = { D : S()}, are their spectral decompositions. Let be the state the successor of , and relations p(||) = q(i | ) = p(|| ) and H( ) H() are valid. For the matrix (ij ) of the
i D
12

In this sense, the physical entropy H() (19), (21) determines the direction of the thermodynamic time arrow [2], H( ) H() H = 0, t = t t > 0. The equality occurs in the equlibrial (stationary) state + of the system t t and its environment.

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 103 21

n

operator in the base {1 , 2 , ..., n } is obtained that ij = uki ukj q(k|) and thus for

operators ln and Tr( ln ) is valid that ln = ln q(i|) {i }

n n

k =1

i =1

and Tr( ln ) =

i =1 k =1

u2 q(k|) ki

ln q(i |)

(124)

= q(i| ) ln q(i|)
i =1

For the information divergence of the distributions q(| ), q(|) and the entropy H( ) is valid that I [q(| )q(|)] =

i =1

q(i| ) ln

n q(i | ) 0, H( ) q(i| ) ln q(i|). ) q (i | i =1

(125)

By (119) for is writable that H() H( ) Tr( ln ). By (123) Tr( ln ) H( ) H() are valid; the rst equality is for I [q(| )q(|)] = 0, H( ) = H(), q(i | ) = q(i |), i = 1, 2, ..., n, = (126) the second equality is for = . The Gibbs theorem expresses, in the deductive (matematical-logical) way, the phenomenon of Gibbs paradox.13 From formulas (47), (55), (56) and (68), (72), (73) for the narrow-band BE and FD capacities follows that TW T0 = max 0 TW (127) and it is seen that the quantity temperature is decisive for studied information transfers. The last relation envokes, inevitably, such an opinion, that these transfers are able be modeled by a direct reversible Carnot cycle with efciency max (0, 1). Conditions leading to C[|] < 0 mean, in such a direct thermodynamic model, that its efciency should be max < 0. This is the contradiction with the Equivalence Principle of Thermodynamics [19]; expresses only that the transfer is running in the opposite direction (as for temperatures). e
kT
W

e kT0 1, e kT0

TW T0 TW

e0 ; > 0, T0 > 0 TW T0

As for BE channel; for the supposition W < 0 the inequalities TW < T0 and p(W ) < p would be gained which is the contradiction with (35), (36) and (47). It would be such a situation with the information is transferred in a different direction and under a different operation mode. Our sustaining on the meaning about the original organization of the transfer, for TW > T0 , then leads to the contradiction mentioned above saying only that we are convinced mistakenly about the actual direction of the information transfer. In the case TW = T0 for the capacity CBE from (50) is valid that CBE = 0. Then W = WKrit [= 0] for p(W ) = p. 2p2 TW < T0 and p(W ) < p is 1 p2 gained which is the contradiction with (68). For TW = T0 is for CFD from (71) valid As for FD channel; for the supposition W <
13

Derived by the information-thermodynamic way together with the I. and I I. Thermodynamic Principle and with the Equivalence Principle of Thermodynamics in [16, 17, 19].

104 22 Thermodynamics Fundamentals and Its Application in Science

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CFD =

Let be noticed yet the relations between the wideband BE and FD capacities and the model heat efciency max . For the BE capacity (98) is gained that C ( KBE ) = 2 kTW 3h TW T0 2 kTW 2 kTW = = Cmax (KBE ) (128) max max 1 TW 3h 3h Cmax (KBE ) = sup H () = H (i ) = H()

h( p) p + ln p ln(1 + p).14 1 p 1+ p

C (KBE ) > 0, TW > T0 ,

C ( KBE )

TW T0 (max 0)

0, TW T0
2 kTW = 3h

It is the information capacity for such a direct Carnot cycle where H ( X ) = For the wide-band FD capacity from (105) is valid C ( KFD ) = 2 kTW 2 kT0 , TW T0 and for TW > T0 , 3h 6h 2 kTW 2TW T0 2 kTW 2TW T0 = max C ( KFD ) = 3h 2TW 3h 2( TW T0 ) 2TW T0 = C ( KBE ) 2( TW T0 ) Cmax (KBE ).

(129)

Due to 1 max = Then,

T0 2 kTW is valid T0 = TW (1 max ) and also C (KFD ) = (1 + max ). TW 6h C (KFD ) = C ( KFD )

TW T0 (max 0)

max 1

2 kTW , 3h

(130)

1 1 2 kTW H (i ) = H() = 2 2 6h

C ( KFD )

2 kTW 2 kTW , 6h 3h

1 H(), H() 2

Again the phenomenon of the not-zero capacity is seen here when the difference between the coding temperature TW and the noise temperature T0 is zero. Capacities C (KFD ) 0 T are, surely, considerable for TW 0 , T0 and being given by the property of the FD phase 2 space cells. Capacities C (KBE ) < 0 and C (KFD ) < 0 are without sense for the given direction of information transfer.

14

Nevertheless the capacity CFD for this case W < WKrit is set in [12, 13]. Similar results as this one and (74) are gained for the MaxwellBoltzman (MB) system in [13].

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 105 23

Nevertheless, it will be shown that all these processes themselves are not organized cyclically by themselves. Further the relation between the information transfer in a wideband BE (photonic) channel organized in a cyclical way and a relevant (reverse) heat cycle will be dealt with. But, rstly, the way in which the capacity formula for an information transfer system of photons was derived in [30] will be reviewed.

6.1. Thermodynamic derivation of wideband photonic capacity

A transfer channel is now created by the electromagnetic radiation of a system L KLL of = photons being emitted from an absolute black body at temperature T0 and within a frequency bandwidth of = R+ , where is the frequency. Then the energy of such radiation is the energy of noise. A source of input messages, signals transmits monochromatic electromagnetic impulses (numbers ai of photons) into this environment with an average input energy W. n This source is dened by an alphabet of input messages, signals { ai }i=1 , with a probability distribution pi = p( ai ), i = 1, 2, ... , n.15 The output (whole, received) signal is created by additive superposition of the input signal and the noise signal. The input signal ai , within a frequency , is represented by the occupation number m = m(), which equates to the number of photons of an input eld with an energy level () = h. The output signal is represented by the occupation number l = l (). The noise signal, created by the number of photons emitted by absolute black body radiation at temperature T0 , is represented by the occupation number n = n(). The medium values of these quantities (spectral densities of the input, noise and output photonic stream) are denoted as m, n and l. In accordance with the Planck radiation law, the spectral density r of a photonic stream of absolute black body radiation at temperature and within frequency , is given by the Planck distribution, r () = h p(, ) p(, T0 ) p(, TW ) , n() = , l () = , p(, ) = e k 1 p(, ) 1 p(, T0 ) 1 p(, TW ) (131)

Thus, for the average energy P of radiation at temperature within the bandwidth = R+ is gained that P() =
0

(, )d =

dP() 2 k2 2 2 k2 = where (, ) = r ()h and . 6 h d 3 h

(132)

Then, for the average noise energy P1 at temperature T0 , and for the average output energy P2 at temperature TW , both of which occur within the bandwidth = R+ is valid that P1 ( T0 ) = 2 k2 T0 2 2 k2 TW 2 , P2 ( TW ) = . 6 h 6 h (133)

The entropy H of radiation at temperature is derived from Clausius denition of heat entropy and thus 1 dP( ) 2 k 2P( ) H= = d = (134) 3 h k 0 k d
15

To distinguish between two frequencies mutually deferring at an innitesimally small d is needed, in accordance with Heisenberg uncertainty principle, a time interval spanning the innite length of time, t ; analog of the thermodynamic stationarity.

106 24 Thermodynamics Fundamentals and Its Application in Science

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Thus, for the entropy H1 of the noise signal and for the entropy H2 of the ouptut signal on the channel L is 2 kT0 2P 2 kTW 2P2 = 1 , H2 = = (135) H1 = 3 h kT0 3 h kTW The information capacity CTW ,T0 of the wide-band photonic transfer channel L is given by the maximal entropy defect [2, 30]) by CT0 ,TW = H2 H1 =
TW T0

1 dP() 2 k d = k d 3 h

TW T0

d =

2 k ( TW T0 ) . 3 h

(136)

For P2 = P1 + W, where W is the average energy of the input signal is then valid that 2 k2 T0 2 2 k2 TW 2 = + W TW = T0 6h 6h Then, in accordance with (102), (103), (104) [30] CT0 ,W (KLL ) = 2 kT0 3h 1+ 6h W 1 2 k2 T0 2 (138) 1+ 6h W 2 k2 T0 2 (137)

7. Reverse heat cycle and transfer channel

A reverse and reversible Carnot cycle Orrev starts with the isothermal expansion at temperature T0 (the diathermic contact [31] is made between the system L and the cooler B ) when L is receiving the pumped out, transferred heat Q0 from the B . During the isothermal compression, when the temperature of both the system L and the heater A is at the same value TW , TW > T0 > 0, the output heat QW is being delivered to the A QW = Q0 + A (139) where A is the input mechanical energy (work) delivered into L during this isothermal compression. It follows from [2, 8, 28] that when an average amount of information I is being recorded, transmitted, computed, etc. at temperature , there is a need for the average energy W k I; at this case W = A. Thus Orrev is considerable as a thermodynamic model of information transfer process in the channel K L [14]. The following values are = changes of the information entropies dened on K16 : H (Y ) =

QW A Q0 output (= I ), H ( X ) = input, H (Y | X ) = noise kTW kTW kTW

(140)

where k is Boltzman constant. The information transfer in K L is without losses caused by = the friction, noise heat (Q0x = 0) and thus H ( X |Y ) = 0. By assuming that for the changes (140) and H ( X |Y ) = 0 the channel equation (4), (5) and (23) is valid The result is A QW 0 = max = H ( X ) kTW kTW Q0 + A Q0 A T (Y; X ) = = = H ( X ). kTW kTW kTW T ( X; Y ) =
16

(141)

In information units Hartley, nat, bit; H () = H (), H (|) = H (|).

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 107 25

In a general (reversible) discrete heat cycle O (with temperatures of its heat reservoires changing in a discrete way) considered as a model of the information transfer process in an transfer channel K L [17, 19] is, for the elementary changes H (k ) [maxk ] of information = entropies of L, valid that17 H (k ) [maxk ] =

But the other information arrangement, description of a revese Carnot cycle will be used further, given by Q0 H ( X ), QW H (Y ) and A H (Y | X ), H ( X |Y ) = 0 (142)

Q(k ) [maxk ] , k = 1, 2, ..., n kk

(143)

where n 2 is the maximal number of its elementary Carnot cycles Ok .18 The change of heat of the system L at temperatures k is Q(k ).

In a general (reversible) continuous cycle O [with temperatures changing continuously, n in the previous discrete system, at will be Q( )] considered as an information transfer process in a transfer channel K L is valid that = Q() dH () = = k Q() d andH ()= k
0

Q( ) d( ); Q()= k

Q( )d (144)

For the whole cycle Orrev , TW > T0 > 0, let be H ( X |Y ) = 0 and then H(X) =
TW S( TW ) S( T0 ) A( ) 2QW = = dH () = ( TW T0 ) (145) k k Orrev k T0 kTW 2 TW Q ( ) TW S( TW ) 2QW W W = = dH () = H (Y ) = [ H ( X ) = H (Y ) max ] k kW kTW 0 0 TW 0

H (Y | X ) = H (Y ) H ( X ) =

dH ()

TW T0

dH () =

T0 0

dH ()

T0 0

QW ( ) S( T0 ) 2QW 2QW T0 = = T0 = = H (X) k k kTW TW kTW 2

TW 0

T (Y; X ) = H (Y ) H (Y | X ) =

dH ()

T0 0

dH () =

TW T0

dH ()

Orrev

A( ) 2QW = max = H (Y ) max = H ( X ) = I k kTW

Obviously, T ( X; Y ) = H ( X ) H ( X |Y ) = T (Y | X ). Further it is obvious that T ( X; Y ) is the capacity CTW ,T0 of the channel K L too, = CTW ,T0 = T ( X; Y ) = H ( X ) =
Orrev

A( ) = k

TW T0

QW ( ) k

(146)

=
17 18

2QW max ( TW T0 ), CTW ,T0 = H (Y ) kTW 2

h and h is Planck constant. 2

In reality for the least elementary heat change Q = h is right where h = It is provable that the Carnot cycle itself is elenentary, not dividible [18].

108 26 Thermodynamics Fundamentals and Its Application in Science

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7.1. Triangular heat cycle

Elementary change d of temperature of the environment of the general continuous cycle O and thus of its working medium L (both are in the diathermic contact at ) causes the elementary reversible change of the heat Q() delivered, (radiated) into L, just about the value Q( ), Q( ) = Q() d, Q(W ) =
W 0

Q( ) d

(147)

Q() (148) For the whole change of entropy SL (W ), or for the entropy SL (W ) respectively, delivered into the medium L by its heating within the temperature interval (0, W , is valid that Q( ) = dSL ( ), dSL () = SL (W ) =
Def W 0

The heat Q(W ) is the whole heat delivered (reversibly) into L (at the end temperature W ). For the innitezimal heat Q( ) delivered (reversibly) into L at temperature and in accordance with the Clausius denition of heat entropy SL [22] is valid that

dSL () =

W 0

Q() =

W 0

Q( ) d

= SL (W ) (149)

when SL (0) = 0 is set down. By (148) for the whole heat Q(W ) deliverd into L within the temperature interval (0, W also is valid that Q(W ) =
W 0

dSL ( )
W)

(150)

Then, by medium value theorem19 is valid that (0, Q(W ) =

T0 S L ( W ) S L (0)

0 + W = W and 2 2
W)

dSL ( ) = [SL (W ) SL (0)] (0,

TW

(151)

For the extremal values T0 a TW of the cooler temperature of O and by (151) Q0 = Q( T0 ) = Q 0 = Q W =

0

QW ( ) and QW = Q( TW ) =

QW ( )
0 0

(152) T0 2

SL ( T0 ) S L (0) S L (0)

dSL ( ) = [SL ( T0 ) SL (0)] (0,T ) , (0,T ) = dSL ( ) = [SL ( TW ) SL (0)] (0,T ) , (0,T
W W)

SL ( TW )

TW 2

With SL (0) = 0 for the (end) temperatures , T0 , TW of L and the relevant heats and their entropies is valid Q( ) = SL ( ) 2Q( ) and then SL ( ) = 2 TW 2QW and then SL ( TW ) = QW = SL ( TW ) 2 TW T0 2Q0 Q0 = SL ( T0 ) and then SL ( T0 ) = 2 T0 (153)

19

Of Integral Calculus.

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 109 27

For the change SL of the thermodynamic entropy SL of the system L, at the tememperature running through the interval T0 , TW , by gaining heat from its environment (the environment of the cycle O ), is valid SL = SL ( TW ) SL ( T0 ) = 2 Q W Q 0 TW T0

TW T0

Q()

(154)

By (149) for the entropy SL (W ) of L at variable temperature 0, W , W TW , is gained that S L ( W ) =

W 0

SL () 2 S L ()d + d = 1 2
W 0 0

d 1 = 2 2
W

W 0

dS L ()

(155)

=
and then S L ( W ) = and thus

1 2

W 0 W

SL ()

SL ( )

dSL ( )

2Q(W ) W (156)

SL ( )

d = dSL ( )

By the result of derivation (155)-(156) for an arbitrary temperature of medium L is valid that20 2Q( ) l (157) SL ( ) = l , l = Q( ) = 2 , = 2 2 Obviously, from (154) for T0 , TW is derivable that SL = l ( TW T0 ) = l TW (1 ), = T0 TW (158)

Let such a reverse cycle is given that the medium L of which takes, through the elementary isothermal expansions at temperatures T0 , TW , the whole heat Q0 Q0 = or, with medium values Q0 =
TW T0 TW T0

Q() = Q() =
0 W)

TW T0

ld =

l 2 TW 2 T0 = QW Q(159) 0 2

SL ( TW ) SL ( T0 )

dSL () Q W TW + T0 Q 0 2 2 TW T0 T0 TW

= W(T ,T
and thus equivalently

[SL ( TW ) SL ( T0 )] =

Q0 = ( TW + T0 ) [ TW T0 ] = TW 2 (1 2 ), =

For a reverse reversible Carnot cycle O rrev , equivalent with the just considered general continuous heat cycle O , drawing up the same heat Q0 , consumpting the same mechanical
20

If

f (x) dx = x l x, l R.

d f ( x ), or

d f (x) dx , then ln | f ( x )| = ln | x | + ln L, L > 0, ln | f ( x )| = ln( L | x |), = f (x) x

f (x) =

110 28 Thermodynamics Fundamentals and Its Application in Science

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work A and giving, at its higher temperature tW (the average temperature of the heater of our general cycle), the same heat QW , is valid that Q0 = QW where = the transform ratio. Then QW = Q0 2tW l 2tW = TW 2 T0 2 = l tW ( TW T0 ) T0 + TW 2 T0 + TW T + TW A = QW (1 ) = l tW ( TW T0 ) 1 0 2tW l = ( TW T0 ) (2tW T0 TW ) 2 (160) (161)
T0 + TW 2

tW

is

For the elementary work A(, ) corresponding with the heat Q() pumped out (reversibly) from L at the (end, output) temperature of L and for the entropy SL () of the whole environment of O (including L with O ) is valid SL () Q() d d =

A(, d) = dSL () = l d

(162)

A(, d) = SL ()d = l d and A(d, d) = l dd = dSL ()d() = A

T0

ld d = l ( T0 )d = A(, d; T0 )

(163)

For the whole work A(W ; T0 ) consumpted by the general reverse cycle O between temperatures T0 and W , being coverd by elementary cycles (162), is valid that A(W ; T0 ) =
W T0 T0

dSL ( ) d =

W T0

T0

ld d = l

W T0

( T0 )d(164)

l l l 2l (W 2 T0 2 ) l T0 (W T0 ) = W 2 + T0 2 T0 W = (W T0 )2 2 2 2 2 T 2 2 = A = TW (1 ) , when it is valid that W = TW , = 0 TW O(W ,T0 ) TW + W = TW and then tW = TW = const. 2

But, then for the results for A in (160), (161) and (164) follows that tW = (165)

Thus our general cycle O is of a triangle shape, O = Orrev with the apexes

[lT0 , T0 ], [lTW , TW ], [lT0 , TW ]

and its efciency is 1 =

(166)

1 1 = max . Thus, the return to the initial (starting) state of 2 2 the medium L is possible by using the oriented abscissas (in the S T diagram)

[lTW , TW ], [lT0 , TW ] and [lT0 , TW ], [lT0 , T0 ]

(167)

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 111 29

For works A(, d; T0 ) of elementary Carnot cycles covering cycle Orrev (166), the range of their working temperatures is d and, for the given heater temperature T0 , W is, by (162)-(163) valid that d d = l ( T0 ) = l ( T0 )d = [SL ( ) SL ( T0 )] d

A(, d; T0 ) = QW ()

(168)

QW () = l ( T0 ) and for used in (160) is gained that + T0 = 2 T0 2 Q0 () = QW () () = l ( T0 ) 2 For the whole heats Q0 a QW being changed mutually between the working medium L of the whole triangular cycle Orrev and its environment (166), and for the work A, in its T + TW equivalent Carnot cycle O rrev with working temperatures 0 and TW , will be valid 2 21 that Q0 = QW = A =
TW T0 TW T0 0 TW T0 T0 0

ld d=

l l T 2 (1 2 ) = W = l ( TW T0 ) T0 + ( TW T0 )2 (169) 2 W 2

TW

ld d = l ( TW T0 ) TW = l TW 2 (1 ) ld d = lTW 2 (1 ) l TW 2 (1 )
Orrev

1 2

TW

(170) A

l l = l TW 2 (1 ) [1 (1 + )] = TW 2 (1 )2 = 2 2

7.2. Capacity corections for wideband photonic transfer channel

The average output energy P2 (W ) of the message being received within interval (0, TW of the temperature of the medium L KLL from [30], when 0 < 0 W and 0 T0 = and W TW are valid, is given by the sum of the input average energy W (W , 0 ) and the average energy P1 (0 ) of the additive noise P2 (W ) = P1 (0 ) + W (W , 0 ) (171)

The output message bears the whole average output information H2 (W ). By the medium value theorem is possible, for a certain maximal temperature W TW of the temperature (0, W , consider that the receiving of the output message is performed at the average (constant) temperature W = W . Then for the whole change of the output information 2 entropy H2 = H2 (W ) [the thermodynamic entropy SL (W ) in information units] is valid H2 (W ) =
21

P2 (W ) P ( ) + W ( W , 0 ) = 1 0 = H1 (W , 0 ) + H [W (W , 0 )] kW kW
2 k2 2 k2 = 2 . , l= 6 h 3 h

(172)

Further it willbe layed down =

112 30 Thermodynamics Fundamentals and Its Application in Science

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By (153) is valid that Q( ) = 2 and Q( ) = ld. Thus for (0, T0 a (0, TW is valid dHW (Y ) = Q(W ) l 2ld = dW , dHW (Y | X ) = kW k kW (173)

With W = TW and 0 = T0 and with the reducing temperature P2 = W + P1 = QW = TW 2 = Y H2 = H (Y ) =

TW 0

TW is possible to write 2 (174)

l l P 2(W + P1 ) 2TW 2 lT = = W dW = TW = T2 = W k k kTW kTW k k 2 2ld l P 2T0 2 lT 2 = T0 2 = T1 = = 0 W kTW kTW kTW kTW k 2

P1 = Q0 = T0 2 = Y | X H1 = H (Y | X ) =
T0 0

W = Q W Q 0 = X W 2 ( TW 2 T0 2 ) H [W ( TW , T0 )] = H ( X ) = T = W kTW k 2

(175)

By the channel equation (4), (5) and by equations (23)-(24) and also by denitions (174)-(175) and with the loss entropy H ( X |Y ) = 0 it must be valid for the transinformation T (; ) that T (Y; X ) = H (Y ) H (Y | X ) = l ( TW T0 ) (1 + ) = H ( X ) k (176) 2 k2 T , = 0, 3 h TW

T ( X; Y ) = H ( X ) H ( X |Y ) = H ( X ) = T ( X, Y ) and by using l = T (Y; X ) =

2 k 2 k T (1 2 ) = T (1 ) (1 + ) = CT0 ,W (KLL ) (1 + ) 3h W 3h W

For the given extremal temperatures T0 , TW the value T ( X; Y ) stated this way is the only one, and thus also, it is the information capacity C T0 ,TW (W ) of the channel KLL (the rst correction) C T0 ,TW = (W ) = T ( X; Y ) = 2 kT0 3h 1+ 6h W 1 (1 + ) 2 k2 T0 2 (177)

The information capacity correction (177) of the wideband photonic channel KLL [30], stated this way, is (1 + )-times higher than the formulas (102) and (138) say. The reason is in using two different information descriptions of the oriented abscissa [l0, 0], [lTW , TW ] in derivation (138) and (177) which abscissa [l0, 0], [lTW , TW ] is on one line in S T diagram and is composed from two oriented abscissas, [l0, 0],[lT0 , T0 ] and [lT0 , T0 ], [lTW , TW ] (178) The rst abscissa represents the phase of noise generation and the second one the phase of input signal generation. The whole composed abscissa represents the phase of whole output signal generation.

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 113 31

For the sustaining, in the sense repeatable, cyclical information transfer, the renewal of the initial or starting state of the transfer channel KLL L, after any individual information = transfer act - the sending input and receiving output message has been accomplished, is needed. Nevertheless, in derivations of the formulas (102), (177) and (138) this return of the physical medium L, after accomplishing any individual information transfer act, into the starting state is either not considered, or, on the contrary, is considered, but by that the whole transfer chain is opened to cover the energetic needs for this return transition from another, outer resources than from those ones within the transfer chain itself. In both these two cases the channel equation is fullled. This enables any individual act of information transfer be realized by external and forced out, repeated starting of each this individual transfer act.22 23 If for the creation of a cycle the resources of the transfer chain are used only, the need for another correction, this time in (177) arises. To express it it will be used the full cyclical thermodynamic analogy K of KLL used cyclically, K LL . The information transfer will be modeled by the cyclical thermodynamic process Orrev of reversible changes in the channel K K LL L and without opening the transfer chain. (Also K K BE ). = = = 7.2.1. Return of transfer medium into initial state, second correction Now the further correction for capacity formulas (102), (138) and (177) will be dealt with for that case that the return of the medium L into its initial, starting state is performed within the transfer chain only. It will be envisiged by a triangular reverse heat cycle Orrev created by the oriented abscissas within the apexes in the S T diagram (166), [lT0 , T0 ], [lTW , TW ], [lT0 , TW ]. The abstract experiment from [30] will be now, formally and as an analogy, realized by this reverse and reversible heat cycle Orrev O rrev , described informationaly, and thought as modeling information transfer process in a channel K K LL|BE L. Thus the denotation = = K K is usable. By (153)-(157) it will be Q( ) = 2 k2 2 l l l = 2 , QW = TW 2 , Q0 = T0 2 6h 2 2 2 (179)

The working temperature 0 of cooling and W of heating are changing by (157), 0 = 1 SL (0 ) T0 , TW and W = TW = const. l (180)

and the heat entropy SL () of the medium L is changing by (155)-(156), dSL = Q( ) 1 2Q( ) d and then SL ( ) = l = (181)

Using integral (149) it is possible to write that Q() =

22 23

Q( ) =

Q( ) d =

ld

(182)

For these both cases is not possible to construct a construction-relevant heat cycles described in a proper information way. But the modeling by the direct cycle such as in (128) is possible for the I I. Principle of Thermodynamics is valid in any case and giving the possibility of the cycle description.

114 32 Thermodynamics Fundamentals and Its Application in Science

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For the whole heats Q0 and QW being changed mutually between L with the cycle Orrev and its environment and, for the whole work A for the equivalent Carnot cycle O rrev with T + TW and TW is valid, by (169)-(170), that working temperatures 0 2 W = Q0 = l T 2 (1 2 ) = X, 2 W QW Q0 = A = QW = l TW 2 (1 ) = Y l T 2 (1 )2 = Y | X 2 W

(183)

For the whole work A delivered into the cycle Orrev , at the temperature TW , and the entropy SL of its working medium L is valid A A = = TW Orrev TW
Orrev
TW T0

l ( T0 ) d = TW

d TW
TW T0

(184)

A 1 = TW 2

TW

TW

T0

T0

dSL ( )

[SL ( TW ) SL ( T0 )]

d 2TW

l l A ( TW T0 )2 = TW (1 )2 = 2TW 2 TW

Following (4), (5) and (23) and the triangular shape of the cycle Orrev , the changes of information entropies by expressions (142), (169)-(170) are dened, valid for the equivalent O rrev 24 , see (142), H (X) = H (Y ) = H (Y | X ) =
Def Def Def

Q0 = kTW

TW

T0 TW T0 TW T0

0 0

Q( ) d = kTW

TW

T0 TW T0

0 0 TW T0

ld`
TW

1 d kTW

(185)

QW = kTW A 1 = kTW 2

TW

Q( ) d = kTW

ld`
TW T0

1 d kTW ld 1 d kTW

TW T0

Q( ) d 1 = kTW 2
TW T0

T (Y; X ) = H (Y ) H (Y | X ) =

l 2kTW

TW 0

TW T0

d d

and by gguring these formulas with l = H (X) = H (Y ) = H (Y | X ) = T (Y; X ) =

=
H ( X |Y ) =
24

l 2 kTW TW (1 2 ) = (1 2 ) 2k 6h l 2 kTW TW (1 ) = (1 ) k 3h l 2 kTW A T (1 )2 = (1 )2 = 2k W 6h Orrev kTW l l l T (1 ) T (1 )2 = T (1 ) (2 1 + ) k W 2k W 2k W 2 kT l W T (1 2 ) = (1 2 ) = H ( X ) = T ( X; Y ) 2k W 6h 0

2 k is gained that 3h

In accordance with the input energy delivered and the extremal temperatures used in [30].

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 115 33

It is visible that the quantity H (Y ) [= H ( X ) + H (Y | X )] is introduced correctly, for by (185) is valid that H (Y ) = l l l T (1 )2 + T (1 2 ) = T (1 ) (1 + 1 + )(186) 2k W 2k W 2k W l = TW (1 ) k

For the transinformation and the information capacity of the transfer organized this way is valid (177), 1 (187) T ( X; Y ) = C T0 ,TW (W ) 2 With the extremal temperatures T0 and TW the information capacity C T0 ,TW (W ) is given by T ( X; Y ) = C T0 ,TW (W ) and then Cmax =

T0 TW

lim C T0 ,TW (W ) = H (Y )

(188)

From the difference Q0 = W = Q0 QW (in L) follows that the temperature 6h W TW = T0 1 + . 2 k2 T0 2 Then, for the transinformation, in the same way as in (187), is now valid 2 k 2 k 1+ 2 kT0 6h W 1+ T ( X; Y ) = 1 2 = ( TW T0 ) = 1+ 1 6h 3h 2 3h 2 2 k2 T0 2 (189) The transiformation T ( X; Y ) is the capacity C (K ) and it is possible to write 2 kT0 6h W T ( X; Y ) = C (K ) = C T0 ,TW (W ) = 1+ 1 ( T0 + TW ) (190) 6hTW 2 k2 T0 2

= C TW (W ) =

W = C T0 (W ) = kTW

kT0

W 1+ 6h W 2 k2 T0 2

= C ( K LL|BE )

which value is 2 less than (177) and

2 less than (138). 1+

The classical aproximation CT0 (W ) of C T0 ,TW (W ) is gained for T0 0. This value is near Shannon capacity of the wideband Gaussian channel with noise energy kT0 and with the whole average input energy (energy) W; in the same way as in (104) is now gained 3h W W W . 2 kT0 CT0 (W ) = (1 + ) = (1 + ) (192) 6h 2kT0 kT0 2 k2 T0 2

For T0 0 the quantum approximation C (W ) of the capacity C T0 ,TW (W ) is obtained, independent on the noise energy (the noise power deminishes near the abslute 0 K) 4 k2 T0 2 W 2 kT0 W + 2 (1 + ) = (191) C (W ) = lim 6h 6h 6h T0 0 62 h2

116 34 Thermodynamics Fundamentals and Its Application in Science

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The mutual difference of results (189) and and (102), (138) [12, 30] is given by the necessity of the returning the transfer medium, the channel K K LL| B E L into its initial state = = after each individual information transfer act has been accomplished and, by the relevant temperatutre reducing of the heat Q0 [by TW in (183)-(189)]. Thus, our thermodynamic cyclical model K Orrev for the repeatible information transfer through the channel = K LL|BE is of the information capacity (189), while in [12, 30] the information capacity of the one-act information transfer is stated.25 By (189) the whole energy costs for the cyclical information transfer considered is countable.26

8. Conclusion
After each completed transmission of an input message and receipt of an output message (one-act transfer) the transferring system must be reverted to its starting state, otherwise the constant (in the sense repeatable) ow of information could not exist. The author believes that either the opening of the chain was presupposed in the original derivation in [30], or that the return of transferring system to its starting state was not considered at all, it was not counted-in. In our derivations this needed state transition is considered be powered within the transfer chain itself, without its openning. Although our derivation of the information capacity for a cyclical case (using the cyclic thermodynamic model) results in a lower value than the original one it seems to be more exact and its result as more precise from the theoretic point of view, extending and not ceasing the previous, original result [12, 30] which remains of its technology-drawing value. Also it forces us in being aware and respecting of the global costs for (any) communication and its evaluation and, as such, it is of a gnoseologic character.

Author details
Bohdan Hejna Institute of Chemical Technology Prague, Department of Mathematics, Studentsk 6, 166 28 Prague 6, Czech Republic

9. References
[1] Bell, D. A. Teorie informace; SNTL: Praha, 1961. [2] Brillouin, L. Science and Information Theory; Academia Press: New York, 1963. [3] Cholevo, A. S. On the Capacity of Quantum Communication Channel. Problems of Information Transmission 1979, 15 (4), 311. [4] Cholevo, A. S. Verojatnostnyje i statisti eskije aspekty kvantovoj teorii; Nauka: Moskva, 1980. c [5] Cover, T. M.; Thomas, J. B. Elements of Information Theory; Wiley: New York, 1991. [6] Davydov, A. S. Kvantov mechanika; SPN: Praha, 1978. [7] Emch, G. G. Algebrai eskije metody v statisti eskoj mechanike i kvantovoj torii polja; Mir: c c e Moskva, 1976.
25

26

For one-act information transfer the choose between two information descriptions is possible which result in capacity (138) or (177). 2 For the energy T ( X; Y ) TW on the output the energy TW greater is needed on the input of the transfer channel 1+ 2 which is in accordance with the I I. Principle of thermodynamics for > 1 is valid. 1+

Information Capacity of Quantum Transfer Information Capacity of Quantum Channels and Thermodynamic Analogies

Transfer Channels and Thermodynamic Analogies 117 35

[8] Gershenfeld, N. Signal entropy and the thermodynamics of computation. IBM Systems Journal 1996, 35 (3/4), 577586. DOI 10.1147/sj.353.0577. [9] Halmos, P. R. Kone nomernyje vektornyje prostranstva; Nauka: Moskva, 1963. c [10] Haek, O.; Noi ka, J. Technick mechanika pro elektrotechnick obory II.; SNTL: Praha, 1968. c [11] Hejna, B.; Vajda, I. Information transmission in stationary stochastic systems. AIP Conf. Proc. 1999, 465 (1), 405418. DOI: 10.1063/1.58272. [12] Hejna, B. Informa n kapacita stacionrnch fyziklnch systmu. Ph.D. Dissertation, c TIA AV CR, Praha, FJFI CVUT, Praha, 2000. [13] Hejna, B. Generalized Formula of Physical Channel Capacities. International Journal of Control, Automation, and Systems 2003, 15. [14] Hejna, B. Thermodynamic Model of Noise Information Transfer. In AIP Conference Proceedings, Computing Anticipatory Systems: CASYS07 Eighth International Conference; Dubois, D., Ed.; American Institute of Physics: Melville, New York, 2008; pp 6775. ISBN 978-0-7354-0579-0. ISSN 0094-243X. [15] Hejna, B. Proposed Correction to Capacity Formula for a Wide-Band Photonic Transfer Channel. In Proceedings of International Conference Automatics and Informatics08; Atanasoff, J., Ed.; Society of Automatics and Informatics: Soa, Bulgaria, 2008; pp VII-1VIII-4. [16] Hejna, B. Gibbs Paradox as Property of Observation, Proof of II. Principle of Thermodynamics. In AIP Conf. Proc., Computing Anticipatory Systems: CASYS09: Ninth International Conference on Computing, Anticipatory Systems, 38 August 2009; Dubois, D., Ed.; American Institute of Physics: Melville, New York, 2010; pp 131140. ISBN 978-0-7354-0858-6. ISSN 0094-243X. [17] Hejna, B. Informa n termodynamika I.: Rovnovn termodynamika penosu informace; c r VCHT Praha: Praha, 2010. ISBN 978-80-7080-747-7. [18] Hejna, B. Informa n termodynamika II.: Fyzikln systmy penosu informace; VCHT Praha: c r Praha, 2011. ISBN 978-80-7080-774-3. [19] Hejna, B. Information Thermodynamics, Thermodynamics - Physical Chemistry of Aqueous Systems, Juan Carlos Moreno-Pirajan (Ed.), ISBN: 978-953-307-979-0, InTech, 2011 Available from: http://www.intechopen.com/articles/show/title/information-thermodynamics [20] Helstroem, C. W. Quantum Detection and Estimation Theory; Pergamon Press: London, 1976. [21] Hork, Z.; Krupka, F. Technick fyzika; SNTL/ALFA: Praha, 1976. [22] Hork, Z.; Krupka, F. Technick fysika; SNTL: Praha, 1961. [23] Jaglom, A. M.; Jaglom, I. M. Pravdpodobnost a teorie informace; Academia: Praha, 1964. e [24] Chodasevi , M. A.; Sinitsin, G. V.; Jasjukevi , A. S. Ideal fermionic communication channel in c c the number-state model;Division for Optical Problems in Information technologies, Belarus Academy of Sciences, 2000. [25] Kal k, J.; Skora, K. Technick termomechanika; Academia: Praha, 1973. c [26] Karpuko, F. V.; Chodasevi , M. A. Sravnitelnoje issledovanije skorostnych charakteristik c bozonnych i fermionnych kommunikacionnych kanalov; Ves NAN B, The National Academy c of Sciences of Belarus, 1998. [27] Landau, L. D.; Lifschitz, E. M. Statistical Physics, 2nd ed.; Pergamon Press: Oxford, 1969. [28] Landauer, M. Irreversibility and Heat Generation in the Computing Process. IBM J. Res. Dev. 2000, 44 (1/2), 261. [29] Lavenda, B. H. Statistical Physics; Wiley: New York, 1991.

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[30] Lebedev, D.; Levitin, L. B. Information Transmission by Electromagnetic Field. Information and Control 1966, 9, 122. [31] Mark, Z. Termodynamika a statistick fyzika; CVUT: Praha, 1995. [32] Marx, G. vod do kvantov mechaniky; SNTL: Praha, 1965. [33] Moore, W. J. Fyzikln chemie; SNTL: Praha, 1981. [34] Prchal, J. Signly a soustavy; SNTL/ALFA: Praha, 1987. [35] Shannon, C. E. A Mathematical Theory of Communication. The Bell Systems Technical Journal 1948, 27, 379423, 623656. [36] Sinitsin, G. V.; Chodasevi , M. A.; Jasjukevi , A. S. Elektronnyj kommunikacionnyj kanal v c c modeli svobodnogo vyrodennogo fermi-gaza; Belarus Academy of Sciences, 1999. [37] Vajda, I. Teria informcie a tatistickho rozhodovania; Alfa: Bratislava, 1982. [38] Watanabe, S. Knowing and Guessing; Wiley: New York, 1969.

Chapter 5 Chapter 0

Thermodynamics Microscopic Connotations

A. Plastino, Evaldo M. F. Curado and M. Casas
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51370

1. Introduction
Thermodynamics is the science of energy conversion. It involves heat and other forms of energy, mechanical one being the foremost one. Potential energy is the capacity of doing work because of the position of something. Kinetic energy is due to movement, depending upon mass and speed. Since all objects have structure, they possess some internal energy that holds such structure together, a kind of strain energy. As for work, there are to kinds of it: internal and external. The later is work done on something". The former is work effected within something, being a capacity. Heat is another king of energy, the leit-motif of thermodynamics. Thermodynamics studies and interrelates the macroscopic variables, such as temperature, volume, and pressure that are employed to describe thermal systems and concerns itself with phenomena that can be experimentally reproducible. In thermodynamics one is usually interested in special systems states called equilibrium ones. Such states are steady ones reached after a system has stabilized itself to such an extent that it no longer keeps changing with the passage of time, as far as its macroscopic variables are concerned. From a thermodynamics point of view a system is dened by its being prepared in a certain, specic way. The system will always reach, eventually, a unique state of thermodynamic equilibrium, univocally determined by the preparation-manner. Empiric reproducibility is a fundamental requirement for physics in general an thermodynamics in particular. The main source of the strength, or robustness, of thermodynamics, lies on the fact does it deals only with phenomena that are experimentally reproducible. Historically, thermodynamics developed out the need for increasing the efciency of early steam engines, particularly through the work of the French physicist Nicolas Sadi-Carnot (1824) who believed that a heat engines efciency was to play an important role in helping France win the Napoleonic Wars. Scottish physicist Lord Kelvin was the rst to formulate a succint denition of thermodynamics in 1854: Thermodynamics is the subject of the relation of heat to forces acting between contiguous parts of bodies, and the relation of heat to electrical agency". Chemical thermodynamics studies the role of entropy in the process of chemical reactions and provides the main body of knowledge of the eld. Since Boltzmann in the 1870s,

2012 Plastino et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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statistical thermodynamics, or statistical mechanics, that are microscopic theories, began to explain macroscopic thermodynamics via statistical predictions on the collective motion of atoms.

1.1. Thermodynamics laws

The laws of physics are established scientic regularities regarded as universal and invariable facts of the universe. A law" differs from hypotheses, theories, postulates, principles, etc., in that it constitutes an analytic statement. A theory starts from a set of axioms from which all laws and phenomena should arise via adequate mathematical treatment. The principles of thermodynamics, often called its laws", count themselves amongst the most fundamental regularities of Nature [1]. These laws dene fundamental physical quantities, such as temperature, energy, and entropy, to describe thermodynamic systems and they account for the transfer of energy as heat and work in thermodynamic processes. An empirically reproducible distinction between heat and work constitutes the hard-core" of thermodynamics. For processes in which this distinction cannot be made, thermodynamics remains silent. One speaks of four thermodynamics laws: The zeroth law of thermodynamics allows for the assignment of a unique temperature to systems that are in thermal equilibrium with each other. The rst law postulates the existence of a quantity called the internal energy of a system and shows how it is related to the distinction between energy transfer as work and energy transfer as heat. The internal energy is conserved but work and heat are not dened as separately conserved quantities. Alternatively, one can reformulate the rst law as stating that perpetual motion machines of the rst kind can not exist. The second law of thermodynamics expresses the existence of a quantity called the entropy S and states that for an isolated macroscopic system S never decreases, or, alternatively, that perpetual motion machines of the second kind are impossible. The third law of thermodynamics refers to the entropy of a system at absolute zero temperature (T = 0) and states that it is impossible to lower T in such a manner that reaches the limit T = 0. Classical thermodynamics accounts for the exchange of work and heat between systems with emphasis in states of thermodynamic equilibrium. Thermal equilibrium is a condition sine qua non for macroscopically specied systems only. It shoul be noted that, at the microscopic (atomic) level all physical systems undergo random uctuations. Every nite system will exhibit statistical uctuations in its thermodynamic variables of state (entropy, temperature, pressure, etc.), but these are negligible for macroscopically specied systems. Fluctuations become important for microscopically specied systems. Exceptionally, for macroscopically specied systems found at critical states, uctuations are of the essence.

1.2. The Legendre transform

The Legendre transform is an operation that transforms one real-valued function of f a real variable x into another f T , of a different variable y, maintaining constant its information

Thermodynamics Microscopic Connotations

Thermodynamics Microscopic Connotations 121 3

content. The derivative of the function f becomes the argument to the function f T . f T (y) = xy f ( x ); y = f ( x ) reciprocity. (1)

The Legendre transform its own inverse. It is used to get from Lagrangians the Hamiltonian formulation of classical mechanics. Legendre reciprocity relations constitute thermodynamics essential formal ingredient [2]. In general, for two functions I and one has

I ( A1 , . . . , A M ) = +

k =1

k Ak ,

(2)

with the Ai extensive variables and the i intensive ones. Obviously, the Legendre transform main goal is that of changing the identity of our relevant independent variables. For we have

( 1 , . . . , M ) = I

k =1

k Ak .

(3)

The three operative reciprocity relations become [2] = Ak ; k I = k ; Ak

M I Ak = k , i i k

(4)

the last one being the so-called Euler theorem.

1.3. The axioms of thermodynamics

Thermodynamics can be regarded as a formal logical structure whose axioms are empirical facts [2], which gives it a unique status among the scientic disciplines [1]. The four axioms given below are equivalent to the celebrated laws of thermodynamics of the prevous Subsection [2]. For every system there exists a quantity E, the internal energy, such that a unique Es value is associated to each and every state s. The difference Es1 Es2 for two different states s1 and s2 in a closed system is equal to the work required to bring the system, while adiabatically enclosed, from one state to the other. There exist particular states of a system, the equilibrium ones, that are uniquely determined by E and by a set of extensive macroscopic parameters A , = 1, . . . , M. The number and characteristics of the A depends on the nature of the system. For every system there exists a state function S( E, A ) that (i) always grows if internal constraints are removed and (ii) is a monotonously (growing) function of E. S remains constant in quasi-static adiabatic changes.

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S and the temperature T = [ E ] A1 ,...,A M vanish for the state of minimum energy and are S non-negative for all other states. From the second and 3rd. Postulates one extracts the following two essential assertions 1. Statement 3a) for every system there exists a state function S, a function of E and the A S = S( E, A1 , . . . , A M ). (5)

2. Statement 3b) S is a monotonous (growing) function of E, so that one can interchange the roles of E and S in (5) and write E = E(S, A1 , . . . , A M ), Eq. (6) clearly indicates that dE = E E dA dE = TdS + P dA , dS + S A (7) (6)

with P generalized pressures and the temperature T dened as [2] T= E . S [ A ] (8)

Eq. (7) will play a key-role in our future considerations. If we know S( E, A1 , . . . , An ) or, equivalently because of monotonicity, E(S, A1 , . . . , An )) we have a complete thermodynamic description of a system [2]. For experimentalists, it is often more convenient to work with intensive variables dened as follows [2]. Let S A0 . The intensive variable associated to the extensive Ai , to be called Pi are the derivatives P0 T = [ E ] , 1/T = . S A1 ,...,An E . ] A j S,A1 ,...,A j1 ,A j+1 ,...,An (9)

Pj j /T = [

(10)

Any one of the Legendre transforms that replaces any s extensive variables by their associated intensive ones (, s will be Lagrange multipliers in SM) Lr1 ,...,rs = E Pj A j , ( j = r1 , . . . , rs )
j

contains the same information as either S or E. The transform Lr1 ,...,rs is a function of n s extensive and s intensive variables. This is called the Legendre invariant structure of thermodynamics. As we saw above, this implies certain relationships amongst the relevant

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systems variables, called the reciprocity relations (RR), that are crucial for the microscopic discussion of Thermodynamics.

2. Classical statistical mechanics

In 1903 Gibbs formulated the rst axiomatic theory for statistical mechanics [1, 3], revolving around the concept of phase space. The phase space (PS) precise location is given by generalized coordinates and momenta. Gibbs postulates properties of an imaginary (Platonic) ad-hoc notion: the ensemble" (a mental picture). The ensemble consists of extremely many (N) independent systems, all identical in nature with the one of actual physical interest, but differing in PS-location. That is, the original system is to be mentally repeated many times, each with a different arrangement of generalized coordinates and momenta. Here Liouvilles theorem of volume conservation in phase space for Hamiltonian motion plays a crucial role. The ensemble amounts to a distribution of N PS-points, representative of the actual system. N is large enough that one can properly speak of a density D at any PS-point = q1 , . . . , q N ; p1 , . . . , p N , with D = D (q1 , . . . , q N ; p1 , . . . , p N , t) D (), with t the time, and, if we call d the volume element, N= d D;

t.

(11)

Randomly extracting a system from the ensemble, the probability of selecting it being located in a neighborhood of would yield P() = D ()/N. Consequently, P d = 1. (13) Liouvilles theorem follows from the fact that, since phase-space points can not be destroyed", if N12 = then
2 1

(12)

D d,

(14)

dN12 = 0. (15) dt An appropriate analytical manipulation involving Hamiltons canonical equations of motion then yields the theorem in the form [1]
N N D D D+ pi + q = 0, pi qi i i i

(16)

entailing the PS-conservation of density. Equilibrium means simply D = 0, i. e.,

N D D p + q = 0. pi i qi i i

(17)

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2.1. The classical axioms

Gibbs refers to PS-location as the phase" of the system [1, 3]. The following statements completely explain in microscopic fashion the corpus of classical equilibrium thermodynamics [1]. The probability that at time t the system will be found in the dynamical state characterized by equals the probability P() that a system randomly selected from the ensemble shall possess the phase will be given by Eq. (12) above. All phase-space neighborhoods (cells) have the same a priori probability. D depends only upon the systems Hamiltonian. The time-average of a dynamical quantity F equals its average over the ensemble, evaluated using D.

3. Information
Information theory (IT) treats information as data communication, with the primary goal of concocting efcient manners of encoding and transferring data. IT is a branch of applied mathematics and electrical engineering, involving the quantication of information, developed by Claude E. Shannon [4] in order to i) nd fundamental limits on signal processing operations such as compressing data and ii) nding ways of reliably storing and communicating data. Since its 1948-inception it has considerably enlarged its scope and found applications in many areas that include statistical inference, natural language processing, cryptography, and networks other than communication networks. A key information-measure (IM) was originally called (by Shannon) entropy, in principle unrelated to thermodynamic entropy. It is usually expressed by the average number of bits needed to store or communicate one symbol in a message and quanties the uncertainty involved in predicting the value of a random variable.Thus, a degree of knowledge (or ignorance) is associated to any normalized probability distribution p(i ), (i = 1, . . . , N ), determined by a functional I [{ pi }] of the { pi } [47] which is precisely Shannons entropy. IT was la axiomatized in 1950 by Kinchin [8], on the basis of four axioms, namely, I is a function ONLY of the p(i ), I is an absolute maximum for the uniform probability distribution, I is not modied if an N + 1 event of probability zero is added, Composition law. As for the last axiom, consider two sub-systems [1 , { p1 (i )}] and [2 , { p2 ( j)}] of a composite system [, { p(i, j)}] with p(i, j) = p1 (i ) p2 ( j). Assume further that the conditional probability distribution (PD) Q( j|i ) of realizing the event j in system 2 for a xed i event in system 1. To this PD one associates the information measure I [ Q]. Clearly, p(i, j) = p1 (i ) Q( j|i ). (18)

Then Kinchins fourth axiom states that

Thermodynamics Microscopic Connotations

Thermodynamics Microscopic Connotations 125 7

I ( p ) = I ( p1 ) + p1 ( i ) I Q ( j | i ) .
i

(19)

An important consequence is that, out of the four Kinchin axioms one nds that Shannonss measure S = p(i ) ln [ p(i )],
i =1 N

(20)

gives us the only way of complying with Kinchins axioms.

4. Statistical mechanics and information theory

It has been argued [9] that the statistical mechanics (SM) of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. From the mechanical viewpoint, the vocables statistical mechanics" suggest that for solving physical problems we ought to acknowledge a degree of uncertainty as to the experimental conditions. Turning this problem around, it also appears that the purely statistical arguments are incapable of yielding any physical insight unless some mechanical information is a priori assumed [9]. This is the conceptual origin of the link SM-IT pioneered by Jaynes in 1957 via his Maximum Entropy Principle (MaxEnt) [5, 6, 10] which allowed for reformulating SM in information terms. Since ITs central concept is that of information measure (IM) Descartes scientic methodology considers that truth is established via the agreement between two independent instances that can neither suborn nor bribe each other: analysis (purely mental) and experiment [11]. The analytic part invokes mathematical tools and concepts: Mathematics world Laboratory. The mathematical realm is called Platos Topos Uranus (TP). Science in general, and physics in particular, may thus be seen as a [TP Experiment"] two-way bridge. TP concepts are related to each other in the form of laws" that adequately describe the relationships obtaining among suitable chosen variables that describe the phenomenon at hand. In many cases these laws are integrated into a comprehensive theory (e.g., classical electromagnetism, based upon Maxwells equations) [1, 1215]. Jaynes MaxEnt ideas describe thermodynamics via the link [IT as a part of TP] [Thermal experiment], or in a more general scenario: [IT] [Phenomenon at hand]. It is clear that the relation between an information measure and entropy is [IM] [Entropy S]. One can then assert that an IM is not necessarily an entropy, since the rst belongs to the Topos Uranus and the later to the laboratory. Of course, in some special cases an association I M entropy S can be established. Such association is both useful and proper in very many situations [5]. If, in a given scenario, N distinct outcomes (i = 1, . . . , N) are possible, three alternatives are to be considered [6]: 1. Zero ignorance: predict with certainty the actual outcome. 2. Maximum ignorance: Nothing can be said in advance. The N outcomes are equally likely.

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3. Partial ignorance: we are given the probability distribution { Pi }; i = 1, . . . , N. If our state of knowledge is appropriately represented by a set of, say, M expectation values, then the best", least unbiased probability distribution is the one that [6] reects just what we know, without inventing" unavailable pieces of knowledge [5, 6] and, additionally, maximizes ignorance: the truth, all the truth, nothing but the truth [6]. Such is the MaxEnt rationale. In using MaxEnt, one is not maximizing a physical entropy, but only maximizing ignorance in order to obtain the least biased distribution compatible with the a priori knowledge. Statistical mechanics and thereby thermodynamics can be formulated on an information theory basis if the density operator is obtained by appealing to Jaynes maximum entropy principle (MaxEnt), that can be stated as follows: Assume that your prior knowledge about the system is given by the values of M expectation values < A1 >, . . . , < A M >. In such circumstances is uniquely determined by extremizing I () subject to M constraints given, namely, the M conditions < A j >= Tr [ A j ], a procedure that entails introducing M Lagrange multipliers i . Additionally, since normalization of is necessary, a normalization Lagrange multiplier should be invoked. The procedure immediately leads one [6] to realizing that I S, the equilibrium Boltzmanns entropy, if the a priori knowledge < A1 >, . . . , < A M > refers only to extensive quantities. Of course, I, once determined, affords for complete thermodynamical information for the system of interest [6].

5. A new micro-macroscopic way of accounting for thermodynamics

Gibbs and MaxEnt approaches satisfactorily describe equilibrium thermodynamics. We will here search for a new, different alternative able to account for thermodynamics from rst principles. Our idea is to give axiom-status to Eq. (7), which is an empirical statement. Why? Because neither in Gibbs nor in MaxEnts axioms we encounter a direct connection with actual thermal data. By appealing to Eq. (7) we would instead be actually employing empirical information. This is our rationale. Consequently, we will concoct a new SM-axiomatics by giving postulate status to the following macroscopic statement: Axiom (1) dE = TdS + P dA .

(21)

This is a macroscopic postulate to be inserted into a microscopic axiomatics corpus. We still need some amount of microscopic information, since we are building up a microscopic theory. We wish to add as little as possible, of course (Ockhams razor). At this point it is useful to remind the reader of Kinchins postulates, recounted above. We will content ourselves with borrowing for our theoretical concerns just his his rst axiom. Thus, we conjecture at this point, and will prove below, that the following assertion sufces for our theoretical purposes:

Thermodynamics Microscopic Connotations

Thermodynamics Microscopic Connotations 127 9

Axiom (2) If there are W microscopic accessible states labelled by i, whose microscopic probability we call pi , then S = S ( p 1 , p 2 , . . . , pW ) . (22) Thus, we are actually taking as a postulate something that is actually known from both quantum and classical mechanics. Axiom (3) The internal energy E and the external parameters A are to be considered as the expectation values of suitable operators, that is, the hamiltonian H and the hermitian operators R (i.e., A < R >). Thus, the A (and also E) will depend on the eigenvalues of these operators and on the probability set. (Note that energy eigenvalues depend of course upon the R .

The reader will immediately realize that Axiom (2) is just a way of re-expressing Boltzmanns atomic" conjecture. Thus, macroscopic quantities become statistical averages evaluated using a microscopic probability distribution [16]. Our present three new axioms are statements of fact. What do we mean? That they are borrowed from either experiment or pre-existent theories. Somewhat surprisingly, our three axioms do not actually incorporate any knew knowledge at all. The merely re-express known previous notions. Ockhams razor at its best! Our theory could no be more economical. We need now to prove that the above three postulates allow one to reconstruct the imposing edice of statistical mechanics. We will tackle this issue by showing below that they our axioms are equivalent to those of Jaynes [17]. At this point we need to recall the main goal of statistical mechanics, namely, nding the probability distribution (or the density operator) that best describes our physical system. In order to do so Jaynes appealed to his MaxEnt postulate, that we restate below for the sake of xing notation. MaxEnt axiom: assume your prior knowledge about the system is given by the values of M
expectation values

Then, is uniquely xed by extremizing the information measure I () subject to normalization plus the constraints given by the M conditions constituting our assumed foreknowledge A =< R >= Tr [ R ]. (24) This leads, after a Lagrange-constrained extremizing process, to the introduction of M Lagrange multipliers , that one assimilates to the generalized pressures P . The truth, the whole truth, nothing but the truth [6]. Jaynes rationale asserts that if the entropic measure that reects our ignorance were not of maximal character, we would actually be inventing information not at hand.

A1 < R1 >, . . . , A R < R M > .

(23)

While working through his variational process, Jaynes discovers that, after multiplying by Boltzmanns constant k B the right-hand-side of his expression for the information measure, it converts itself into an entropy, I S, the equilibrium thermodynamic one, with the caveat that A1 =< R1 >, . . . , A M =< R M > refer to extensive quantities. Having , his universal form I () yields complete microscopic information with respect to the system of interest. To achieve our ends one needs now just to prove that the new axiomatics, with (21) and (22), is equivalent to MaxEnt.

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6. New connection between macroscopic and microscopic approaches

In establishing our new connections between the micro- and macro-scenarios we shall work with the classical instance only, since the corresponding quantum treatment constitute in this sense just a straightforward extension. Our main idea is to pay attention to the generic change pi pi + dpi as constrained by Eq. ( 21). In other word, we insist on studying the change dpi that takes place in such a manner that (21) holds. Our main macroscopic quantities S, A j , and E will vary with dpi . These changes are not arbitrary but are constrained by (21). Note here an important advantage to be of our approach. We need not specify beforehand the information measure employed. Since several possibilities exist (see for instance Gell-Mann and Tsallis [18]), this entails that the choice of information nature is not predetermined by macroscopic thermodynamics. For a detailed discussion of this issue see Ferri, Martinez, and Plastino [19]. The pertinent ingredients at hand are an arbitrary, smooth function f ( p) permitting one expressing the information measure via I S({ pi }) = pi f ( pi ),
i

(25)

M quantities A representing values of extensive quantities R , that adopt, for a micro-state i, the value ai with probability pi , still another arbitrary smooth, monotonic function g( pi ) (g(0) = 0; g(1) = 1). With the express purpose of employing generalized, non-Shannonian entropies, we slightly generalize here the expectation-value denitions by recourse to g via (26):
A R = ai g( pi ); = 2, . . . , M, i W

such that S({ pi }) is a concave function,

(26)

E = i g ( p i ) ,
i

(27)

where i is the energy associated to the microstate i. We take A1 E and pass to a consideration of the probability variations dpi that should generate accompanying changes dS, dA , and dE in, respectively, S, the A , and E. The essential issue at hand is that of enforcing compliance with dE TdS +

=1

dA = 0,

(28)

with T the temperature and generalized pressures. By recourse to (25), (26), and (27) we i) recast now (28) for

Thermodynamics Microscopic Connotations

Thermodynamics Microscopic Connotations 129 11

and ii) expand the resulting equation up to rst order in the dpi . Remembering that the Lagrange multipliers are identical to the generalized pressures P of Eq. (7), one thus encounter, after a little algebra [2026], Ci
(1)
M = [=1 ai + i ]

pi pi + dpi ,

(29)

Ci i [Ci
(1)

(2)

S = T pi

+ Ci ]dpi i Ki dpi = 0,

(2)

(30)

so that, appropriately rearranging things Ti

(1)

Ti

(2)

= f ( pi ) + pi f ( pi )
(31)

M = [(=1 ai + i ) g ( pi ) K ], ( 1/kT ),

and we are in a position to recast (30) in the fashion Ti

(1)

+ Ti

(2)

= 0; ( f or any i),

(32)

an expression whose importance will become manifest later on. Eqs. (30) or (32) yield one and just one pi expression, as demonstrated in Refs. [2026]. However, it will be realized below that, at this stage, an explicit expression for this probability distribution is not required. We pass now to traversing the opposite road that leads from Jaynes MaxEnt procedure and ends up with our present equations. This entails extremization of S subject to constraints in E, A , and normalization. For details see [2026]. Setting 1 = 1/T one has

pi [ S H

=2

R pi ] = 0,
i

(33)

(normalization Lagrange multiplier ) is easily seen in the above cited references to yield as a solution the very set of Eqs. (30). The detailed proof is given in the forthcoming Section. Eqs. (30) arise then from two different approaches: our methodology, based on Eqs. (21) and (22), and following the well known MaxEnt route. Accordingly, we see that both MaxEnt and our axiomatics co-imply one another. They are indeed equivalent ways of constructing equilibrium statistical mechanics. As a really relevant fact

130 12 Thermodynamics Fundamentals and Its Application in Science

Will-be-set-by-IN-TECH

One does not need to know the analytic form of S[ pi ] neither in Eqs. (30) nor in (33).

7. Proof
Here we prove that Eqs. (30) can be derived from the MaxEnt approach (33). One wishes to extremize S subject to the constraints of xed valued for i) U, ii) the M values A (entailing Lagrange multipliers (1) and (2) M ), and iii) normalization (Lagrange multiplier ). One has also (34) A = R = pi ai ,
i with ai = i |R |i the matrix elements in the basis i of R . The ensuing variational problem one faces, with U = i pi i , is

{ pi } S U that immediately leads, for = , to pm

i

=1

A pi = 0,
i

(35)

pi f ( pi ) [ pi ( ai + i ) + pi ] =1

= 0,

(36)

so that the the following two quantities vanish

M f ( p i ) + p i f ( p i ) [ ( = 1 a i + i ) + ]

if K,
M f ( p i ) + p i f ( p i ) ( = 1 a i + i ) + K ]

0 = Ti

(1)

+ Ti .

(2)

(37)

We realize now that (32) and the last equality of (37) are one and the same equation. MaxEnt does lead to (32).

8. Conclusions
We have formally proved above that our axiomatics allows one to derive MaxEnt equations and viceversa. Thus, our treatment provides an alternative foundation for equilibrium statistical mechanics. We emphasized that, opposite to what happens with both Gibbs and Jaynes axioms, our postulates have zero new informational content. Why? Because they are borrowed either from experiment or from pre-existing theories, namely, information theory and quantum mechanics. The rst and second laws of thermodynamics are two of physics most important empirical facts, constituting pillars to our present view of Nature. Statistical mechanics (SM) adds an underlying microscopic substratum able to explain not only these two laws but the whole of thermodynamics itself [2, 6, 2730]. Basic SM-ingredient is a microscopic probability

Thermodynamics Microscopic Connotations

Thermodynamics Microscopic Connotations 131 13

distribution (PD) that controls microstates-population [27]. Our present ideas yield a detailed picture, from a new perspective [2026], of how changes in the independent external thermodynamic parameters affect the micro-state population and, consequently, the entropy and the internal energy.

Acknowledgement
This work was partially supported by the MEC Grant FIS2005-02796 (Spain).

Author details
A. Plastino Universidad Nacional de La Plata, Instituto de Fsica (IFLP-CCT-CONICET), C.C. 727, 1900 La Plata, Argentina Physics Departament and IFISC-CSIC, University of Balearic Islands, 07122 Palma de Mallorca, Spain Evaldo M. F. Curado Centro Brasileiro de Pesquisas Fisicas, Rio de Janeiro, Brazil M. Casas Physics Departament and IFISC-CSIC, University of Balearic Islands, 07122 Palma de Mallorca, Spain

9. References
[1] R. B. Lindsay and H. Margenau, Foundations of physics, NY, Dover, 1957. [2] E. A. Desloge, Thermal physics NY, Holt, Rhinehart and Winston, 1968. [3] J. Willard Gibbs, Elementary Principles in Statistical Mechanics, New Haven, Yale University Press, 1902. [4] C. E. Shannon, Bell System Technol. J. 27 (1948) 379-390. [5] E. T. Jaynes Papers on probability, statistics and statistical physics, edited by R. D. Rosenkrantz, Dordrecht, Reidel, 1987. [6] A. Katz, Principles of Statistical Mechanics, The information Theory Approach, San Francisco, Freeman and Co., 1967. [7] T. M. Cover and J. A. Thomas, Elements of information theory, NY, J. Wiley, 1991. [8] A. Plastino and A. R. Plastino in Condensed Matter Theories, Volume 11, E. Ludea (Ed.), Nova Science Publishers, p. 341 (1996). [9] D. M. Rogers, T. L. Beck, S. B. Rempe, Information Theory and Statistical Mechanics Revisited, ArXiv 1105.5662v1. [10] D. J. Scalapino in Physics and probability. Essays in honor of Edwin T. Jaynes edited by W. T. Grandy, Jr. and P. W. Milonni (Cambridge University Press, NY, 1993), and references therein. [11] B. Russell, A history of western philosophy (Simon & Schuster, NY, 1945). [12] P. W. Bridgman The nature of physical theory (Dover, NY, 1936). [13] P. Duhem The aim and structure of physical theory (Princeton University Press, Princeton, New Jersey, 1954). [14] R. B. Lindsay Concepts and methods of theoretical physics (Van Nostrand, NY, 1951).

132 14 Thermodynamics Fundamentals and Its Application in Science

Will-be-set-by-IN-TECH

[15] H. Weyl Philosophy of mathematics and natural science (Princeton University Press, Princeton, New Jersey, 1949). [16] D. Lindley, Boltzmanns atom, NY, The free press, 2001. [17] W.T. Grandy Jr. and P. W. Milonni (Editors), Physics and Probability. Essays in Honor of Edwin T. Jaynes, NY, Cambridge University Press, 1993. [18] M. Gell-Mann and C. Tsallis, Eds. Nonextensive Entropy: Interdisciplinary applications, Oxford, Oxford University Press, 2004. [19] G. L. Ferri, S. Martinez, A. Plastino, Journal of Statistical Mechanics, P04009 (2005). [20] E. Curado, A. Plastino, Phys. Rev. E 72 (2005) 047103. [21] A. Plastino, E. Curado, Physica A 365 (2006) 24 [22] A. Plastino, E. Curado, International Journal of Modern Physics B 21 (2007) 2557 [23] A. Plastino, E. Curado, Physica A 386 (2007) 155 [24] A. Plastino, E. Curado, M. Casas, Entropy A 10 (2008) 124 [25] International Journal of Modern Physics B 22, (2008) 4589 [26] E. Curado, F. Nobre, A. Plastino, Physica A 389 (2010) 970. [27] R.K. Pathria, Statistical Mechanics (Pergamon Press, Exeter, 1993). [28] F. Reif, Statistical and thermal physics (McGraw-Hill, NY, 1965). [29] J. J.Sakurai, Modern quantum mechanics (Benjamin, Menlo Park, Ca., 1985). [30] B. H. Lavenda, Statistical Physics (J. Wiley, New York, 1991); B. H. Lavenda, Thermodynamics of Extremes (Albion, West Sussex, 1995).

Section 3

Property Prediction and Thermodynamics

Chapter 6

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds
Zdeka Kolsk, Milan Zbransk and Alena Randov
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/49998

1. Introduction
Thermodynamic data play an important role in the understanding and design of chemical processes. To determine values of physico-chemical properties of compounds we can apply experimental or non-experimental techniques. Experimental techniques belong to the most correct, accurate and reliable. All experimental methods require relevant technical equipment, time necessary for experiment, sufficient amount of measured compounds of satisfactory purity. Compound must not affect technical apparatus and should not be decomposed during experiment. Other aspect is a valid legislation, which limits a usage of dangerous compounds by any users. If due to any of these conditions mentioned above causes the experiment cannot be realized, some non-experimental approaches can be applied.

2. Non-experimental approaches to determine physico-chemical properties of compounds

If due to any of conditions results in that experimental determination cannot be realized and data on physico-chemical property are necessary, we have to employ some nonexperimental approaches, either calculation methods or estimation ones. Due to the lack of experimental data for several industrially important compounds, different estimation methods have been developed to provide missing data. Estimation methods include those based on theory (e.g. statistical thermodynamics or quantum mechanics), various empirical relationships (correlations of required property with variable, experimentally determined compound characteristics, e.g. number of carbon atoms in their molecule, molecular weight, normal boiling temperature, etc.), and several classes of additivity-principle methods
2012 Kolsk et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

136 Thermodynamics Fundamentals and Its Application in Science

(Baum, 1989; Pauling et al., 2001). Estimation methods can be divided into several groups from many aspects, e.g. into methods based on theoretical, semi-theoretical relations and the empirical ones. Books and papers of last decades divide estimation methods depending on the required input data into QPPR or QSPR approaches (Baum, 1989). QPPR methods (Quantity-Property-Property-Relationship) are input data-intensive. They require for calculation of searched value property knowledge of other experimental data. We can use them successfully only when we have input data. On the other hand QSPR (Baum, 1989) methods (Quantity-Structure-Property-Relationship) need only knowledge of the chemical structure of a compound to predict the estimated property. QSPR methods use some structural characteristics, such as number of fragments (atoms, bonds or group of atoms in a molecule), topological indices or other structural information, molecular descriptors, to express the relation between the property and molecular structure of compound (Baum, 1989; Pauling et al., 2001; Gonzles et al., 2007a). Empirical and group contribution methods seem to be the most suitable (Pauling et al., 2001; Majer et al., 1989) due to their simplicity, universality and fast usage.

2.1. Group contribution methods

Group contribution methods are presented as empirical QSPR approaches. The easiest models were based on study of property on number of carbon atoms nC or methylen groups nCH2 in molecules of homological series. In Fig. 1 is presented dependence of normal boiling temperature Tb on number of carbon atoms nC (bottom axis) or methylen groups nCH2 (top axis) in molecules of homological series n-alkanols C1-C12 (Majer & Svoboda, 1985; NIST database). As we can see, this dependence is clearly linear in some range of nC=C2-C10. But increasing discrepancy is evident either for low number of carbon atoms C1 or for higher one nC>C10. Due to these departures from linear behaviour some parameters covering structural effects on property were inclusive to these easy models (e.g. Chickos et al., 1996). From these approaches structural fragments and subsequently group contribution methods have been established. Group contribution methods are based on the so called additive principle. That means any compound can be divided into fragments, usually atoms, bonds or group of atoms, etc. All fragments have a partial value called a contribution. These contributions are calculated from known experimental data. Property of a compound is obtained by a summing up the values of all contributions presented in the molecule. Example of division of molecule of ethanol into atomic, bond and group fragments is presented in Fig. 2. When we divide this molecule into atomic fragments, the total value of property X of ethanol is given by summing up the values for two carbon atom contributions X(C), six hydrogen atom contributions X(H) and one oxygen atom contribution X(O). The second way is the division of ethanol molecules into the following bond fragments with their contribution: X(C-C), X(C-O), X(C-H) and X(O-H). Due to increasing quality and possibility of computer technique a fragmentation into more complex group structural fragments is applied in present papers (Baum, 1989; Pauling et al., 2001). Some of ways to divide the molecule ethanol into group structural fragments are presented in Fig. 2. Ethanol molecule can be divided either into: (i)

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 137

CH3-, -CH2- and -OH, or: (ii) CH3- and CH2OH. More complex compounds are described by more complex structural fragments.

Figure 1. Dependence of normal boiling temperature of n-alkanols in homological series C1-C12

Figure 2. Example of division of ethanol molecule into atomic, bond and group structural fragments

Group contribution methods are essentially empirical estimation methods. A large variety of these models have been designed during last centuries, differing in a field of their applicability and in the set of experimental data. They were developed to estimate, e.g. critical properties (Lydersen, 1955; Ambrose, 1978; Ambrose, 1979; Joback & Reid, 1987;

138 Thermodynamics Fundamentals and Its Application in Science

Gani & Constantinou, 1996; Poling et al., 2001; Marrero & Gani, 2001; Brown et al., 2010; Monago & Otobrise, 2010; Sales-Cruz et al., 2010; Manohar & Udaya Sankar, 2011; Garcia et al., 2012), parameters of state equations (Pereda et al., 2010; Schmid & Gmehling, 2012), acentric factor (Constantinou & Gani, 1994; Brown et al., 2010; Monago & Otobrise, 2010), activity coefficients (Tochigi et al., 2005; Tochigi & Gmehling, 2011), vapour pressure (Poling et al., 2001; Miller, 1964), liquid viscosity (Joback & Reid, 1987; Conte et al., 2008; Sales-Cruz et al., 2010), gas viscosity (Reichenberg, 1975), heat capacity (Joback & Reid, 1987; Ruzicka & Domalski, 1993a; Ruzicka & Domalski, 1993b; Kolsk et al., 2008), enthalpy of vaporization (e.g. Chickos et al., 1995; Chickos & Wilson, 1997; Marrero & Gani, 2001; Kolsk et al. 2005, etc.), entropy of vaporization (Chiskos et al., 1998; Kolsk et al. 2005), normal boiling temperature (Joback & Reid, 1987; Gani & Constantinou, 1996; Marrero & Gani, 2001), liquid thermal conductivity (Nagvekar & Daubert, 1987), gas thermal conductivity (Chung et al., 1984), gas permeability and diffusion coefficients (Yampolskii et al., 1998), liquid density (Campbell & Thodos, 1985; Sales-Cruz et al., 2010; Shahbaz et al., 2012), surface tension (Brock, 1955; Conte et al., 2008; Awasthi et al., 2010), solubility parameters of fatty acid methyl esters (Lu et al., 2011), flash temperatures (Liaw & Chiu, 2006; Liaw et al., 2011). Large surveys of group contribution methods for enthalpy of vaporization and liquid heat capacity have been presented in references (Zbransk et al., 2003; Kolsk, 2004; Kolsk et al., 2005; Kolsk et. al, 2008; Zbransk et al, 2010a). Group-contribution-based property estimation methods ca be also used to predict the missing UNIFAC group-interaction parameters for the calculation of vaporliquid equilibrium (Gonzles at al., 2007b). Group contribution methods can be used for pure compounds, even inorganic compounds (e.g. Williams, 1997; Briard et al., 2003), organometallic compounds (e.g. Nikitin et al., 2010) and also for mixtures (e.g. Awasthi et al., 2010; Papaioannou et al., 2010; Teixeira et al., 2011; Garcia et al., 2012). Also e.g. estimation of thermodynamic properties of polysacharides was presented (Lobanova et al., 2011). Discussion about determination of properties of polymers has been also published (Satyanarayana et al., 2007; Bogdanic, 2009; Oh & Bae, 2009). Property models based on the group contribution approach for lipid technology have been also presented (Daz-Tovar et al., 2007). During last years also models for ionic liquids and their variable properties were developed, e.g. for density, thermal expansion and viscosity of cholinium-derived ionic liquids (Costa et al., 2011; Costa et al., 2012), viscosity (Adamov et al., 2011), the glass-transition temperature and fragility (Gacino et al., 2011), experimental data of mixture with ionic liquid were compared with group contribution methods (Cehreli & Gmehling, 2010) or thermophysical properties were studied (Gardas et al., 2010). Some of these group contribution methods were developed for only limited number of compounds, for some family of compounds, e.g. for fluorinated olefins (Brown et al., 2010), hydrocarbons (Chickos et al., 1995), fatty acid methyl esters (Lu et al., 2011), etc., most of approaches were established for a wide range of organic compounds.

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 139

2.1.1. Group contribution methods by Marrero-Gani

In this chapter for most of estimations the modified group contribution method by Marrero and Gani (Marrero & Gani, 2001; Kolsk et al., 2005; Kolsk et. al. 2008) was applied, which has been originally developed for estimation of different thermodynamic properties at one temperature only (Constantinou & Gani, 1996; Marrero & Gani, 2001). Determination of group contribution parameters is performed in three levels, primary, secondary and third. At first, all compounds are divided into the primary (first) order group contributions. This primary level uses contributions from simple groups that allow description of a wide variety of organic compounds. Criteria for their creation and calculation have been described (Marrero & Gani, 2001; Kolsk et al., 2005; Kolsk et al., 2008). The primary level groups, however, are insufficient to capture a proximity effect (they do not implicate an influence of their surroundings) and differences between isomers. Using primary level groups enables to estimate correctly properties of only simple and monofunctional compounds, but the estimation errors for more complex substances are higher. The primary level contributions provide an initial approximation that is improved at the second level and further refined at the third level, if that is possible and necessary. The higher levels (second and third) involve polyfunctional and structural groups that provide more information about a molecular structure of more complex compounds. These higher levels are able to describe more correctly polyfunctional compounds with at least one ring in a molecule, or non-ring chains including more than four carbon atoms in a molecule, and multi-ring compounds with a fused or non-fused aromatic or non-aromatic rings. The differences between some isomers are also able to distinguish by these higher levels. Complex polycyclic compounds or systems of fused aromatic or nonaromatic rings are described by the third order contributions. They are still bigger and more complex than the first, even the second order ones. The multilevel scheme enhances the accuracy, reliability and the range of application of group contribution method for an almost all classes of organic compounds. After these all three levels the total value of predicted property X is obtained by the summing up of all group contributions, which occur in the molecule. First order groups, second and third order ones, if they are in. n m o X N C M D z O E x i xi j xj k xk 0 i j k 1 1 1 (1)

where X stands the estimated property, x0 is an adjustable parameter for the relevant property, Cxi is the first-order group contribution of type i, Dxj is the second-order group contribution of type j, Exk is the third-order group contributions of the type k and Ni, Mj, Ok denote the number of occurrences of individual group contributions. The more detail description of parameters calculation is mentioned in original papers (Marrero & Gani, 2001; Kolsk et al., 2005; Kolsk et al., 2008) To develop reliable and accurate group contribution model three important steps should be realized: (i) to collect input database, rather of critically assessed experimental data, from which parameters, group contributions, would be calculated; (ii) to design structural

140 Thermodynamics Fundamentals and Its Application in Science

fragments for description of all chemical structures for compounds of input database; (iii) to divide all chemical structures into defined structural fragments correctly. It can be realized either manually, when databases of chemical structures and structural fragments inclusive several members only, either via computer program, when databases contain hundreds of compounds and structural fragments are more complex. To calculate group contribution parameters for thermophysical properties the ProPred program has been used (Marrero, 2002). Description and division chemical structures for other estimations have been made handy. Molecular structures for electronical splitting of all compounds from the basic data set were input in the Simplified Molecular Input Line Entry Specification, so-called the SMILES format (Weininger et al., 1986; Weininger, 1988; Weininger et al., 1989; Weininger, 1990). For more universal usage of computer fragmentation a suitable computer program has been developed (Kolsk & Petrus, 2010). The main goal of the newly developed program is to provide a powerful tool for authors using group contribution methods for automatic fragmentation of chemical structures.

2.2. Estimation of selected physico-chemical properties of compounds

The models for estimation of several physical or physico-chemical properties of pure organic compounds, such as enthalpy of vaporization, entropy of vaporization (Kolsk et al., 2005), liquid heat capacity (Kolsk et al., 2008) and a Nafion swelling (Randov et al, 2009) is presented below. Most of them are developed to estimate property at constant temperature 298.15 K and at normal boiling temperature (Kolsk et al., 2005; Kolsk et al., 2008; Randov et al., 2009), liquid heat capacity as a temperature dependent (Kolsk et al., 2008). Hitherto unpublished results for estimation of a flash temperature or organic compounds and for determination of reactivation abbility of reactivators of acetylcholinesterase inhibited by inhibitor are presented in this chapter.

2.2.1. Enthalpy of vaporization and entropy of vaporization

Enthalpy of vaporization, HV, entropy of vaporization, SV are important thermodynamic quantities of a pure compound, necessary for chemical engineers for modelling of many technological processes with evaporation, for extrapolation and prediction of vapour pressure data, or for estimation of the other thermodynamic properties, e.g. solubility parameters. It can be also used for extrapolation and prediction of vapour pressure data. There are several methods to determine these properties, experiment-based and modelbased. Experiment-based methods, such as calorimetry or gas chromatography, provide generally reliable data of good accuracy. In the case of model-based methods, we can distinguish several groups of methods on the basis of the input information they require. Methods based on the Clausius-Clapeyron equation and vapour pressure data, variable empirical correlations, methods based on the tools of statistical thermodynamics or quantum mechanics. During last decades the group contribution methods are widely used

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 141

for their universality and simplicity. More rich survey of estimation methods for enthalpy of vaporization is presented in papers (Kolsk, 2004; Kolsk et al., 2005). Large databases of critically assessed data have been used for group contribution calculations: data for 831 compounds have been used for estimations at 298.15 K, and data for 589 compounds have been used for estimations at the normal boiling temperature. Organic compounds were divided into several classes (aliphatic and acyclic saturated and unsaturated hydrocarbons, aromatic hydrocarbons, halogenated hydrocarbons, compounds containing oxygen, nitrogen or sulphur atoms and miscellaneous compounds). Especially calorimetrically measured experimental data from the compilation (Majer & Svoboda, 1985) and data from some other sources mentioned in original paper (Kolsk et al., 2005) were employed. Results for estimations of these three properties are presented in the following Tables, Table 1 for enthalpy of vaporization at 298.15 K, Table 2 for enthalpy of vaporization at normal boiling temperature and Table 3 for entropy of vaporization at normal boiling temperature, NC means a number of compounds used for development of model and contributions calculation, NG is number of applied structural fragments (groups), AAE is absolute average error and ARE is average relative error (Kolsk et al., 2005). Table 1 shows that values for 831 compounds were used for estimation of enthalpy of vaporization at 298.15 K. When only first level groups were used, the prediction was performed with the AAE and the ARE of 1.3 kJ/mol and 2.8%, resp. Values of 116 group contributions were calculated at this step. Then, 486 compounds were described by the second order groups. Prediction of these compounds improved after the use of these contributions from the value of 1.3 kJ/mol to 0.8 kJ/mol (from 2.8% to 1.8%) in comparison when using only the first level groups. At the end only 55 compounds were suitable for refining by the third order groups. The results were refined from the values of 1.4 kJ/mol to 1.1 kJ/mol (from 2.5% to 2.1%). The total prediction error was cut down from the value of 1.3 kJ/mol to 1.0 kJ/mol for AAE and from 2.8% to 2.2 % for ARE after usage of all three-level groups, as it is obvious from this table. A similar pattern of results for other predicted properties are presented in Tables 2 and 3.

Estimation level FIRST SECOND 486 compounds THIRD 55 compounds ALL LEVELS

NC 831 486 after only the FIRST 55 After FIRST + SECOND 831

NG 116 91 15 222

AAE / kJ/mol 1.3 0.8 (1.3) 1.1 (1.4) 1.0

ARE / % 2.8 1.8 (2.8) 2.1 (2.5) 2.2

Table 1. Results for estimation of enthalpy of vaporization at 298.15 K (Kolsk et al., 2005)

142 Thermodynamics Fundamentals and Its Application in Science

Estimation level FIRST SECOND 377 compounds THIRD 23 compounds ALL LEVELS

NC 589 377 after only the FIRST 23 After FIRST + SECOND 589

NG 111 100 14 225

AAE / kJ/mol 1.2 0.9 (1.2) 1.1 (1.3) 0.9

ARE / % 3.2 2.5 (3.4) 2.1 (2.7) 2.6

Table 2. Results for estimation of enthalpy of vaporization at normal boiling temperature (Kolsk et al., 2005)

Estimation level FIRST SECOND 377 compounds THIRD 23 compounds ALL LEVELS

NC 589 377 after only the FIRST 23 After FIRST + SECOND 589

NG 111 100 14 225

AAE / J/(Kmol) 2.1 1.8 (2.3) 1.9 (2.5) 1.7

ARE / % 2.2 1.9 (2.4) 1.9 (2.5) 1.8

Table 3. Results for estimation of entropy of vaporization at normal boiling temperature (Kolsk et al., 2005)

As an example of the use of all three levels we have chosen the molecule of 1,1,4,7tetramethylindane. Its chemical structure is shown in Fig. 3 and its division into individual first, second and third order groups with the result for vaporization enthalpy at 298.15 K is presented in Table 4. When we sum up all group contribution of the first level, we have got value of 64.48 kJ/mol. The first level provides an initial approximation with the relative error of estimated value exceeding 5 % in comparison with experimental value 61.37 kJ/mol. Estimated value of vaporization enthalpy at 298.15 K is then improved at the second level and further refined at the third level, after those the relative error reduced to 1.2 %.

Figure 3. Chemical structure of 1,1,4,7-tetramethylindane

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 143

Estimation level FIRST

Group fragment no. x0 1 13 15 18 107 109

Group fragment definition Adjustable parameter CH3 aCH aC fused with nonaromatic subring aC-CH3 CH2 (cyclic) C (cyclic)

Its frequency 1 2 2 2 2 2 1

Group contribution value for HV at 298.15 K / kJ/mol 9.672 2.266 4.297 6.190 8.121 4.013 3.667 64.48

Estimated value SECOND Estimated value THIRD Estimated value

55

Ccyc-CH3

-1.355 63.59

6 19

aC-CHncyc (fused rings) (n in 0..1) AROM.FUSED[2]s1s4

2 1

0.279 -0.615 62.13

Table 4. Results for estimation of enthalpy of vaporization at 298.15 K for 1,1,4,7-tetramethylindane, aC means carbon atom in aromatic ring, abbreviation cyc is used for cycle (Kolsk et al., 2005)

Group contribution methods by Ducros (Ducros et al., 1980; Ducros et al., 1981; Ducros & Sannier, 1982; Ducros & Sannier, 1984), by Chickos (Chickos et al., 1996), the empirical method, equations nos. 6 and 7 by Vetere (Vetere, 1995) and method by Ma and Zhao (Ma & Zhao, 1993) were used for comparison of results obtained in this work for estimation at 298.15 K and at normal boiling temperature, resp. While the new approach (Kolsk et al., 2005) was applied for enthalpy of vaporization at 298.15 K for 831 organic compounds with the ARE of 2.2 %, the Ducross method could be applied to only 526 substances with the ARE of 3.1 % and the Chickoss one for 800 compounds with the ARE of 4.7 %. For comparison of the results of estimation at the normal boiling temperature the new model provided for 589 compounds, the ARE was 2.6 % for enthalpy of vaporization and 1.8 % for entropy of vaporization (Kolsk et al., 2005), the Veteres method was capable of estimating the values of for the same number of compounds with the following results: 4.6 % (Eq. 6, Vetere, 1995) and 3.4 % (Eq. 7, Vetere, 1995), model by Ma and Zhao (Ma & Zhao, 1993) for 549 compounds with the ARE of 2.5 %. The error for the enthalpy of vaporization, based on an independent set of various 74 compounds not used for correlation, has been determined to be 2.5%. Group contribution description and values for next usage of readers are presented in original paper (Kolsk et al., 2005).

2.2.2. Liquid heat capacity

Isobaric heat capacity of liquid Clp is an important thermodynamic quantity of a pure compound. Its value must be known for the calculation of an enthalpy difference required

144 Thermodynamics Fundamentals and Its Application in Science

for the evaluation of heating and cooling duties. Liquid heat capacity also serves as an input parameter for example in the calculation of temperature dependence of enthalpy of vaporization, for extrapolation of vapour pressure and the related thermal data by their simultaneous correlation, etc. In work (Kolsk et al., 2008) the three-level group contribution method by Marrero and Gani (Marrero & Gani, 2001) mentioned above, which is able to calculate liquid heat capacity at only one temperature 298.15 K, was applied, and this approach has been extended to estimate heat capacity of liquids as a function of temperature. Authors have employed the combination of equation for the temperature dependence of heat capacity and the model by Marrero and Gani to develop new model (Kolsk et al., 2008). For parameter calculation 549 organic compounds of variable families of compounds were taken. In Table 5 are presented results of this estimation. NG means number of applied structural groups and ARE is the average relative error. More detailed results are presented in original paper (Kolsk et al., 2008). Estimation level First Second Third NG 111 88 25 ARE / % 1.9 1.6 1.5

Table 5. Results for estimation of liquid heat capacity in temperature range of pure organic compounds (Kolsk et al., 2008)

Also these estimated values were compared with results obtained by other estimation methods (Zbransk & Rika, 2004; Chickos et al., 1993) for the basic dataset (compounds applied for parameter calculation) and also for 149 additional compounds not used in the parameter calculation (independent set). The first method (Zbransk & Rika, 2004) was applied for all temperature range, the method proposed by Chickos (Chickos et al., 1993) was only used for temperature 298.15 K with the following results: new model was applied for 404 compounds with ARE of 1.5 %, the older method by Zbransk (Zbransk & Rika, 2004) for the same number of compounds with the ARE of 1.8 % and the Chickoss one for 399 compounds with the ARE of 3.9 %. For the heat capacity of liquids authors used recommended data from the compilations by (Zbransk et al., 1996; Zbransk et al., 2001). Because the experimental data are presented permanently, it is necessary to update database of critically assessed and recommended data. Therefore authorss work has been also aimed at updating and extending two publications prepared earlier within the framework of the IUPAC projects (Zbransk et al., 1996; Zbransk et al., 2001). These publications contain recommended data on liquid heat capacities for almost 2000 mostly organic compounds expressed in terms of parameters of correlating equations for temperature dependence of heat capacity. In new work (Zbransk et al., 2010b) authors collected experimental data on heat capacities of pure liquid organic and inorganic compounds that have melting temperature below 573 K published in the primary literature between 1999 and 2006. Data from more than 200 articles are included

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 145

into the database. Compounds were divided into several families, such as hydrocarbons (saturated, cyclic, unsaturated, aromatic), halogenated hydrocarbons containing atoms of fluorine, chlorine, iodine, bromine, compounds containing oxygen (alcohols, phenols, ethers, ketones, aldehydes, acids, esters, heterocycles, other miscellaneous compounds), compounds containing nitrogen (amines, nitriles, heterocycles, other miscellaneous compounds), compounds containing sulphur (thioles, sulphides, heterocycles) and compounds containing silicon. Also data of organometallic compounds, compounds containing atoms of phosphorus and boron as well as some inorganic compounds were included. Also the list of families of compounds has been extended by a new group denoted as ionic liquids due to an increased interest in physical-chemical properties of these compounds in recent years. Data for approximately 40 ionic liquids were included. Altogether new data for almost 500 compounds, out of them about 250 compounds were not covered the in previous works (Zbransk et al., 1996; Zbransk et al., 2001), were compiled and critically evaluated.

2.2.3. Nafion swelling

Prediction of the physical and chemical properties of pure substances and mixtures is a serious problem in the chemical process industries. One of the possibilities for prediction of the properties is the group contribution method. The anisotropic swelling of Nafion 112 membrane in pure organic liquids (solvents) was monitored by an optical method. Nafion is a poly(tetrafluoroethylene) (PTFE) polymer with perfluorovinyl pendant side chains ended by sulfonic acid groups. The PTFE backbone guarantees a great chemical stability in both reducing and oxidizing environments. Nafion membrane is important in chemical industry. It is used in fuel cells, membrane reactors, gas dryers, production of NaOH, etc. (Randov et al., 2009). In many applications Nafion is immersed in liquid, which significantly affects the membrane properties, namely swelling and transport properties of permeates (Randov et al., 2009). The change in the size of the membrane sample is taken as a measure of swelling. All experimental data were presented (Randov et al., 2009) and these results were used as a basis for application of the group contribution method to the relative expansion in equilibrium. From a total of 38 organic liquids under study, 26 were selected as an evaluational set from which the group and structural group contributions were assigned. The remaining 12 compounds were used as the testing set. Due to limited number of compounds the more complex and known group contribution methods could not been taken. Authors have to develop new group structural fragments. The proposed method utilizes the four kinds of the structural units: constants, C-backbone, functional groups, and molecular geometry (Randov et al., 2009). Constants were presented as alcohols, ketones, ethers, esters, carboxylic acids. As C-backbone were taken groups CH3, -CH2- and >CH-. Functional groups as hydroxyl OH-, carbonyl -C=O and ether O- and fragments for molecular geometry for cycles and branched chains were taken. The relative expansions Aexp (for the drawing direction) and/or Bexp (for the perpendicular direction) were calculated from the side lengths of the dry membrane sample (a10, a20, b10, b20) and the side lengths of the swelled membrane sample in equilibrium (a1, a2, b1, b2) according to the eq. (3). Description of mentioned sizes is presented in Fig. 4.

146 Thermodynamics Fundamentals and Its Application in Science

Figure 4. Description of membrane dimensions a10, a20, b10, b20 side lengths of the dry membrane and a1, a2, b1, b2 side lengths of the swelled membrane in equilibrium (Randov et al., 2009)

ua1

a1 a10 a10

, ua 2

a2 a20 a20

, ub1

b1 b10 b10

, ub 2

b2 b20 b20

(3)

Calculation approach is presented in original paper (Randov et al., 2009). Value of 1.5% in relative expansions was determined to be the experimental error. Maximum differences between the experimental and calculated relative expansions in both sets did not exceed the value of 3% (Randov et al., 2009). The values of 13 contributions for individual membrane relative expansions were determined on the basis of experimental data on relative expansion of Nafion membrane. Obtained results are in good agreement with experimental data. Maximum differences between experimental and calculated values are nearly the same, only twice greater than the experimental error.

2.2.4. Flash temperature of organic compounds

The flash temperature Tf and lower flammability limit (LFL) are one of the most important variables to consider when designing chemical processes involving flammable substances. These characteristics are not fundamental physical points. Flash temperature is one of the most important variables used to characterize fire and explosion hazard of liquids. The flash temperature is defined as the lowest temperature at which vapour above liquid forms flammable mixture with air at a pressure 101 325 Pa. Usual approach for flash temperature estimation is linear relationship between flash temperature Tf and normal boiling temperature Tb (Dvok, 1993). Some models for flash temperature were presented earlier (Liaw & Chiu, 2006; Liaw et al., 2011). In this work to estimate flash temperature of organic compound authors applied the modified group contribution method (Kolsk et al., 2005) and calculate group contribution values data for 186 compounds (Steinleitner, 1980) were used. The database for calculation of parameters contains data for aliphatic and acyclic saturated and unsaturated

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 147

hydrocarbons, aromatic hydrocarbons, alcohols, halogenated hydrocarbons, compounds containing oxygen, nitrogen or sulphur atoms and miscellaneous compounds. To collect more data for development of reliable method was not able due to that all databases collect some values obtained via closed cup type measuring method and others measured by open cup one and data both of methods vary. Flash temperature was calculated by relationship (4) similar to eq. (1):

Tf Tf NiCi M j D j z Ok Ek
1 1 1 i j k

(4)

where Tf is an adjustable parameter, Ci is the first-order group contribution of type i, Dj is the second-order group contribution of type j, Ek is the third-order group contribution of the type k and Ni, Mj, Ok denote the number of occurrences of individual group contributions. Determination of contributions and of adjustable parameters was performed by a three-step regression procedure (Marrero & Gani, 2001). To evaluate the method error the following statistical quantities for each compound, absolute error AE (eq. 5) and relative error ARE (eq. 6) were used:
AE Tf

Tf exp Tf est
100

(5)

T f exp Tf est RE Tf Tf exp

(6)

where subscripts exp and est mean experimental and estimated value of the flash temperature. 186 compounds from the basic data set were described by the first level group contributions (Kolsk et al., 2005). From this large database only 114 compounds could be selected to be described by the original second level groups as defined earlier (Kolsk et al., 2005). The total absolute and the relative average errors for all 186 compounds were equal to 6.3 K and 2.0 %. Results for individual estimation levels are presented in Table 6.

Estimation level FIRST SECOND THIRD ALL LEVELS

NC 186 105 11 186

AAE / K 7.9 5.7 2.9 6.5

ARE / % 2.4 1.8 0.8 2.0

Table 6. Results for Estimation of flash temperature, NC is number of compounds

Individual calculated structural fragments of the first, second and third estimation levels are presented in Tables 7-9, resp.

148 Thermodynamics Fundamentals and Its Application in Science

Structural fragment Tf CH3 CH2 CH C CH2=CH CH=CH CH2=C CH=C C=C CH#C C#C -F -Cl CH2SH

Contribution /K 194.35 5.38 13.28 15.77 13.59 11.51 34.57 19.63 27.52 29.27 14.94 15.04 2.99 29.32 56.33

Structural fragment aCH aC aC aC aN aC-CH3 aC-CH2 aC-CH aC-C aC-CH=CH2 OH -SH CH2 CH C

Contribution /K 12.39 21.15 26.84 31.53 25.51 28.32 37.11 37.38 19.88 50.66 64.22 55.62 10.89 22.89 -9.50

Structural fragment aC-OH CH2Cl CHCl CCl CHCl2 CCl3 aC-Cl aC-F aC-Br -I -Br CH=CH CH=C N O

Contribution /K 85.26 45.56 42.83 37.51 67.42 100.38 50.70 53.47 64.97 78.85 59.25 18.21 37.59 52.99 -3.39

Table 7. Group contribution of the first level for estimation of flash temperature

Structural fragment

(CH3)2CH (CH3)3C CH(CH3)CH(CH3) CH(CH3)C(CH3)2 CHn=CHm-CHp=CHk (k,m,n,p in 0..2) CH3-CHm=CHn (m,n in 0..2) CH2-CHm=CHn (m,n in 0..2) CHp-CHm=CHn (m,n in 0..2; p in 0..1) CHOH COH CHm(OH)CHn(OH) (m,n in 0..2)

Contribution Structural /K fragment CHm=CHn-Cl -1.45 (m,n in 0..2) aC-CHn-X (n in -3.98 1..2) X: Halogen aC-CHn-OH (n 7.68 in 1..2) 22.69 aC-CH(CH3)2 0.53 -2.01 2.23 3.78 -3.92 -4.98 13.41 aC-CF3 (CHn=C)cycCH3 (n in 0..2) CHcyc-CH3

Contribution Structural fragment /K -0.50 1.04 5.51 1.80 0.13 0.46 -5.70 CHcyc-OH Ccyc-CH3 >Ncyc-CH3 AROMRINGs1s2 AROMRINGs1s3 AROMRINGs1s4 AROMRINGs1s2s4

Contribution /K -1.31 -0.23 -1.11E-17 -2.24 1.72 -0.84 -2.84

CHcyc-CH2 17.80 CHcyc-CH=CHn 8.52 (n in 1..2) CHcyc-C=CHn (n in 1..2) -1.20 CHcyc-Cl 1.59

AROMRINGs1s2s4s5 6.22 PYRIDINEs3s5 9.98E-18

(CH=CHOCH=CH)cyc -4.24 (3 F) (perFlouro) -0.13 2.66E-17

Table 8. Group contribution of the second level for estimation of flash temperature

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 149

Contribution Structural Contribution Structural Contribution Structural fragment /K fragment /K fragment /K CHcyc-CHcyc OH-(CHn)m-OH -1.87 AROM.FUSED[2] 8.69 -33.36 (different rings) (m>2, n in 0..2) aC-aC (different -6.04 CH multiring 0.98 AROM.FUSED[4a] -26.07 rings) aC-CHm-aC aC-CHncyc (fused -4.34 (different rings) (m 12.92 rings) (n in 0..1) in 0..2) Table 9. Group contribution of the third level for estimation of flash temperature

2.2.5. Reactivation ability of some reactivators of acetylcholinesterase

In the last years regarding to valid legislation on dangerous compounds it is necessary to know many of important characteristics of chemical compounds. Due to this new models for their estimation were developed. New models for estimation of reactivation ability of reactivators for acetylcholinesterase inhibited by (i) chloropyrifos (O,O-diethyl O-3,5,6trichloropyridin-2-yl phosphorothioate) as a representative of organophosphate insecticide and by (ii) sarin ((RS)-propan-2-yl methylphosphonofluoridate) as a representative of nerve agent is now presented. Both of these family compounds, organophosphate pesticide and nerve agent, are highly toxic and have the same effect to living organisms, which is based on an inhibition of acetylcholinesterase (AChE). New compounds able to reactivate the inhibited AChE, so-called reactivators of AChE, are synthesized. Reactivation ability of these reactivators is studied using standard reactivation in vitro test (Kua & Kassa, 2003). Reactivation ability of reactivators means the percentage of original activity of AChE (Kua & Patoka, 2004). New models for determination values of reactivation ability of reactivators AChE inhibited by (i) chloropyrifos and (ii) sarin have been developed. Concentration of reactivators was c=110-3 moldm-3. In comparison with previous cases (estimations of thermophysical properties) authors have only less experimental data for development of model (about 20 for each of cases). Due to their long names and complex chemical structures these compounds in this chapter only are presented as their codes taken from original papers (Kua & Kassa, 2003; Kua et al., 2003a; Kua et al., 2003b; Kua et al., 2003c; Kua & Patoka, 2004; Kua & Cabal, 2004a; Kua & Cabal, 2004b; Kua et. al., 2006. Data of reactivation ability for these reactivators were given by the mentioned author team (Kua et al.). Classical group contribution method includes groups describing some central atom, central atom with its bonds, or central atom with its nearest surrounding. However these models commonly used experimental data of hundreds or thousands compounds for parameters calculation. Due to for much small database in these cases it was necessary to design new fragments depending on the molecular structures available compounds. Structural fragments in this work cover larger and more complex part of molecules in comparison with other papers focused to group contribution methods. Reactivation potency is given in the group contribution method by the following relation, eq. 7:
Rp

xi Rpi
i 1

(7)

150 Thermodynamics Fundamentals and Its Application in Science

where Rpi is value of individual fragment i presented in molecule by which it contributes to total value of Rp, x is number of frequency of this fragment i in molecule. Parameters Rpi were obtained by minimization function SRp, eq. 8:
SRp

Rpi ,calc Rpi ,exp

i 1

(8)

where suffix exp presents experimental data and suffix calc the calculated values of Rp, m is number of compounds in dataset. The results obtained by this new approach were compared with experimental data using the following statistical quantities - an absolute error of individual compounds AE (eq. 9) and the average absolute error of dataset AAE (eq. 10):
Rpi ,calc Rpi ,exp AEi
m R pi ,calc Rp i ,exp AAE m i 1

(9)

(10)

Parameters of new model were calculated from the experimental data of the basic dataset. For model for reactivators AChE inhibited by chloropyrifos the input database included data of reactivation ability Rp for 24 reactivators (K 135, K 078, TO 096, TO 100, K 076, TO 094, TO 063, TO 097, TO 098, K 347, TO 231, K 117, K 074, K 033, K 106, K 107, K 110, K 114, HI-6, K 282, K 283, K 285, K 129, K 099) of concentration c=110-3 moldm-3. Values for 17 groups with the AAE of 1.85 % of Rp were calculated. Designed groups with their calculated values of Rpi are presented in Table 10. These calculated parameters were tested on the test set of 5 independent compounds (TO 238, K 111, K 113, Methoxime, K 280) of which experimental data were not applied to group contributions determination. The AAE of Rp prediction for this test-set was 1.45 %. Table 11 presents experimental data and predicted values for these 5 independent compounds. Also illustration of usage of this method for two compounds from this test set is added below. As it is clear from Table 10 the highest values of contributions are given for fragments P3, P7 for monoaromatic reactivators and P11, P12 and P14 for two aromatic rings in reactivator molecule. On the other hand the smallest contribution (the negative ones) to total value of reactivation ability yields fragments P5 a P6 for monoaromatic compounds and P16 and P17 for two aromatic ring reactivators. These values resulted in fact that reactivation ability of new reactivators for reactivation AChE inhibited by chloropyrifos should be increased by presence of the following functional groups in molecules: another quarternary nitrogen atom in aliphatic ring bonded to aromatic quarternary nitrogen atom, the oxime groups in para- or meta- positions and presence of other aliphatic rings bonded to aromatic ring in other position than quarternary nitrogen and oxime groups. In all cases it is clear that reactivation ability decreases with presence of cycle ring, double bond and also in a less range with the presence of oxygen atoms presented in molecules. Also ortho- position of oxime group does not contribute positively.

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 151

no.

Fragment description

Rpi /%

no.

Fragment description

Rpi /%

P1

two oxime groups in positions o- due to a Oxime group (=NOH) in position odue to a quarternary nitrogen N+ 26.365 P9 quarternary nitrogen atom in 26.580 aromatic ring atom in aromatic ring two oxime groups in Oxime group (=NOH) in position ppositions m- due to a + due to a quarternary nitrogen N 15.365 P10 quarternary nitrogen atom N+ atom in aromatic ring in aromatic ring Other quarternary nitrogen atom N+ two oxime groups in with 4 CHx- groups in molecule, in positions p- due to a 46.792 P11 aliphatic ring bonded to nitrogen quarternary nitrogen atom N+ atom N in aromatic ring in aromatic ring two oxime groups, one in position o-, other in position Number of members bonded in m- due to a quarternary -1.047 P12 aliphatic ring after the group P3 nitrogen atom N+ in aromatic ring two oxime groups, one in position o-, other in position Cycle ring bonded to nitrogen atom P13 p- due to a quarternary N in aromatic ring 10.365 nitrogen atom N+ in aromatic ring two oxime groups, one in position m-, other in position Oxygen atom O bonded in aliphatic p- due to a quarternary P14 ring bonded to one aromatic ring 32.437 nitrogen atom N+ in aromatic ring Oxygen atom O bonded in Presence of other aliphatic ring 88.073 P15 aliphatic ring between two bonded to aromatic one aromatic rings Number of members bonded in aliphatic ring following group NCycle between two aromatic CHx- (nitrogen atom N is a part of -2.344 P16 rings aromatic ring), (which are not included in other groups) Double bond between two P17 aromatic rings

P2

15.737

P3

47.105

P4

52.105

P5

25.842

P6

56.105

P7

-5.842

P8

10.474 22.105

Table 10. List of structural fragments and their values for estimation of reactivation ability of reactivators for acetylcholinesterase inhibited by chloropyrifos

152 Thermodynamics Fundamentals and Its Application in Science

Reactivator TO 238 K 111 K 113 Methoxime K 280

Rp,exp / % 48.00 8.00 37.00 45.00 4.00

Rp,calc / % 49.55 5.26 36.63 47.11 4.48

Deviation / % 1.55 -2.74 -0.37 2.11 0.48

Table 11. Results for estimation of reactivation ability of the test dataset of 5 reactivators of acetylcholinesterase inhibited by chloropyrifos

Illustration of new method for reactivation ability prediction of two reactivators (TO 238 and K 280) of which experimental data were not used for parameters calculation follows.

TO 238

K 280

Figure 5. Chemical structure of two reactivators of acetylcholinesterase signed as TO 238 and K 280

Example of usage of the new model for reactivation ability prediction for TO 280 reactivator:

Rp,calc(TO 238) = P1 + 2P6 + P7 = 26.365 + 2(-32.437) + 88.073 = 49.546 % Rp,exp(TO 238) = 48.00 % AE = Rp,calc(TO 238) - Rp,exp(TO 238) = 1.55 %.
Example of usage of the new model for reactivation ability prediction for K 280 reactivator:

Rp,calc(K 280) = P9 + P17 = 26.580 + (-22.105) = 4.475 % Rp,exp(K 280) = 4.00 % AE = Rp,calc(K 280) - Rp,exp(K 280) = 0.48 %.
For model development for reactivators AChE inhibited by sarin the input database included data of reactivation ability Rp for 18 reactivators (K 127, K 128, K 141, K 276, K 311, K 277, K 077, K 142, K 131, K 100, K 233, K 194, K 191, K 067, K 119, K 053, Pralidoxime, HI6) of concentration c=110-3 moldm-3 were taken. Due to the smaller database in comparison with the chloropyrifos-inhibited case it was not possible to apply the same structural fragments. Values for 11 new structural different groups with the AAE of 3.39 % of Rp have been calculated. Designed groups with their calculated values of Rpi are presented in Table 12. These calculated parameters were tested on the test set of 4 independent compounds (TO 055, TO 058, K 197, Obidoxime) of which experimental data were not applied to group contributions determination. The AAE of Rp prediction for this test-set was 2.18 %. Table 13 presents experimental data and predicted values for 4 independent compounds.

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 153

no. Fragment description Quarternary nitrogen atom N inclusive in aromatic ring Presence of oxime group ortho- position of substituent on aromatic ring meta- position of substituent on aromatic ring para- position of substituent on aromatic ring Presence of cycle in a molecule

P1

P2 P3

Other member of ring between two quarternary nitrogen atoms N+ or/and -6.41 22.50 P7 bonded at the last quarternary nitrogen atom + of molecule N Presence of oxygen atom O in molecule 2.16 -31.21 P8 other than mentioned in the following group 46.03 P9 Presence of group >C=O in molecule Presence of group -NHx(x = 0, .., 2) in molecule Presence of a double bond between two carbon atoms in a ring between two quarternary nitrogen atoms N+ in molecule 7.88

Rpi no. /%

Fragment description

Rpi /%

P4

14.49 P10

-12.20

P5 P6

40.01 P11 -10.03

1.66

Table 12. List of structural fragments and their values for estimation of reactivation ability of reactivators for acetylcholinesterase inhibited by sarin

As it is shown in Table 12, the highest and the positive values of group contributions are given for fragments P1, P3-P5, P8 and P9. On the other hand the smallest contribution (the negative ones) to the total value of reactivation ability yield fragments P6, P7 and P10. Also the value of fragment P2 for oxime group seems to have a negative effect to the total value but it should be said, that the oxime group has to be summed up with some group for its position on aromatic ring. It results in a fact that the oxime group in meta- position has the negative influence to the total value of reactivation ability, on the other hand the total value of Rp increases with oxime group in positions of ortho- or para-. These values resulted in fact that reactivation ability of new reactivators for reactivation AChE inhibited by sarin should be increased by the presence of the following function groups in molecules: another quarternary nitrogen atom in aromatic ring, the oxime groups in ortho- or para positions, presence of oxygen atom or group >C=O in molecule. It is clear that reactivation ability decreases with presence of cycle ring and also with presence of the group NHx (x = 0, .., 2) in molecules. Also meta- position of oxime group, as same as the longer ring (CHx)n (x = 0, .., 2) bonded at quarternary nitrogen atoms, that means group P7, do not contribute positively.
Reactivator TO 055 TO 058 K 197 Obidoxime Rp,exp / % 30.00 25.00 4.00 41.00 Rp,calc / % 32.38 27.63 4.08 44.70 Deviation / % 2.38 2.63 0.08 3.70

Table 13. Results for estimation of reactivation ability of the test dataset of 4 reactivators of acetylcholinesterase inhibited by sarin

154 Thermodynamics Fundamentals and Its Application in Science

Illustration of new method for reactivation ability prediction of two reactivators (TO 055 and TO 058) of which experimental data were not used for parameters calculation follows.

TO 055

TO 058

Figure 6. Chemical structure of two reactivators of acetylcholinesterase signed as TO 055 and TO 058

Example of usage of the new model for reactivation ability prediction for TO 055 reactivator: Rp,calc(TO 055) = 3P1 + 3P2 + 3P5 + 3P6 + 3P7 + P10 = 3(22.50) + 3(-31.21) + 3(40.01) + 3(-10.03) + 3(-6.41) + (-12.20) = 32.38 %; Rp,exp(TO 055) = 30.00 %

AE = Rp,calc(TO 055) - Rp,exp(TO 055) = 2.38 %.

Example of usage of the new model for reactivation ability prediction for TO 055 reactivator: Rp,calc(TO 058) = 2P1 + 2P2 + 2P5 + 2P6 + 3P7 + 2P8 = 2(22.50) + 2(-31.21) + 2(40.01) + 2(10.03) + 3(-6.41) + 2(2.16) = 27.63 %; Rp,exp(TO 058) = 25.00 %

AE = Rp,calc(TO 058) - Rp,exp(TO 058) = 2.63 %.

As it is clear, in comparison with the previous cases, these models are applicable only for the same inhibitors but for new reactivators of ACHE inhibited by the same inhibitors (the first for chloropyrifos, the second one for sarin). But on the other hand, it can be also used as a tool for easy prediction of reactivation potency of some newly synthesized reactivators without any other in vitro standard tests.

3. Conclusion
Most of the industrial applications and products contain a mixture of many components and for the production it is important to know the properties of individual substance and the properties of aggregates. The accomplishments of all of these experiments are too expensive and time-consuming, so the calculation or estimation methods are good way to solve this problem. The group contribution methods are the important and favourible estimation method, because they permit to determine value of property of extant or hypothetic compound. Group contribution methods are the suitable tool for estimation of many physico-chemical quantities of pure compounds and mixtures too as it was showed and confirmed above for some cases. It can be used for estimation of pure compounds, as well as mixtures, for one temperature estimation, as well as for temperature range, etc. The biggest advantage of these methods is they need knowledge only chemical structure of compounds

Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 155

without any other input information. The presented models have been developed for estimation of many variable properties, enthalpy of vaporization, entropy of vaporization, liquid heat capacity, swelling of Nafion, flash temperature and reactivation ability of reactivators of acetylcholinesterase inhibited by organophosphate compounds. Proposed models and their structural fragments, accuracy and reliability depend mainly on frequency of input data and their accuracy, correctness and reliability. The most of presented models of group contribution methods, not only in the cases presented in this chapter, can be applied for the wide variety of organic compounds, when groups describing these molecules are presented. Some of models can be applied from only limited families of compounds due to their parameters were calculated only for limited database of compounds. Group contribution methods can be applied either for estimation or prediction of properties at one temperature or as a temperature function depending on their development. The accuracy of developed models is the higher, the input database is more reliable.

Author details
Zdeka Kolsk Faculty of Science, J. E. Purkyn University, Usti nad Labem, Czech Republic Milan Zbransk and Alena Randov Institute of Chemical Technology, Prague, Czech Republic

Acknowledgement
This work was supported by the GA CR under the project P108/12/G108. Authors also thank to Ing. Michal Karlk from ICT Prague, Czech Republic, for data for flash temperature estimation and Prof. Kamil Kua from Department of Toxicology, Faculty of Millitary Health Science Hradec Kralove, Czech Republic, for data on reactivation ability.

4. References
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156 Thermodynamics Fundamentals and Its Application in Science

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Williams, J. D. (1997). Prediction of melting and heat capacity of inorganic liquids by the method of group contributions. Thesis, New Mexico State Univ., Las Cruces, NM, USA Briard, A. J.; Bouroukba, M.; Petitjean, D. & Dirand, M. (2003). Models for estimation of pure n-alkanes' thermodynamic properties as a function of carbon chain length. Journal of Chemical and Engineering Data, Vol.48, No.6, pp. 1508-1516, ISSN 0021-9568 Nikitin, E. D.; Popov, A. P.; Yatluk, Y. G. & Simakina, V. A. (2010). Critical Temperatures and Pressures of Some Tetraalkoxytitaniums. Journal of Chemical and Engineering Data, Vol.55, No.1, pp. 178-183, ISSN 0021-9568 Papaioannou, V.; Adjiman, C. S.; Jackson, G. & Galindo, A. (2010). Group Contribution Methodologies for the Prediction of Thermodynamic Properties and Phase Behavior in Mixtures. In: Molecular Systems Engineering. Pistikopoulos E. N.; Georgiadis, M. C.; Due, V.; Adjiman, C. S.; Galindo, A. (Eds.), 135-172, Wiley-VCH, ISBN 978-3-527-31695-3, Weinheim Teixeira, M. A.; Rodriguez, O.; Mota, F. L.; Macedo, E. A. & Rodrigues, A. E. (2010). Evaluation of Group-Contribution Methods To Predict VLE and Odor Intensity of Fragrances. Industrial & Engineering Chemistry Research, Vol.50, No.15, pp. 9390-9402, ISSN 0888-5885 Lobanova, O.; Mueller, K.; Mokrushina, L. & Arlt, W. (2011). Estimation of Thermodynamic Properties of Polysaccharides. Chemical Engineering & Technology, Vol.34, No.6, pp. 867876, ISSN 0930-7516 Satyanarayana, K. C.; Gani, R.; & Abildskov, J. (2007). Polymer property modeling using grid technology for design of structured products. Fluid Phase Equilibria, Vol.261, No.12, pp. 5863, ISSN 0378-3812 Bogdanic, G. (2009). Additive Group Contribution Methods for Predicting the Properties of Polymer Systems. In: Polymeric Materials. Nastasovic, A. B. & Jovanovic, S. M. (Eds.), 155-197, Transworld Research Network, ISSN 978-81-7895-398-4, Kerala Oh, S. Y. & Bae, Y. C. (2009). Group contribution method for group contribution method for estimation of vapor liquid equilibria in polymer solutions. Macromolecular Research, Vol.17, No.11, pp. 829-841, ISSN 1598-5032 Daz-Tovar, C.; Gani, R. & Sarup, B. (2011). Lipid technology: Property prediction and process design/analysis in the edible oil and biodiesel industries. Fluid Phase Equilibria, Vol.302, No.1-2, pp. 284293, ISSN 0378-3812 Costa, A. J. L.; Esperanca, J. M. S. S.; Marrucho, I. M. & Rebelo, L. P. N. (2011). Densities and Viscosities of 1-Ethyl-3-methylimidazolium n-Alkyl Sulfates. Journal of Chemical & Engineering Data, Vol.56, No.8, pp. 3433-3441, ISSN 0021-9568 Costa, A. J. L.; Soromenho, M. R. C.; Shimizu, K.; Marrucho, I. M.; Esperanca, J. M. S. S.; Lopes, J. N. C. & Rebelo, L. P. N. (2012). Density, Thermal Expansion and Viscosity of Cholinium-Derived Ionic Liquids. Chemphyschem: a European journal of chemical physics and physical chemistry, Ahead of Print, ISSN 1439-7641 Adamova, G.; Gardas, Ramesh L.; Rebelo, L. P. N.; Robertson, A. J. & Seddon, K. R. (2011). Alkyltrioctylphosphonium Chloride Ionic Liquids: Synthesis and Physicochemical Properties. Dalton Transactions, Vol.40, No.47, pp. 12750-12764, ISSN 1477-9226

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Gacino, F. M.; Regueira, T.; Lugo, L.; Comunas, M. J. P. & Fernandez, J. (2011). Influence of Molecular Structure on Densities and Viscosities of Several Ionic Liquids. Journal of Chemical & Engineering Data, Vol.56, No.12, pp. 4984-4999, ISSN 0021-9568 Cehreli, S. & Gmehling, J. (2010). Phase Equilibria for Benzene-Cyclohexene and Activity Coefficients at Infinite Dilution for the Ternary Systems with Ionic Liquids. Fluid Phase Equilibria, Vol.295, No.1, pp. 125-129, ISSN 0378-3812 Gardas, R. L.; Ge, R.; Goodrich, P.; Hardacre, C.; Hussain, A. & Rooney, D. W. (2010). Thermophysical Properties of Amino Acid-Based Ionic Liquids. Journal of Chemical & Engineering Data, Vol.55, No.4, pp. 1505-1515, ISSN 0021-9568 Marrero J. (2002). Programm ProPred, Version 3.5, Jorge Marrero, Department of Chemical Engineering, DTU Denmark, released date: May 15, 2002 Weininger, D.; Weininger, A. & Weininger, J. (1986). Smiles. A Modern Chemical Language and Information System. Chemical Design Automation News, Vol.1, No.8, pp. 2-15, ISSN 0886-6716 Weininger, D. (1988). Smiles. A Chemical Language and Information-System. 1. Introduction to Metodology and Encoding Rules. Journal of Chemical Information and Computer Sciences, Vol.28, No.1, pp. 31-36, ISSN 0095-2338 Weininger, D.; Weininger, A. & Weininger, J. (1989). Smiles. 2. Algorithm for Generation of Unique Smiles Notation. Journal of Chemical Information and Computer Sciences, Vol.29, No.2, pp. 97-101, ISSN 0095-2338 Weininger, D. (1990). Smiles. 3. Depict Graphical Depiction of Chemical Structures. Journal of Chemical Information and Computer Sciences, Vol.30, No.3, pp. 237-243, ISSN 0095-2338 Kolsk, Z. & Petrus P. (2010). Tool for group contribution methods computational Fragmentation Collection of Czechoslovak Chemical Communications, Vol.75, No.4, pp. 393 404, ISSN 0010-0765 Randov, A.; Bartovsk, L.; Hovorka, .; Poloncarzov, M.; Kolsk, Z. & Izk, P. (2009). Application of the Group Contribution Approach to Nafion Swelling. Journal of Applied Polymer Science, Vol.111, No.4, pp. 1745-1750, ISSN 0021-8995 Ducros, M.; Gruson, J. F. & Sannier H. (1980). Estimation of enthalpies of vaporization for liquid organic compounds. Part 1. Applications to alkanes, cycloalkanes, alkenes, benzene hydrocarbons, alkanethiols, chloro- and bromoalkanes, nitriles, esters, acids, and aldehydes. Termochimica Acta, Vol.36, No.1, pp. 39-65, ISSN 0040-6031 Ducros, M.; Gruson, J. F. & Sannier H. (1981). Estimation of the enthalpies of vaporization of liquid organic compounds. Part 2. Ethers, thioalkanes, ketones and amines. Termochimica Acta, Vol.44, No.2, pp. 131-140, ISSN 0040-6031 Ducros, M. & Sannier, H. (1982). Estimation of the enthalpies of vaporization of liquid compounds. Part 3. Application to unsaturated hydrocarbons. Termochimica Acta, Vol.54, No.1-2, pp. 153-157, ISSN 0040-6031 Ducros, M. & Sannier, H. (1984). Determination of vaporization enthalpies of liquid organic compounds. Part 4. Application to organometallic compounds. Termochimica Acta, Vol.75, No.3, pp. 329-340, ISSN 0040-6031

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Vetere A. (1995). Methods to predict the vaporization enthalpies at the normal boiling temperature of pure compounds revisited. Fluid Phase Equilibria, Vol.106, No.1-2, pp. 110 , ISSN 0378-3812 Ma, P. & Zhao, X. (1993). Modified Group Contribution Method for Predicting the Entropy of Vaporization at the Normal Boiling Point. Industrial & Engineering Chemistry Research, Vol.32, No.12, pp. 3180-3183, ISSN 0888-5885 Zbransk, M. & Rika, V. (2004). Estimation of the Heat Capacities of Organic Liquids as a Function of Temperature Using Group Additivity. An Amendment. J. Phys. Chem. Ref. Data, Vol.33, No.4, pp. 1071-1081, ISSN 0047-2689 Chickos, J. S.; Hesse, D. G. & Liebman, J. F. (1993). A Group Additivity Approach for the Estimation of Heat-Capacities of Organic Liquids and Solids at 298 K. Structural Chemistry, Vol.4, No.4, pp. 261-269, ISSN 1040-0400 Zbransk, M.; Rika, V.; Majer, V. & Domalski E. S. (1996). Heat capacity of liquids: Volume II. Critical review and recommended values. Journal of Physical and Chemical Reference Data, Monograph, 815-1596, American Chemical Society: Washington, D.C., ISSN 1063-0651 Zbransk, M.; Rika, V. & Domalski E. S. (2001). Heat Capacity of Liquids: Critical Review and Recommended Values. Supplement I. Journal of Physical and Chemical Reference Data, Vol.30, No.5, pp. 1199-1689 Zbransk, M.; Kolsk, Z.; Rika, V. & Domalski, E. S. (2010b). Heat Capacity of Liquids: Critical Review and Recommended Values. Supplement II. Journal of Physical and Chemical Reference Data, Vol.39, No.1, pp. 013103/1-013103/404, ISSN 0047-2689 Dvok, O. (1993). Estimation of the flash point of flammable liquids. Chemick prmysl, Vol.43, No.5, pp. 157-158., ISSN 0009-2789 Steinleitner, H. G. (1980). Tabulky holavch a nebezpench ltek, Transl. Novotn, V.; Benda, E. Svaz porn ochrany SSR , 1st ed. Praha Kua, K. & Kassa, J. (2003). A Comparison of the Ability of a New Bisperidinium Oxime-1,4(hydroxyiminomethylpyridinium)-4-(4-carbamoylpyridinium)butane Dibromide and Currently used Oximes to Reactivate Nerve Agent-Inhibited Rat Brain Acetylcholinesterase by In Vitro Methods. Journal of Enzyme Inhibition, Vol.18, No.6, pp. 529-533, ISSN 8755-5093 Kua, K.; Bielavsk, J.; Cabal, J. & Kassa, J. (2003a). Synthesis of a New Reactivator of TabunInhibited Acetylcholnesterase. Bioorganic & Medicinal Chemistry Letters, Vol.13, No.20, pp. 3545-3547, ISSN 0960-894X Kua, K.; Bielavsk, J.; Cabal, J. & Bielavsk, M. (2003b). Synthesis of a Potential Reactivator of Acetylcholinesterase-(1-(4-hydroxyiminomethylpyridinium)-3-(carbamoylpyridinium)propane dibromide. Tetrahedron Letters, Vol.44, No.15, pp. 3123-3125, ISSN 0040-4039 Kua, K.; Patoka, J. & Cabal, J. (2003c). Reactivation of Organophosphate Inhibited Acetyylcholinesterase Activity by -bis-(4-hydroxyiminomethylpyridinium)alkanes in vitro. Journal of Applied Biomedicine, Vol.1, No.4, pp. 207-211. ISSN 1214-0287 Kua K. & Patoka J. (2004). Reactivation of Cyclosarine-Inhibited Rad Brain Acetylcholinesterase by Pyridinium-Oximes. Journal of Enzyme Inhibition and Medicinal Chemistry. Vol.19, No.1, pp. 39-43, ISSN 1475-6366

162 Thermodynamics Fundamentals and Its Application in Science

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Chapter 7

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State

Ronald J. Bakker
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50315

1. Introduction
Physical and chemical properties of natural fluids are used to understand geological processes in crustal and mantel rock. The fluid phase plays an important role in processes in diagenesis, metamorphism, deformation, magmatism, and ore formation. The environment of these processes reaches depths of maximally 5 km in oceanic crusts, and 65 km in continental crusts, e.g. [1, 2], which corresponds to pressures and temperatures up to 2 GPa and 1000 C, respectively. Although in deep environments the low porosity in solid rock does not allow the presence of large amounts of fluid phases, fluids may be entrapped in crystals as fluid inclusions, i.e. nm to m sized cavities, e.g. [3], and fluid components may be present within the crystal lattice, e.g. [4]. The properties of the fluid phase can be approximated with equations of state (Eq. 1), which are mathematical formula that describe the relation between intensive properties of the fluid phase, such as pressure (p), temperature (T), composition (x), and molar volume (Vm).
p T , Vm , x

(1)

This pressure equation can be transformed according to thermodynamic principles [5], to calculate a variety of extensive properties, such as entropy, internal energy, enthalpy, Helmholtz energy, Gibbs energy, et al., as well as liquid-vapour equilibria and homogenization conditions of fluid inclusions, i.e. dew point curve, bubble point curve, and critical points, e.g. [6]. The partial derivative of Eq. 1 with respect to temperature is used to calculate total entropy change (dS in Eq. 2) and total internal energy change (dU in Eq. 3), according to the Maxwell's relations [5].

p dS dV T V , nT

(2)

2012 Bakker, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

164 Thermodynamics Fundamentals and Its Application in Science

p T dU p dV T V , n T

(3)

where nT is the total amount of substance in the system. The enthalpy (H) can be directly obtained from the internal energy and the product of pressure and volume according to Eq. 4.
H U pV

(4)

The Helmholtz energy (A) can be calculated by combining the internal energy and entropy (Eq. 5), or by a direct integration of pressure (Eq. 1) in terms of total volume (Eq. 6).
A U TS
dA pdV

(5) (6)

The Gibbs energy (G) is calculated in a similar procedure according to its definition in Eq. 7.
G U p V T S

(7)

The chemical potential (i) of a specific fluid component (i) in a gas mixture or pure gas (Eq. 8) is obtained from the partial derivative of the Helmholtz energy (Eq. 5) with respect to the amount of substance of this component (ni).
A i n i T , V , n

(8)
j

The fugacity (f) can be directly obtained from chemical potentials (Eq. 9) and from the definition of the fugacity coefficient (i) with independent variables V and T (Eq. 10). f RT ln i0 f i

i i0

(9)

where i0 and fi0 are the chemical potential and fugacity, respectively, of component i at standard conditions (0.1 MPa).

RT ln i

RT p dV RT ln z . n V i T , V , nj

(10)

where i and z (compressibility factor) are defined according to Eq. 11 and 12, respectively.

fi xi p

(11)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 165

pV nT RT

(12)

2. Two-constant cubic equation of state

The general formulation that summarizes two-constant cubic equations of state according to van der Waals [7], Redlich and Kwong [8], Soave [9], and Peng and Robinson [10] is illustrated in Eq. 13 and 14, see also [11]. In the following paragraphs, these equations are abbreviated with Weos, RKeos, Seos, and PReos.
p

2 RT Vm 1 Vm Vm 3 4 Vm 4
nT RT nT 2 2 2 V nT 1 V nT 3 V nT 4 V nT 2 4 2

(13)

(14)

where p is pressure (in MPa), T is temperature (in Kelvin), R is the gas constant (8.3144621 Jmol-1K-1), V is volume (in cm3), Vm is molar volume (in cm3mol-1), nT is the total amount of substance (in mol). The parameters 1, 2, 3, and 4 are defined according to the specific equations of state (Table 1), and are assigned specific values of the two constants a and b, as originally designed by Waals [7]. The a parameter reflects attractive forces between molecules, whereas the b parameter reflects the volume of molecules. W b a RK b aT -0.5 b S b a b PR b a b b

1 2 3 4

Table 1. Definitions of 1, 2, 3, and 4 according to van der Waals (W), Redlich and Kwong (RK), Soave (S) and Peng and Robinson (PR).

This type of equation of state can be transformed in the form of a cubic equation to define volume (Eq. 15) and compressibility factor (Eq. 16).
a0 V 3 a1V 2 a2 V a3 b0 z 3 b1z 2 b2 z b3 0 0

(15) (16)

where a0, a1, a2, and a3 are defined in Eq. 17, 18, 19, and 20, respectively; b0, b1, b2, and b3 are defined in Eq. 21, 22, 23, and 24, respectively.
a0 p

(17) (18)

a1

nT p 3 4 1 nT RT

166 Thermodynamics Fundamentals and Its Application in Science

a2

nT 2 p 4 2 1 3 1 4

nT 2 RT 3 4 nT 2 2

(19) (20) (21)

a3

nT 3 p 1 4 2 nT 3 RT 4 2 nT 3 1 2

b0
2

RT p

b1

RT RT 4 1 p 3 p

(22)

b2

RT 2 RT 2 4 3 4 1 p p p
b3 RT 2 1 2 1 p 4 p

(23)

(24)

The advantage of a cubic equation is the possibility to have multiple solutions (maximally three) for volume at specific temperature and pressure conditions, which may reflect coexisting liquid and vapour phases. Liquid-vapour equilibria can only be calculated from the same equation of state if multiple solution of volume can be calculated at the same temperature and pressure. The calculation of thermodynamic properties with this type of equation of state is based on splitting Eq. 14 in two parts (Eq. 25), i.e. an ideal pressure (from the ideal gas law) and a departure (or residual) pressure, see also [6]. p where
pideal nT RT V

pideal presidual

(25)

(26)

The residual pressure (presidual) can be defined as the difference (p, Eq. 27) between ideal pressure and reel pressure as expressed in Eq. 14 .
p presidual nT RT nT RT nT 2 2 2 V V nT 1 V nT 3 V nT 4 V nT 2 4 2

(27)

The partial derivative of pressure with respect to temperature (Eq. 28) is the main equation to estimate the thermodynamic properties of fluids (see Eqs. 2 and 3).

p T

pideal p T T

(28)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 167

where
n R nT R nT RT (nT 1 ) p T 2 V V nT 1 T V nT 1 T 1 V nT 3V nT 4V nT 4
2 2 2

( nT 2 2 ) T
2

nT 2 2
2

nT 3V nT 4V nT 2 4 2

nT 3V nT 4V nT 4 T

(29)

The parameters 1, 3, and 4 are usually independent of temperature, compare with the b parameter (Table 1). This reduces Eq. 29 to Eq. 30. n R nT R (nT 2 2 ) p 1 T 2 2 2 T V V nT 1 T V nT 3V nT 4 V nT 4

(30)

Other important equations to calculate thermodynamic properties of fluids are partial derivatives of pressure with respect to volume (Eq. 31 and 32).

p V

V nT 1
2nT RT

nT RT

nT 2 2 V 2 nT 3V nT 4V nT 2 42
2nT 2 2
2

2V nT 3 nT 4

(31)

2p V2

V nT 1

nT 3V nT 4V nT 4

2V nT 3 nT 4

2nT 2
2

(32)

nT 3V nT 4 V nT 2 4 2

Eqs. 31 and 32 already include the assumption that the parameters 1, 2, 3, and 4 are independent of volume. Finally, the partial derivative of pressure in respect to the amount of substance of a specific component in the fluid mixture (ni) is also used to characterize thermodynamic properties of fluid mixtures (Eq. 33).

p ni

RT V nT 1
2

V nT 1
1 nT 2 2

nT RT

(nT 1 ) ni
2

V nT 3V nT 4 V nT 4

( nT 2 2 ) ni
2

(33)

nT 3V nT 4V nT 2 4 2

(nT 3 ) (nT 4 ) (nT 4 ) n n V 2nT 4 n i i i

168 Thermodynamics Fundamentals and Its Application in Science

3. Thermodynamic parameters
The entropy (S) is obtained from the integration defined in Eq. 2 at constant temperature (Eqs. 34 and 35).
S1 S0

dS

V1 V0 V1 V0

p
V , nT

dV

(34)

S1 S0

pideal p dV T T

(35)

The limits of integration are defined as a reference ideal gas at S0 and V0, and a real gas at S1 and V1. This integration can be split into two parts, according to the ideal pressure and residual pressure definition (Eqs. 25, 26, and 27). The integral has different solutions dependent on the values of 3 and 4: Eq. 36 for 3 = 0 and 4 = 0, and Eqs. 37 and 38 for 3 > 0.

V V n V 1 1 (nT 2 2 ) S1 S0 nT R ln 1 nT R ln 1 T 1 0 V V n V V V T 0 0 0 T 1 1 1

(36)

V V n V S1 nT R ln 1 nT R ln 1 T 1 0 S0 V V n V 0 0 T 1 1 (37) 2V1 nT ( 3 4 ) q 2V nT ( 3 4 ) q 1 (nT 2 2 ) 1 (nT 2 2 ) ln ln 0 q q T T 2V1 nT ( 3 4 ) q 2V0 nT ( 3 4 ) q where

q nT 4 4 2 ( 3 4 )2

(38)

The RKeos and Seos define q as nT b , whereas in the PReos q is equal to nT b 8 , according to the values for 3 and 4 listed in Table 1. Eqs. 36 and 37 can be simplified by assuming that the lower limit of the integration corresponds to a large number of V0. As a consequence, part of the natural logarithms in Eqs. 36 and 37 can be replaced by the unit value 1 or 0 (Eqs. 39, 40, and 41).
V0 lim V n 1 0 T 1
1 lim 0 V 0

V0

(39)

V0

(40)

V0

2V nT ( 3 4 ) q lim 0 2V n ( ) q 1 T 3 4 0

(41)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 169

The entropy change that is caused by a volume change of ideal gases corresponds to the second term on the right-hand side of Eqs. 36 and 37. This term can be used to express the behaviour of an ideal mixture of perfected gases. Each individual gas in a mixture expands from their partial volume (vi) to the total volume at a pressure of 0.1 MPa, which results in a new expression for this term (Eq. 42)
V nT R ln 1 V 0 ideal.mix

ni R ln v1
i

V
i

(42)

where ni is the amount of substance of component i in the fluid mixture. In addition, the partial volume of an ideal gas is related to the standard pressure p0 (0.1 MPa) according to the ideal gas law (Eq. 43, compare with Eq. 26).
vi ni RT p0

(43)

Finally, the entropy of fluid phases containing gas mixtures at any temperature and total volume according to the two-constant cubic equation of state is given by Eq. 44 for 3 = 0 and 4 = 0, and Eq. 45 for 3 > 0. S

S0

ni R ln n 0RT
i

p V
i

2 V nT 1 1 (nT 2 ) nT R ln V V T

(44)

S0

ni R ln n 0RT
i

p V
i

2 V nT 1 1 (nT 2 ) 2V nT ( 3 4 ) q (45) nT R ln ln 2V n ( ) q V q T 4 T 3

The subscripts "1" for the upper limit of integration is eliminated to present a pronounced equation. The standard state entropy (S0) of a mixture of ideal gases is defined according to the arithmetic average principle (Eq. 46). S0

ni si0
i

(46)

where si0 is the molar entropy of a pure component i in an ideal gas mixture at temperature T. The internal energy (U, see Eq. 3) is obtained from the pressure equation (Eq. 14) and its partial derivative with respect to temperature (Eqs. 28 and 30):
U1 U0 V1

dU

V1

V0

T T

p dV (nT 2 2 ) nT 2 2 T dV T

(47)

U1

U0

V0

V2 n

T 3V

nT 4 V nT 4

(48)

170 Thermodynamics Fundamentals and Its Application in Science

Similar to the integral in the entropy definition (see Eqs. 44 and 45), Eq. 48 has different solutions dependent on the values of 3 and 4: Eq. 49 for 3 = 0 and 4 = 0, and Eq. 50 for 3 > 0.
U U0 1 V ( nT 2 2 ) nT 2 2 T T

(49)

U0

(nT 2 2 ) 2V nT ( 3 4 ) q 1 2 nT 2 T ln q T 2V nT ( 3 4 ) q

(50)

The definition of q is given in Eq. 38. The standard state internal energy ( U0) of a mixture of ideal gases is defined according to the arithmetic average principle (Eq. 51).
U0

ni ui0
i

(51)

where ui0 is the molar internal energy of a pure component i in an ideal gas mixture at temperature T. Enthalpy (Eq. 52 for 3 = 0 and 4 = 0, and Eq. 53 for 3 > 0), Helmholtz energy (Eq. 55 for 3 = 0 and 4 = 0, and Eq. 56 for 3 > 0), and Gibbs energy (Eq. 58 for 3 = 0 and 4 = 0, and Eq. 59 for 3 > 0) can be obtained from the definitions of pressure, entropy and internal energy according to standard thermodynamic relations, as illustrated in Eq. 4, 5, and 7. Standard state enthalpy (H0), standard state Helmholtz energy (A0), and standard state Gibbs energy (G0) of an ideal gas mixture at 0.1 MPa and temperature T are defined in Eqs. 54, 57, and 60, respectively.
H U0 nT RTV 1 V nT 1 V (nT 2 2 ) 2nT 2 2 T T

(52)

H U0

nT RTV nT 2 2 V 2 V nT 1 V nT 3V nT 4 V nT 2 4 2

(nT 2 2 ) 2V nT ( 3 4 ) q 1 nT 2 2 T ln q T 2V nT ( 3 4 ) q
H0 U 0 nT RT

(53)

(54) (55)

A U 0 TS0

ni RT ln n 0RT
i

p V
i

V nT 1 nT 2 2 nT RT ln V V

A U0

V nT 1 nT RT ln V i i 2V nT ( 3 4 ) q nT 2 2 ln 2V n ( ) q q 4 T 3 TS0

ni RT ln n 0RT

p V

(56)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 171

A0

U0 TS0

(57)

p V 2nT 2 2 V nT 1 nT RTV G U0 TS0 RT ni ln 0 nT RT ln n RT V V nT 1 V i i G U0 p V V nT 1 nT RTV TS0 RT ni ln 0 nT RT ln n RT V V nT 1 i i 2V nT ( 3 4 ) q nT 2 2 nT 2 2V ln 2 q V nT 3V nT 4 V nT 2 4 2 2V nT ( 3 4 ) q

(58)

(59)

G0

U0 TS0 nT RT

(60)

The Helmholtz energy equation (Eqs. 55, 56, and 57) is used for the definition of chemical potential (i) of a component in either vapour or liquid phase gas mixtures (compare with Eq. 8), Eq. 61 for 3 = 0 and 4 = 0, and Eq. 62 for 3 > 0, calculated with two-constant cubic equations of state.

pV U0 S V nT 1 T 0 RT ln 0 RT RT ln n RT ni ni V i nT RT (nT 1 ) 1 nT 2 2 ni ni V nT 1 V

(61)

pV U0 S nT RT (nT 1 ) V nT 1 T 0 RT ln 0 RT RT ln n RT ni ni ni V V nT 1 i n 2 1 n 2 q 2V nT ( 3 4 ) q T 2 T22 ln ni 2V nT ( 3 4 ) q q q ni n n n 2 q 1 T 2 T 3 T 4 n ni ni q 2V nT ( 3 4 ) q i n nT 2 2 n q 1 T 3 T 4 2V nT ( 3 4 ) q ni q ni ni

(62)

where

q ni

n nT 4 n 1 4n nT ( 3 4 ) T 3 T 4 n q T 4 ni ni i

(63)

The definitions of the partial derivative of q in respect to amount of substance (Eq. 63) according to 3 = b and 4 = 0 [8, 9] is illustrated in Eq. 64, and 3 = b and 4 = b [10] in Eq. 65.

172 Thermodynamics Fundamentals and Its Application in Science

q ni q ni

(nT b) ni
8

(64)

(nT b) ni

(65)

The fugacity coefficient (i) is defined according to Eqs. 9 and 10 from the difference between the chemical potential of a real gas mixture and an ideal gas mixture at standard conditions (0.1 MPa), see Eq. 66 for 3 = 0 and 4 = 0, and Eq. 67 for 3 > 0. Fugacity coefficient defined in Eq. 66 is applied to Weos and Eq. 67 is applied to RKeos, Seos, and PReos.
2 pV V nT 1 nT RT (nT 1 ) 1 nT 2 RT ln i RT ln RT ln V V nT 1 ni V ni nT RT

(66)

pV V nT 1 nT RT (nT 1 ) RT ln i ln RT RT ln V V nT 1 ni nT RT 2 n 2 1 2V n ( ) q n q T 3 4 T 2 T22 ln n q ni 2V nT ( 3 4 ) q q i n n n 2 q 1 T 2 T 3 T 4 ni ni q 2V nT ( 3 4 ) q ni n n nT 2 2 q 1 T 3 T 4 q ni ni 2V nT ( 3 4 ) q ni

(67)

4. Spinodal
The stability limit of a fluid mixture can be calculated with two-constant cubic equations of state, e.g. see [6]. This limit is defined by the spinodal line, i.e. the locus of points on the surface of the Helmholtz energy or Gibbs energy functions that are inflection points, e.g. see [12] and references therein. The stability limit occurs at conditions where phase separation into a liquid and vapour phase should take place, which is defined by the binodal. Metastability is directly related to spinodal conditions, for example, nucleation of a vapour bubble in a cooling liquid phase within small constant volume cavities, such as fluid inclusions in minerals (< 100 m diameter) occurs at conditions well below homogenization conditions of these phases in a heating experiment. The maximum temperature difference of nucleation and homogenization is defined by the spinodal. In multi-component fluid systems, the partial derivatives of the Helmholtz energy with respect to volume and amount of substance of each component can be arranged in a matrix that has a determinant (Dspin) equal to zero (Eq. 68) at spinodal conditions.

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 173

AV V Dspin

An

1V

An

AV n An n An n 1 1 1 2 1 AV n An n An n
2 1 2 2 2

(68)

This matrix is square and contains a specific number of columns that is defined by the number of differentiation variables, i.e. volume and number of components in the fluid mixture minus 1. The individual components of this matrix are defined according to Eqs. 69, 70, 71, 72, 73, and 74. The exact definition of these components according to two-constant cubic equations of state can be obtained from the web site http://fluids.unileoben.ac.at (see also [6]). AV V 2A V2 n1 , n2 , 2A n 2 1 n2 , V , 2A n 2 2 n1 , V , AV n (69)

An

1 n1

(70)

An

2 n2

(71)

An V
1

2A n V 1 n2 , 2A n V 2 n1 , 2A n n 1 2 V ,

(72)

An V
2

AV n

(73)

An n
1 2

An

n1

(74)

The determinant in Eq. 68 is calculated with the Laplacian expansion that contains "minors" and "cofactors", e.g. see [13]. The mathematical computation time increases exponential with increasing number of components. Therefore, the LU decomposition [14] can be applied in computer programming to reduce this time. The spinodal curve, binodal curve and critical point of a binary CO2-CH4 mixture with x(CO2) = 0.9 are illustrated in Figure 1, which are calculated with the PReos [10]. The spinodal has a small loop near the critical point, and may reach negative pressures at lower temperatures. The binodal remains within the positive pressure part at all temperatures. The binodal is obtained from equality of fugacity (Eq. 66 and 67) of each component in both

174 Thermodynamics Fundamentals and Its Application in Science

liquid and vapour phase, and marks the boundary between a homogeneous fluid mixture and fluid immiscibility [6, 15].

Figure 1. (a) Temperature-pressure diagram of a binary CO2-CH4 fluid mixture, with x(CO2) = 0.9. The shaded area illustrates T-p condition of immiscibility of a CO2-rich liquid phase and a CH4-rich vapour phase (the binodal). The red dashed line is the spinodal. All lines are calculated with the equation of state according to PReos [10]. The calculated critical point is indicated with cPR. cDK is the interpolated critical point from experimental data [16]. (b) enlargement of (a) indicated with the square in thin lines.

5. Pseudo critical point

The pseudo critical point is defined according to the first and second partial derivatives of pressure with respect to volume (Eqs. 31 and 32). This point is defined in a p-V diagram where the inflection point and extremum coincide at a specific temperature, i.e. Eqs. 31 and 32 are equal to 0. The pseudo critical point is equal to the critical point for pure gas fluids, however, the critical point in mixtures cannot be obtained from Eqs. 31 and 32. The pseudo critical point estimation is used to define the two-constants (a and b) for pure gas fluids in cubic equations of state according to the following procedure. The molar volume of the pseudo critical point that is derived from Eqs 31 and 32 is presented in the form of a cubic equation (Eq. 75). 0
2 Vm3 3 1 Vm2 3 42 3 1 3 4 Vm 1 42 3 4 42 3 4 (75)

The solution of this cubic equation can be obtained from its reduced form, see page 9 in [15]:
x3 f x g 0

(76)

where f 3 4 2 1 1 3 4 (77)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 175

2 g 2 13 1 2 4 2 3 4 3 4 4 2 3 12

(78) (79)

Vm

x 1

The values of f and g in terms of the b parameters for the individual two-constant cubic equations of state are given in Table 2. The molar volume at pseudo critical conditions is directly related to the b parameter in each equation of state: Weos Eq. 80; RKeos Eq. 81; Seos also Eq. 81; and PReos Eq. 82.
Weos : Vm pc
3b

(80) (81)

RKeos :

Vm pc Vm pc

b
3

2 1

3.847322 b

PReos :

1 Q b 3.951373 b

(82)

where Q is defined according to Eq. 83, the superscript "pc" is the abbreviation for "pseudo critical". Q Equation of state van der Waals [7] Redlich and Kwong [8] Soave [9] Peng and Robinson [10] f -3b2 -6b2 -6b2 -6b2

4 8
g -2b3 -6b3 -6b3 -8b3

4 8

(83) b in Eqs. 94-96 42.8453 29.6971 29.6971 26.6656 difference 37 % 21 % 21 % 12 %

b in Eqs. 80-82 31.3727 24.4633 24.4633 23.8191

Table 2. Definitions of f and g according to Eq. 77 and 78, respectively. The values of b are calculated for the critical conditions of pure CO2: Vm,C = 94.118 cm3mol-1, TC = 304.128 K and pC = 7.3773 MPa [18]. The last column gives the percentage of difference between the values of b (Eqs. 80-82 and 94-96).

The temperature at pseudo critical conditions is obtained from the combination of Eqs. 80-82 and the first partial derivative of pressure with respect to volume (Eq. 31).
Weos :
T pc

T pc

8 2 27 bR

0.29629630

bR

(84) (85)

RKeos :

2 3 2 1 2 0.20267686 2 bR bR

PReos :

T pc

3 2 0.17014442 2 bR bR Q 4 2 Q 2Q 4
2

(86)

176 Thermodynamics Fundamentals and Its Application in Science

where Q is defined according to Eq. 83. The order of equations (84, 85, 86) is according to the order of equations of state in Eq. 80, 81,and 82. The parameter 2 is used in Eqs. 84, 85 and, 86 instead of the constant a (see Table 1). Eq. 87 illustrates the transformation of Eq. 85 for the RKeos [8] by substitution of 2 according to its value given in Table 1. T pc

2 1

3a bR

(87)

Any temperature dependency of the a constant has an effect on the definition of the pseudo critical temperature. The pressure at pseudo critical condition (Eqs. 88-90) is obtained from a combination of the pressure equation (Eq.14), pseudo critical temperature (Eqs. 84-87) and pseudo critical molar volume (Eqs. 80-82). Weos : p pc p pc 1 2 27 b2
3

0.03703704

2
b2

(88)

RKeos :

2 1

2
b
2

0.01755999

2
b2

(89)

PReos :

p pc

Q2 2 4Q 2

2
b
2

0.01227198

2
b2

(90)

where Q is defined according to Eq. 83. The order of equations (88, 89, and 90) is according to the order of equations of state in Eqs. 80, 81, and 82. These equations define the relation between the a and b constant in two-constant cubic equations of state and critical conditions, i.e. temperature, pressure, and molar volume of pure gas fluids. Therefore, knowledge of these conditions from experimental data can be used to determine the values of a (or 2) and b, which can be defined as a function of only temperature and pressure (Eqs. 91-93, and 9496, respectively). Weos :

2
1
3

2 2 27 R TC 64 pC

0.421875

R2TC 2 pC
R2TC 2 pC

(91)

RKeos :

2 1
2

R2TC 2 pC

0.42748024

(92)

PReos : 2

4Q 2 Q 2 2 4Q 2 Q 2
2

R T
2

pC

0.45723553

R2TC 2 pC

(93)

Weos :

1 RT b C 8 pC

0.125

RTC pC

(94)

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 177

RKeos :

2 1 3

RT

pC

0.08664035

RTC pC RTC pC

(95)

PReos : b

2Q Q 2
2

RTC pC

0.07779607

(96)

where TC and pC are the critical temperature and critical pressure, and Q is defined according to Eq. 83. The order of equations (91-93, and 94-96) is according to the order of equations of state in Eqs. 80-82. Comparison of the value of b calculated with experimental critical volume (Eqs. 80, 81 and 82) and critical temperature and pressure (Eqs. 94, 95, and 96) is illustrated in Table 2. The difference indicates the ability of a specific equation of state to reproduce fluid properties of pure gases. A large difference indicates that the geometry or morphology of the selected equation of state in the p-V-T-x parameter space is not exactly reproducing fluid properties of pure gases. The empirical modifications of the van-derWaals equation of state according to Peng and Robinson [10] result in the most accurate equation in Table 2 (11% for pure CO2).

6. Critical point and curve

The critical point is the highest temperature and pressure in a pure gas system where boiling may occur, i.e. where a distinction can be made between a liquid and vapour phase at constant temperature and pressure. At temperatures and pressures higher than the critical point the pure fluid is in a homogeneous supercritical state. The critical point of pure gases and multi-component fluid mixtures can be calculated exactly with the Helmholtz energy equation (Eqs. 55-57) that is obtained from two-constant cubic equations of state, e.g. see [17, 18], and it marks that part of the surface described with a Helmholtz energy function where two inflection points of the spinodal coincide. Therefore, the conditions of the spinodal are also applied to the critical point. In addition, the critical curve is defined by the determinant (Dcrit) of the matrix illustrated in Eq. 97, see also [6].
AV V Dcrit An
1V

An

AV n An n An n 1 1 1 2 1 DV Dn Dn
1 2

(97)

The number of rows in Eq.97 is defined by the differentiation variables volume and number of components minus 2. The last row is reserved for the partial derivatives of the determinant Dspin from Eq. 68:

DV

Dspin V

(98)

178 Thermodynamics Fundamentals and Its Application in Science

Dn

Dspin n1 Dspin n2

(99)

Dn

(100)

The derivatives of the spinodal determinant (Eqs. 98-100) are calculated from the sum of the element-by-element products of the matrix of "cofactors" (or adjoint matrix) of the spinodal (Eq. 101) and the matrix of the third derivatives of the Helmholtz energy function (Eq. 102).

CV V CVn CV n

Cn Cn Cn

1V

Cn Cn Cn

V n1 n2

1 n1

(101)

1 n2

AV V K AV n AV n

1K 2

An An An

1V

An An An

VK n1 K n2 K

1 n1 K

(102)

1 n2

Figure 2. Calculated critical points of binary CO2-CH4 fluid mixtures in terms of temperature (red line) and pressure (green line), obtained from the PReos [10]. Solid circles are experimental data [16, 19]. The open squares are the critical point of pure CO2 [20].

where Cxy are the individual elements in the matrix of "cofactors", as Laplacian expansion. The subscript K refers to the variable that is differentiation (volume, amount of substance of the components 1 computation time in software that uses this calculation method, the LU

obtained from the used in the third and 2. To reduce decomposition has

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 179

been used to calculate the determinant in Eq. 97. The determinants in Eqs. 68 and 97 are both used to calculate exactly the critical point of any fluid mixture and pure gases, based on two-constant cubic equations of state that define the Helmholtz energy function. An example of a calculated critical curve, i.e. critical points for a variety of compositions in a binary fluid system, is illustrated in Figure 2. The prediction of critical temperatures of fluid mixtures corresponds to experimental data [16, 19], whereas calculated critical pressures are slightly overestimated at higher fraction of CH4. This example illustrates that the PReos [10] is a favourable modification that can be used to calculate sub-critical conditions of CO 2-CH4 fluid mixtures.

7. Mixing rules and definitions of 1 and 2

All modifications of the van-der-Waals two-constant cubic equation of state [7] have an empirical character. The main modifications are defined by Redlich and Kwong, Soave and Peng and Robinson (see Table 1), and all modification can by summarized by specific adaptations of the values of 1, 2, 3, and 4 to fit experimental data. The original definition [7] of 1 (b) and 2 (a) for pure gases is obtained from the pseudo critical conditions (Eqs. 9193, and 94-96). This principle is adapted in most modifications of the van-der-Waals equation of state, e.g. RKeos [8]. Soave [9] and Peng and Robinson [10] adjusted the definition of 2 with a temperature dependent correction parameter (Eqs. 103-105).

2 aC
1 m1
T TC
2

(103)

(104)

i 0, 1, 2

mi i

(105)

where ac is defined by the pseudo critical conditions (Eqs. 91-93), and is the acentric factor. The summation in Eq. 105 does not exceed i = 2 for Soave [9] and Peng and Robinson [10]. The definition of the acentric factor is arbitrary and chosen for convenience [5] and is a purely empirical modification. These two equations of state have different definitions of pseudo critical conditions (see Eqs. 91-93 and 94-96), therefore, the values of mi must be different for each equation (Table 3). Soave [9] 0.480 1.574 -0.176 Peng and Robinson [10] 0.37464 1.54266 -0.26992

m0 m1 m2

Table 3. Values of the constant mi in Eq. 105.

180 Thermodynamics Fundamentals and Its Application in Science

The two-constant cubic equation of state can be applied to determine the properties of fluid mixtures by using "mixing rules" for the parameters 1 and 2 which are defined for individual pure gases according to pseudo critical conditions. These mixing rules are based on simplified molecular behaviour of each component (i and j) in mixtures [21, 22] that describe the interaction between two molecules:
1mix 2 mix

xi 1(i)
i j

(106)

xi x j 2 (i , j)
i j

(107)

where

2 (i , j)

2 (i) 2 ( j)

(108)

These mixing rules have been subject to a variety of modifications, in order to predict fluid properties of newly available experimental data of mixtures. Soave [9] and Peng and Robinson [10] modified Eq. 108 by adding an extra correction factor (Eq. 109).

2 (i , j )

1
ij

2 (i) 2 ( j)

(109)

where ij has a constant value dependent on the nature of component i and j.

8. Experimental data
As mentioned before, modifications of two-constant cubic equation of state was mainly performed to obtain a better fit with experimental data for a multitude of possible gas mixtures and pure gases. Two types of experimental data of fluid properties were used: 1. homogeneous fluid mixtures at supercritical conditions; and 2. immiscible two-fluid systems at subcritical conditions (mainly in petroleum fluid research). The experimental data consist mainly of pressure, temperature, density (or molar volume) and compositional data, but can also include less parameters. Figure 3 gives an example of the misfit between the first type of experimental data for binary CO2-CH4 mixtures [19] and calculated fluid properties with RKeos [8] at a constant temperature (15 C). The RKeos uses the pseudo critical defined parameters 1 and 2 (Eqs. 92 and 95) and mixing rules according to Eqs. 106-108 and is only approximately reproducing the fluid properties of CO2-CH4 mixtures at subcritical conditions Experimental data of homogeneous supercritical gas mixtures in the ternary CO2-CH4-N2 system [23] are compared with the two-constant cubic equations of state in Table 4. The Weos [7] clearly overestimates (up to 14.1 %) experimentally determined molar volumes at 100 MPa and 200 C. The Seos [9] is the most accurate model in Table 4, but still reach deviations of up to 2.3 % for CO2-rich gas mixtures. The PReos [10] gives highly underestimated molar volumes at these conditions.

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 181

Figure 3. Modelled immiscibility of binary CO2-CH4 gas mixtures (shaded areas) in a pressure - amount CH4 fraction diagram (a) and amount CH4 fraction - molar volume diagram (b) at 15 C. The solid and open circles are experimental data [16]. The red squares are the properties of pure CO 2 [20]. The yellow triangle (Cexp) is the interpolated critical point for experimental data, and the green triangle (CRK) is the calculated critical point [8]. tie1 and tie 2 in (b) are calculated tie-lines between two phases at constant pressures 6.891 and 6.036 MPa, respectively.

CO2 0.8 0.8 0.4 0.2

composition CH4 N2 0.1 0.1 0.2 0.2 0.3 0.3 0.4 0.4

Vm(exp) W RK S cm3mol-1 56.64 64.61 (14.1%) 54.90 (-3.1%) 57.94 (2.3%) 58.92 65.81 (11.7%) 56.61 (-3.9%) 59.61 (1.2%) 61.08 67.08 (9.6%) 58.27 (-4.6%) 61.12 (0.1%) 62.90 68.28 (8.6%) 59.83 (-4.9%) 62.42 (-0.8%)

PR 53.59 (-5.4%) 56.93 (-6.1%) 56.93 (-6.8%) 58.28 (-7.3%)

Table 4. Comparison of supercritical experimental molar volumes [23] at 100 MPa and 200 C with twoconstant cubic equations of state (abbreviations see Table 1). The percentage of deviation from experimentally obtained molar volumes is indicated in brackets.

Figure 3 and Table 4 illustrate that these modified two-constant cubic equations of state still need to be modified again to obtain a better model to reproduce fluid properties at sub- and supercritical conditions.

9. Modifications of modified equations of state

The number of publications that have modified the previously mentioned two-constant cubic equations of state are numerous, see also [11], and they developed highly complex, but purely empirical equations to define the parameters 1 and 2. A few examples are illustrated in the following paragraphs.

9.1. Chueh and Prausnitz [24]

The constant values in the definition of 1 and 2 (Eqs. 92 and 95) are modified for individual gases by Chueh and Prausnitz [24]. This equation is an arbitrary modification of the RKeos

182 Thermodynamics Fundamentals and Its Application in Science

[8]. Consequently, the calculation of the value of 1 and 2 is not any more defined by pseudo critical conditions, which give exact mathematical definition of these constants. Although the prediction of fluid properties of a variety of gas mixtures was improved by these modifications, the morphology of the Helmholtz energy equation in the p-V-T-x parameter space is not any more related to observed fluid properties. The theory of pseudo critical conditions is violated according to these modifications. The mixing rules in Eqs. 106-108 were further refined by arbitrary definitions of critical temperature, pressure, volume and compressibility for fluid mixtures.
2 (i , j)
2 i j R 2TCij 2 pCij

(110)

aij

2.5 i j R2TCij pCij 2

(111)

where i and j are the newly defined constant values of component i and j, and TCij and pCij are defined according to complex mixing rules [see 24]. The values of TCij and pCij are not related to true critical temperatures and pressures of specific binary gas mixtures. The prediction of the properties of homogeneous fluids at supercritical conditions (Table 5) is only slightly improved compared to RKeos [10], but it is not exceeding the accuracy of the Seos [11]. At sub-critical condition (Figure 4), the Chueh-Prausnitz equation is less accurate than the Redlich-Kwong equation (compare Figure 3) in the binary CO2-CH4 fluid mixture at 15 C. composition CH4 N2 0.1 0.1 0.2 0.2 0.3 0.3 0.4 0.4 Vm(exp) cm3mol-1 56.64 58.92 61.08 62.90 CP 56.42 (-0.4%) 57.85 (-1.8%) 59.21 (-3.1%) 60.44 (-3.9%) H 55.96 (-0.6%) 57.68 (-2.1%) 59.17 (-3.1%) 60.38 (-4.0%) B1 56.84 (0.4%) 59.43 (0.9%) 61.67 (1.0%) 63.45 (0.9%) B2 56.53 (-0.2%) 58.81 (-0.2%) 60.79 (-0.5%) 62.40 (-0.8%)

CO2 0.8 0.8 0.4 0.2

Table 5. The same experimental molar volumes as in Table 4 compared with two-constant equations of state according to Chueh and Prausnitz [24] (CP), Holloway [25, 26] (H), Bakker [27] [B1], and Bakker [28] (B2). The percentage of deviation from experimentally obtained molar volumes is indicated in brackets.

9.2. Holloway [25, 26] and Bakker [27]

The equation of Holloway [25, 26] is another modification of the RKeos [8]. The modification is mainly based on the improvement of predictions of homogenous fluid properties of H2O and CO2 mixtures, using calculated experimental data [29]. The value for 1 and 3 (both b) of H2O is arbitrarily selected at 14.6 cm3mol-1, whereas other pure gases are defined according to pseudo critical conditions. The definition of 2 (i.e. a) for H2O as a function of

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 183

temperature was subjected to a variety of best-fit procedures [25, 26]. The fitting was improved from four experimental data points [25] to six [26] (Figure 5), but was restricted to temperatures above 350 C. Bakker [27] improved the best-fit equation by including the entire data set [29], down to 50 C (Eq. 112).

Figure 4. See Figure 3 for details. The RKeos is indicated by dashed lines in (a) and (b). The shaded areas are immiscibility conditions calculated with the Chueh-Prausnitz equation. tie1 and tie 2 in (b) are calculated tie-lines between two phases at constant pressures 6.944 and 5.984 MPa, respectively.

Figure 5. Temperature dependence of the a constant for pure H2O in the modified cubic equation of state [25, 26]. The open circles are calculated experimental data [29]. fit [25] is the range of fitting in the definition of Holloway [25], and fit [26] of Holloway [26]. RK illustrates the constant value calculated from pseudo critical condition [8].

184 Thermodynamics Fundamentals and Its Application in Science

aH O
2

2.0246 10 3 1.4928 106 7.57 108 6 9.4654 10 T T2 T3

(112)

where T is temperature in Kelvin, and the dimension of a is cm6MPaK0.5mol-2. The properties of homogeneous pure CO2, CH4 and N2 fluids [27] were also used to obtain a temperature dependent a constant (Eqs. 113, 114, and 115, respectively). aCO 5.9363 10 3 1.4124 106 1.1767 10 8 6 1.2887 10 2 T T T3
3.5216 10 3 1.155 10 6 1.1767 10 8 1.1764 10 6 T T2 T3

(113)

aCH

(114)

aN

0.20059 10 3 0.15386 106 6 0.060191 10 T T2

(115)

The aij value of fluid mixtures with a H2O and CO2 component (as in Eqs. 106-108 and 110111) is not defined by the value of pure H2O and CO2 (Eqs. 112 and 113), but from a temperature independent constant value (Eqs. 116 and 117, respectively). In addition, a correction factor is used only for binary H2O-CO2 mixtures, see [25, 29].

a0 H 2O
a0 CO2

3.5464 106
4.661 106

MPa cm6 K 0.5 mol 2

MPa cm6 K 0.5 mol 2

(116) (117)

Table 5 illustrates that the equation of Holloway [25] is not improving the accuracy of predicted properties of supercritical CO2-CH4-N2 fluids, compared to Chueh-Prausnitz [24] or Seos [9], and it is only a small improvement compared to the RKeos [8]. The accuracy of this equation is highly improved by using the definitions of a constants according to Bakker [27] (see Eqs. 112-115), and result in a maximum deviation of only 1% from experimental data in Table 5. Experimental data, including molar volumes of binary H2O-CO2 fluid mixtures at supercritical conditions [30, 31, 32] are used to estimate fugacities of H2O and CO2 according to Eq. 118 (compare Eq. 10). RT ln i

Vm , i V m
0

ideal

dp

(118)

where Vm,i - Vmideal is the difference between the partial molar volume of component i and the molar volume of an ideal gas (see also Eq. 43). The difference between Eqs. 118 and 10 is the

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 185

mathematical formulation and the use of different independent variables, which are temperature and pressure in Eq. 118. The integration to calculate the fugacity coefficient can be graphically obtained by measuring the surface of a diagram of the difference between the ideal molar volume and the partial molar volume (i.e. Vm,i - Vmideal) as a function of pressure (Figure 6). The surface obtained from experimental data can be directly compared to calculated curves from equations of state, according to Eq. 10 (Table 6). The dashed line in Figure 6 is calculated with another type of equation of state: a modification of the Lee-Kesler equation of state [33] that is not treated in this manuscript because it is not a two-constant cubic equation of state. Fugacity estimations of H2O are similar according to both equations, and reveal only a minor improvement for the twoconstant cubic equation of state [27]. The experimental data to determine fugacity of CO2 in this fluid mixture is inconsistent at relative low pressures (< 100 MPa). The calculated fugacity [27] is approximately compatible with the experimental data from [31, 32].

Figure 6. Fugacity estimation in a pressure - dv diagram at 873 K and a composition of x(CO2) = 0.3 in the binary H2O-CO2 system, where dv is the molar volume difference of an ideal gas and the partial molar volume of either H2O or CO2 in binary mixtures. Experimental data are illustrated with circles, triangles and squares (solid for CO2 and open for H2O. The red lines are calculated with Bakker [27], and the shaded area is a measure for the fugacity coefficient of H2O (Eq. 118).

186 Thermodynamics Fundamentals and Its Application in Science

Pressure (MPa) 10 50 100 200 300 400 500 600

Exp. fugacity (MPa) 6.692 27.962 45.341 77.278 114.221 160.105 219.252 295.350

B1 fugacity (MPa) 6.659 (-0.5%) 27.3061 (-2.3%) 44.6971 (-1.4%) 75.0515 (-2.9%) 111.072 (-2.8%) 157.145 (-1.8%) 216.817 (-1.1%) 294.216 (-04%)

Table 6. Fugacities of H2O in H2O-CO2 fluid mixtures, x(CO2) = 0.3, at 873.15 K and variable pressures. B1 fugacity is calculated with Bakker [27]. The deviation (in %) is illustrated in brackets.

9.3. Bowers and Helgeson [34] and Bakker [28]

Most natural occurring fluid phases in rock contain variable amounts of NaCl, which have an important influence on the fluid properties. Bowers and Helgeson [34] modified the RKeos [8] to be able to reproduce the properties of homogeneous supercritical fluids in the H2O-CO2-NaCl system, but only up to 35 mass% NaCl. The model is originally restricted between 350 and 600 C and pressures above 50 MPa, according to the experimental data [35] that was used to design this equation. This model was modified by Bakker [28] including CH4, N2, and additionally any gas with a (2) and b (1) constants defined by the pseudo critical conditions (Eqs. 91-93 and 94-96). Experimental data in this multi-component fluid system with NaCl can be accurately reproduced up to 1000 MPa and 1300 K. Table 5 illustrates that this modification results in the best estimated molar volumes in the ternary CO2-CH4-N2 fluid system at 100 MPa and 673 K. Similar to all modifications of the RKeos [8], this model cannot be used in and near the immiscibility conditions and critical points (i.e. sub-critical conditions).

10. Application to fluid inclusion research

Knowledge of the properties of fluid phases is of major importance in geological sciences. The interaction between rock and a fluid phase plays a role in many geological processes, such as development of magma [36], metamorphic reactions [37] and ore formation processes [38]. The fluid that is involved in these processes can be entrapped within single crystal of many minerals (e.g. quartz), which may be preserved over millions of years. The information obtained from fluid inclusions includes 1. fluid composition; 2. fluid density; 3. temperature and pressure condition of entrapment; and 4. a temporal evolution of the rock can be reconstructed from presence of various generation of fluid inclusions. An equation of state of fluid phases is the major tool to obtain this information. Microthermometry [39] is an

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 187

analytical technique that directly uses equations of state to obtain fluid composition and density of fluid inclusions. For example, cooling and heating experiment may reveal fluid phase changes at specific temperatures, such as dissolution and homogenization, which can be transformed in composition and density by using the proper equations of state. The calculation method of fluid properties is extensive and is susceptible to errors, which is obvious from the mathematics presented in the previous paragraphs. The computer package FLUIDS [6, 40, 41] was developed to facilitate calculations of fluid properties in fluid inclusions, and fluids in general. This package includes the group "Loners" that handles a large variety of equations of state according to individual publications. This group allows researchers to perform mathematical experiments with equations of state and to test the accuracy by comparison with experimental data. The equations of state handled in this study can be downloaded from the web site http://fluids.unileoben.ac.at and include 1. "LonerW" [7]; 2. "LonerRK" [8]; 3. "LonerS" [9]; 4. "LonerPR" [10]; 5. "LonerCP" [24]; 6. "LonerH" [25, 26, 27]; and 7. "LonerB" [28, 34]. Each program has to possibility to calculate a variety of fluid properties, including pressure, temperature, molar volume, fugacity, activity, liquid-vapour equilibria, homogenization conditions, spinodal, critical point, entropy, internal energy, enthalpy, Helmholtz energy, Gibbs energy, chemical potentials of pure gases and fluid mixtures. In addition, isochores can be calculated and exported in a text file. The diagrams and tables presented in this study are all calculated with these programs.

Author details
Ronald J. Bakker Department of Applied Geosciences and Geophysics, Resource Mineralogy, Montanuniversitaet, Leoben, Austria

11. References
[1] Dziewonski AM, Anderson DL (1981) Preliminary reference Earth model. Phys. Earth Planet. In. 25: 297-356. [2] Press F, Siever R (1999) Understanding Earth. Freeman, New York, 679 p. [3] Roedder E (1984) Fluid inclusions, Reviews in Mineralogy 12, Mineralogical Association of America, 646 p. [4] Bakker RJ (2009) Reequilibration of fluid inclusions: Bulk diffusion. Lithos 112: 277-288. [5] Prausnitz JM, Lichtenthaler RN, Gomes de Azevedo E (1986) Molecular thermodynamics of fluid-phase equilibria. Prentice-Hall, Englewood Cliffs, NJ, 600 p. [6] Bakker RJ (2009) Package FLUIDS. Part 3: correlations between equations of state, thermodynamics and fluid inclusions. Geofluids 9: 63-74.

188 Thermodynamics Fundamentals and Its Application in Science

[7] Waals JD van der (1873) De continuiteit van den gas- en vloeistof-toestand. PhD Thesis, University Leiden, 134 p. [8] Redlich OR, Kwong JNS (1949) On the thermodynamics of solutions, V: An equation of state, fugacities of gaseous solutions. Chem Rev. 44: 233-244. [9] Soave G (1972) Equilibrium constants from a modified Redlich-Kwong equation of state. Chem. Eng. Sci. 27: 1197-1203. [10] Peng DY, Robinson DB (1976) A new two constant equation of state. Ind. Eng. Chem. Fundam. 15: 59-64. [11] Reid RC, Prausnitz JM, Poling BE (1989) The properties of gases and liquids. McGrawHill Book Company, NJ, 741 p. [12] Levelt-Sengers J (2002) How fluids unmix, discoveries by the school of van der Waals and Kamerlingh Onnes. Koninklijke Nederlandse Akademie van Wetenschappen, Amsterdam, 302 p. [13] Beyer WH (1991) CRC Standard mathematical tables and formulae. CRC Press, Boca Raton, Fl, 609 p. [14] Horn RA, Johnson CR (1985) Matrix analysis. Cambridge University Press, Cambridge, 561 p. [15] Prausnitz JM, Anderson TF, Grens EA, Eckert CA, Hsieh R, O'Connell JP (1980) Computer calculations for the multicomponent vapor-liquid and liquid-liquid equilibria. Prentice-Hall, Englewood Cliffs, NJ, 353 p. [16] Donnelly HG, Katz DL (1954) Phase equilibria in the carbon dioxide - methane system. Ind. Eng. Chem. 46: 511-517. [17] Baker LE, Luks KD (1980) Critical point and saturation pressure calculations for multipoint systems. Soc. Petrol. Eng. J. 20: 15-4. [18] Konynenburg PH van, Scott RL (1980) Critical lines and phase equilibria in binary van der Waals mixtures. Philos. T. Roy. Soc. 298: 495-540. [19] Arai Y, Kaminishi GI, Saito S (1971) The experimental determination of the P-V-T-X relations for carbon dioxide-nitrogen and carbon dioxide-methane systems. J. Chem. Eng. Japan 4: 113-122. [20] Span R, Wagner W (1996) A new equation of state for carbon dioxide covering the fluid region from the triple point temperature to 1100 K at pressures up to 800 MPa. J. Phys. Chem. Ref. Data 25:1509-1596. [21] Lorentz HA (1881) ber die Anwendung des Satzes vom Virial in den kinetischen Theorie der Gase. Ann. Phys. 12: 127-136. [22] Waals JD van der (1890) Molekulartheorie eines Krpers, der aus zwei verschiedenen Stoffen besteht. Z. Ph. Chem. 5: 133-173 [23] Seitz JC, Blencoe JG, Joyce DB, Bodnar RJ (1994) Volumetric properties of CO2-CH4-N2 fluids at 200 C and 1000 bars: a comparison of equations of state and experimental data. Geochim. Cosmochim. Acta 58: 1065-1071.

Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 189

[24] Chueh PL, Prausnitz JM (1967) Vapor-liquid equilibria at high pressures. Vapor-phase fugacity coefficients in non-polar and quantum-gas mixtures. Ind. Eng. Chem. Fundam. 6: 492-498. [25] Holloway JR (1977) Fugacity and activity of molecular species in supercritical fluids. In: Fraser DG, editor. Thermodynamics in geology, pp 161-182. [26] Holloway JR (1981) Composition and volumes of supercritical fluids in the earth's crust. In Hollister LS, Crawford MI, editors. Short course in fluid inclusions: Applications to petrology, pp. 13-38. [27] Bakker RJ (1999a) Optimal interpretation of microthermometrical data from fluid inclusions: thermodynamic modelling and computer programming. Habilitation Thesis, University Heidelberg, 50 p. [28] Bakker RJ (1999b) Adaptation of the Bowers and Helgeson (1983) equation of state to the H2O-CO2-CH4-N2-NaCl system. Chem. Geol. 154: 225-236. [29] Santis R de, Breedveld GJF, Prausnitz JM (1974) Thermodynamic properties of aqueous gas mixtures at advanced pressures. Ind. Eng. Chem. Process, Dess, Develop. 13: 374377. [30] Greenwood HJ (1969) The compressibility of gaseous mixtures of carbon dioxide and water between 0 and 500 bars pressure and 450 and 800 Centigrade. Am. J.Sci. 267A: 191-208. [31] Franck EU, Tdheide K (1959) Thermische Eigenschaften berkritischer Mischungen von Kohlendioxyd und Wasser bis zu 750 C und 2000 Atm. Z. Phys. Chem. Neue Fol. 22: 232-245. [32] Sterner SM, Bodnar RJ (1991) Synthetic fluid inclusions X. Experimental determinations of the P-V-T-X properties in the CO2-H2O system to 6 kb and 700 C. Am. J. Sci. 291: 154. [33] Duan Z, Mller N, Weare JH (1996) A general equation of state for supercritical fluid mixtures and molecular simulation of mixtures PVTX properties. Geochim. Cosmochim. Acta 60: 1209-1216. [34] Bowers TS, Helgeson HC (1983) Calculation of the thermodynamic and geochemical consequences of non-ideal mixing in the system H2O-CO2-NaCl on phase relations in geological systems: equation of state for H2O-CO2-NaCl fluids at high pressures and temperatures. Geochim. Cosmochim. Acta 47: 1247-1275. [35] Gehrig M (1980) Phasengleichgewichte und pVT-daten ternrer Mischungen aus Wasser, Kohlendioxide und Natriumchlorid bis 3 kbar und 550 C. University Karlsruhe, PhD-thesis, Hochschul Verlag, Freiburg, 109 p. [36] Thompson JFH (1995) Magmas, fluids, and ore deposits. Short course 23, Mineralogical Association of Canada. [37] Spear FS (1995) Metamorphic phase equilibria and pressure-temperature-time paths. Mineralogical Society of America, Monograph, 799 p. [38] Wilkinson JJ (2001) Fluid inclusions in hydrothermal ore deposits. Lithos 55: 229-272.

190 Thermodynamics Fundamentals and Its Application in Science

[39] Shepherd TJ, Rankin AH, Alderton DHM (1985) A practical guide to fluid inclusion studies. Blackie, Glasgow, 239 p. [40] Bakker RJ (2003) Package FLUIDS 1. Computer programs for analysis of fluid inclusion data and for modelling bulk fluid properties. Chem. Geol. 194: 3-23. [41] Bakker RJ, Brown PE (2003) Computer modelling in fluid inclusion research. In: Samson I, Anderson A, Marshall D, editors. Short course 32, Mineralogical Association of Canada, pp. 175-212.

Chapter 8

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes

Elisabeth Blanquet and Ioana Nuta
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51377

1. Introduction
The development and the design of materials and/or the processes of their fabrication are generally very time consumer and with expensive operations. Various methods of development can be conceived. Often, "empirical" approaches are adopted: the choice of the experimental parameters is established either on technological or commercial criteria, the optimization being the results of a trial and error approach, or on the results of design of experiments (DOE) approach targeted at a property of a material or a parameter of a very particular process. Another approach is to use process modeling: to simulate the process by a more or less simplified model. The modeling of gas-solid materials fabrication processes brings together several physical and chemical fields with variable complexity, starting from thermodynamics and\or kinetics studies up to the mass and heat transport coupled with databases and with thermodynamic and/or kinetics transport properties. The objective of this chapter is to illustrate the interest areas computer-aided materials design and of processes optimization based on the thermodynamic simulation and giving some interesting examples in different domains. Databases as well as their necessary tools for the implementation of the thermodynamic calculations will be described. The thermodynamic simulations of multicomponent systems contribute at two important points: the selection of the material and the optimization of the conditions of fabrication. In order to obtain a finely targeted product which meet specific functionalities, it is necessary to answer the following questions:

what type of composition, quantity, and microstructure of the material allow to obtain such properties? it is possible to elaborate the material? By what process, with which reagent/ species and which operating conditions? is stable this material during a treatment in temperature, and under a given atmosphere?
2012 Blanquet and Nuta, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

192 Thermodynamics Fundamentals and Its Application in Science

does this material react with its environment (substrate, oven, atmosphere)?

These questions are connected because the properties of the material, essentially conditioned by the microstructure of the final material, are going to depend on its chemical composition, to the process, to the operating conditions and on dimensions of the fabrication equipment. The answers to these questions can be provided and shown from calculation of phase diagrams, evaluation of chemical reactions, calculation of equilibrium pressures, and from reaction diagrams.

2. Description of the methodologies

To evaluate equilibrium state, two possible approaches exist. The first one is to choose a priori a limited number of species and the simple chemical reactions which are susceptible to represent the studied process, and to estimate one or several most favorable reactions. It can be reminded the very classic use of the diagrams of Ellingham for the synthesis of metals from their oxides. The second approach, more complex, is based on the analysis and the consideration of all the species belonging to the chemical system in the studied process. The optimization procedure must have the following stages: a. b. c. d. The analysis of the system with the inventory of all the species reasonably susceptible to be present during the reactions taking place in the process. The construction of a consistent set of thermodynamic data for these species. The thermodynamic calculations at equilibrium of complex system The best representation of the results for the users

Thus, the thermodynamic calculations often give satisfactory results for processes which use high temperatures and residence time or reaction but for processes at low temperature, the kinetic factors must be not neglected. That is why the recent developments of thermodynamic softwares tend to include descriptions of phenomena of diffusion and reaction kinetics. The thermodynamic approach gives the superior limit of possibilities of process (considering the reaction rates as infinite). It can be the only way of modeling for a complex system where the mechanisms of reaction and the kinetic data are badly known. To include some dynamic aspects (mass transport) in the modeling, an approach which takes into account the evaluation of flows will be presented. It concerns applications where the total pressure is low (<10 Pa).

2.1. The analysis of the system

The analysis of the system consists in listing the following points: the range of temperature T, range of pressure P or of volume V, the duration of the process, the list of the reagent species,

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 193

the inventory of the components of the reactor and the nature of the atmosphere. For these last points, it means elaborating a list of all the compounds, the gaseous species, the elements and the solid solutions which result from the combination of the basic elements of the system. This list is automatically generated thanks to interfaces with databases. However, it is advisable to make sure that the used database is very complete. As an example, the list corresponding to the chemical system Si-C-H-Ar (proceeded CVD (Chemical Vapor Deposition) contains about sixty species excluding the hydrocarbons CxHy where x>3 [1].

2.2. Calculation of a thermochemical equilibrium

In a process reactor, at constant pressure, the balance is reached when the total free Gibbs energy function of the system is minimal (equation 1). To determine the nature and the proportion of the present phases at equilibrium, it is necessary to have the description of the energies of Gibbs of all these phases. G Ne Gj qj RT j 1 RT (1)

where qj the number of moles of the species j, Gj the molar free energy of Gibbs of the species j, Ne total number of species. The Gibbs energy can be described from the enthalpy (H) and the entropy (S):

G(T ) H(T ) T S(T )

with
H (T ) K ) H (298
T

(2)

298 K

c P (T )dT

(3)

S(298 K ) S(T )

298 K

c P (T ) T

dT

(4)

The necessary data are thus: Cp(T), H(298K), S(298K) and the data of possible phases transitions Ttrans, Htrans(T). Various formalisms are adopted for the analytical expression of the function Cp (T). Among them, the formalisms of the SGTE (Scientific Group Thermodata Europe ) [2] (equation 5) and of the NASA [3](equation 6) are : cP (T ) bT cT 2 a d T2 (5)

cP (T ) bT cT 2 dT 3 eT 4 a

(6)

194 Thermodynamics Fundamentals and Its Application in Science

where a, b, c, d, e are adjustable parameters. So, it can be described analytically the Gibbs energy G for a stoichiometric compound (equation 7), for a gas (equation 8) and a solution phase (equation 9):

G(T ) A BT CT ln T DT 2 ET 3
P P0

F T

(7)

G(T , P) G(T ) RT ln

(8)

G(T , x)

Giref (T ) Gid (T , xi ) G excs (T , xi )

i i

G id (T , xi ) RT ( xi ln xi ) G
excs

(T , xi ) described from a mod el

(9)

Besides, as neither the enthalpy nor the entropy can be described in an absolute way, a reference state must be used for these two functions of state. For the entropy, the adopted convention consists in taking a zero value at 0 K. In the case of the enthalpy, the most common convention is to choose the stable structure of the element at T = 298K, as standard reference state (e.g. Al cfc, Ti hcp, O2 gas ). For the reference state, H(298K)=0 and S(0K)=0. As the reliability of the results of the thermodynamics simulation depends widely on the quality and on the consistence of the necessary data, it is advisable to attach an importance to the consistence of the available information: thermodynamics measurements, theoretical calculations, characterizations (X-ray diffraction, Environmental Scanning Microscopy), balance of phases (diagrams). In the Table 1 are given some experimental and theoretical techniques usually used to obtain the thermodynamic data. The thermodynamic information are accessible in compilations of binary phases diagrams (for example Hansen [5], Elliot [6], Massalski [7]), ternary (Ternary Alloys [8]), or specialized journals (CALPHAD, Journal of Phase Equilibria, Intermetallics), or tables (JANAF Thermochemical Tables [9], Barin [10], Gurvich [11]). Today, most of data are available in international electronic databases. In Europe, the economic interest group "Scientific Group Thermodata Europe [12]" proposes common data bases for compounds, pure substances and for solutions. Also let us quote the Coach data bank ( more than 5000 listed species) proposed by Thermodata [1], well adapted to simulate gas/solid processes, the FACT bank (oxides/salts) proposed by the company GTT [13] and the Research Center in Calculation Thermodynamics [14], base TCRAS [15], bases NASA combustion [16], NIST [17].

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 195

Experimental H(T) Cp(298K), S(298K) Cp(T) Cp, S(T) G(T) Ttrans, Htrans (T) Calorimetry (dissolution) Temperature measurement at low temperature

Theory Ab initio calculations Estimations : Miedema [4], analogy

Estimations : Neumann-Kopp law(Cp=0 for a condensed compound) volume-specific heat capacity Differential Scanning Calorimetry (DSC) calculations Electromotive force, Mass Spectrometry (activity data, partial pressures at equilibrium) Differential Thermal Analysis (DTA) Thermogravimetric analysis (TGA)

Table 1. The classically used techniques to obtain the thermodynamic data

2.3. Calculations of complex equilibrium

The software of complex equilibrium is based on the minimization at constant temperature T of the Gibbs energy and constant pressure P (equation 1) or Helmholtz energy (equation 10), at constant volume:
F RT

qj RT RT
j 1

Ne

G j

P.V

(10)

qj the number of moles of the species j . The constraints of mass equilibrium of each present element in the chemical system expressed according to the number of atoms on the pure element i (C elements) are translated by the equation (11 ):
Ne ni qeTie with i e 1 1 C

(11)

where Tie represents the stoichiometry of the species e for the element i. These C equations can be translated under the matrix shape (equation 12):

n T * q with Ne C

(12)

There are multiple algorithms allowing this minimization. Various classifications were given, the most exhaustive having been supplied by Smith and Missen [18]. In a simple way, two

196 Thermodynamics Fundamentals and Its Application in Science

groups of algorithms can be distinguished: on one hand the methods of direct minimization, about zero order for the calculation of the function G, on the other hand, the methods of the first order based on the equality of the chemical potential which require the calculation of the function derivatives. These last ones also include the methods of second order, using among others the algorithm of Newton-Ralphson which is based on the second derivatives. It is necessary to note that the methods of the first order must be perfectly controlled because they can lead to a maximum instead of a minimum and consequently to a wrong result. A method of the first group is described below: the matrix T is decomposed into a regular square matrix Tp of dimension C and a matrix Td of dimension (C, Ne-C) such as:

Tp qp Td qd n

(13)

The C species which constitute the matrix column qp are called the main species because they are chosen among the most important species and have by definition a linear independent stoichiometry. The Ne-C remaining species of the matrix Td is called derived species although they are chosen as variables from the minimization. So the Ne-C values qd are given by the procedure of minimization, C values qp is calculated by resolving the linear system:

qp Tp n Tp Td qd

(14)

An iteration of this method is divided into two steps. Firstly, the phase of exploration, every variable is modified by a value + or - h. If Xn-1 is the vector representing the variables after n-1 iterations: the species i having a step hi and Gi the value of the function

Gi G( x1, x 2 ,..., xi 1, xi hi , xi 1`,..., xv)

if Gi+<Gi either,

(15)

Gi G( x1, x 2 ,..., xi 1, xi 2hi , xi 1`,..., xv)

or,

(16)

Gi G( x1, x 2 ,..., xi 1, xi hi , xi 1`,..., xv)

(17)

When the exploration phase is ended, the next step is to move to the second algorithm phase where from the values of G + and Xn + issued from the exploration phase, we calculate X++ = Xn-1 + (Xn+-Xn-1) as well as the corresponding value G++ to obtain the optimal set [19]. To proceed the mimimization procedure, a certain number of more and more friendly softwares are available commercially. It can be listed as example: Gemini1/Gemini2 [1] FactSage [14]

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 197

MTDATA [20] Thermocalc [21]

3. Applications
Thomas [22], Bernard [23] and Pons [24] present few examples on CVD processes to illustrate the use of an a priori thermodynamic analysis. In the following paragraphs, it was chosen to show other few examples which evidence the help of thermodynamic modeling in industrial bottlenecks: Thermal stability of Metal-Organic Precursors used in CVD and ALD processes. Stability of SiC in H2 atmosphere HfO2 plasma etching SiO2 PVD evaporation-condensation deposition process.

In the last two examples which correspond to processes operating at low pressure (<1 Pa), in addition to pure thermodynamic approach, a dynamic approach was presented which includes calculations of the major species flows.

3.1. Microelectronics: Thermal stability of metal-organic precursors used in CVD and ALD processes
In the pursuit of smaller and faster devices manufacture, microelectronics industry scales down feature sizes and thus has to develop new materials and processes. Nowadays, organometallic precursors are widely used in ALD (Atomic Layer Deposition) and CVD (Chemical Vapor Deposition) deposition processes due to low deposition temperature (generally below 523 K). The objective of computational modeling for gaseous phase processes like ALD or CVD is to correlate the as-grown material quality (uniformity, growth rate, cristallinity, composition, etc) to general parameters such as growth conditions, reactor geometry, as well as local parameters that are actual flow, thermal fields and chemical kinetics at the solid/gas interface. The gaseous precursors compounds used for the transport of the elements to be deposited by these processes have to meet several physicochemical properties requirements including relatively high volatility, convenient decomposition behavior and thermal stability. The tantalum organometallic precursor pentakis dimethylamino tantalum (PDMAT), remains an attractive solution for tantalum nitride films deposition. Unfortunately, information on physical and chemical behavior of this kind of precursor is scarce and namely species that are formed during vaporization and transported to the deposition chamber remain generally unknown. Thus, the knowledge of thermodynamics of these gaseous compounds could help in the understanding of the transport and growth mechanisms. Indeed, thanks to thermodynamics, it is possible to evaluate what evolves at equilibrium in the precursor source, in the input lines and in the deposition chamber where deposition reactions occur. To control, optimize and understand any ALD or CVD processes, thermodynamic simulations are very useful and therefore data should be primarily assessed.

198 Thermodynamics Fundamentals and Its Application in Science

3.1.1. Assessment of PDMAT thermodynamic data by mass spectrometry

In order to deposit thin layers of TaN using PDMAT, ALD experiments evidenced a cracking of this precursor in the ALD reactor [25]. Cracking reactions of PDMAT can be complex and occur at the same time. A quantitative interpretation of cracking reactions can be deduced from observed molecules by mass spectrometry [26, 27] with the condition that all products and reactants of the reaction are observed and measured by the mass spectrometer at the same time. Without additional hydrogen contribution, the two following cracking reactions of Ta [N(CH3)2]5(g) could occur: i. either the Ta- [N(CH3)2] bond breaks with the additional break of H-CH2 to produce HN(CH3)2 (the so-called substitution):

Ta N CH3 2 g Ta N CH3 2 NCH3CH2 g HN CH3 2 g , 5 3

ii. or the only bond break of Ta- [N(CH3)2],

(18)

Ta N CH3 2 g Ta N CH3 2 g N CH3 2 g . 5 4

(19)

As no N(CH3)2 (g) radical was detected, the observed HN(CH3)2 (g) molecule could be formed by the following complete and rapid reaction,
N CH 3 2 g H 2 g ou H g HN CH 3 2 g .

(20)

Consequently, it could be assumed that the measured HN(CH3)2 (g) amount is the same as the initial produced amount of N(CH3)2 (g): this radical spontaneously reacts totally according to the reaction (20) after being produced by reaction (19). This mechanism could explain why N(CH3)2 (g) was not detected. So, in this study, the total cracking reaction was finally considered:

Ta N CH3 2

g
5

H2 g Ta N CH3 2

g
4

HN CH3 2 g

(21)

Another cracking reaction could be noticed: OTaN4C8H24 (g) molecule broke down into OTaN3C6H18 (g) according to the following reaction, OTaN4 C8 H 24 g H 2 g OTaN3C6H18 g HN CH3 2 g because the energy of the Ta-N bond is lower than the Ta-O bond. The experimental study of these two reactions (21) and (22) requires to know or measure H2(g) pressure. Hydrogen could come from either equilibrium with cracking cell deposits or either molecules losing one or more hydrogen atoms. In this last case, a new molecule should be present. In this study, as no hydrogen was detected or introduced intentionally in the cell, it was assumed that the amino radical is totally consumed and produces HN(CH3)2 (g) with just a sufficient hydrogen amount. So, it can be assumed that the partial pressure of (22)

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 199

p(HN(CH3)2) is quite equal to the partial pressure of p(N(CH3)2). That allows us to calculate the equilibrium constant of reaction (19):

K p (T )

p( N(CH3 )2 ) p(Ta[ N(CH 3 )2 ]4 p(Ta[ N(CH 3 )2 ]5

(23)

Pressure measurements of these three molecules by mass spectrometry lead to the evaluation of standard enthalpy at 298 K from the third law of thermodynamics:
0 0 r H 298 K RT ln K p (T ) T r fefT

(24)

Measured partial pressures of Ta [N(CH3)2]5 (g), Ta [N(CH3)2]4 (g) and HN(CH3)2 (g) are elsewhere reported [26, 27]. From this, the average value of rH298 K was evaluated to be equal to (855) kJ/mol.

3.1.2. Thermodynamic simulation of PDMAT (thermal cracking)

Thermodynamic simulations, based on the Gibbs free energy minimization of the Ta-C-NH-(O)-(Ar) system were performed using GEMINI software [1] to provide the nature of the species that should be present at equilibrium under experimental conditions. The sets of thermodynamic data which have been used come from SGTE 2007 database [28] and from the mass spectrometry study for Ta [N(CH3)2]5(g), Ta [N(CH3)2]4(g),and NC2H6 (g) gaseous species [26]. Without any available literature data or any estimates, it cannot be considered any thermodynamic description of OTaNxCyHz (g) gaseous species and intermediate TaNxCyHz (g) species such as TaN3C6H16 (g), even though these species are expected to appear as observed in mass spectrometric measurements and to play a role in PDMAT cracking and in Ta containing solid formation [26]. Two kinds of simulations have been performed within a temperature range from 400 to 750 K and at 10 Pa, which is our typical mass spectrometric total pressure in the cracking cell. First, homogeneous equilibrium was investigated - no solid phase is allowed to be formed - which corresponds to no deposition i.e. transport in gas lines held at temperature above the saturated one (Figure 1). Second, a heterogeneous equilibrium - the solid phase is allowed to be formed - has also been simulated, which corresponds to the deposition process occurring in the ALD reactor and in the cracking cell. In all these thermodynamic simulations, it appeared that Ta [N(CH3)2]5(g), (PDMAT) is not stable. In Figure 1 the homogeneous equilibrium calculation show that Ta [N(CH3)2]4(g) is stable but disappears after 450 K and Ta(g) is the only one main tantalum containing species after 415 K - but this species will soon be condensed due to large over saturation-. Added to Ta(g), a lot of cracking gaseous species such as N2 (g), CH4 (g), H2 (g) originate from the complete amine decomposition and indeed among these species, NC2H7 (g) and NC2H6 (g)

200 Thermodynamics Fundamentals and Its Application in Science

do not appear. The heterogeneous equilibrium calculations shows the formation of C solid that corresponds to the amine decomposition and this amount of free carbon increases with increasing temperature. Also, the formation of solid TaN was observed within the whole investigated temperature range and no gaseous tantalum containing species pertained contrary to mass spectrometric experiments.

Figure 1. Homogeneous thermodynamic simulations performed starting from 1 mole of the compound Ta [N(CH3)2]5(g) and 0.001 mol of Ar and for an applied total pressure equal to 10 Pa in order to be compared with the mass spectrometric experiments.

3.1.3. Conclusions
It is to be concluded that discrepancies exist between thermodynamic simulations and mass spectrometric experiments. Indeed, thermodynamics predicted total cracking of both Ta [N(CH3)2]5(g) and amine molecules in the whole investigated temperature ranges, while in mass spectrometric experiments, Ta [N(CH3)2]5(g) and NC2H7 (g) amine have been observed only in the low temperature below 623 K [26, 29]. The deviation vs. equilibrium could be analyzed experimentally by the use of various sizes of cracking cell as well as the deliberate and controlled introduction of H2(g). However, despite these limitations, these results indicate the main features of the precursor thermal behavior which can be very useful in the first stages of the development of any new ALD or CVD (for precursor transport) processes.

3.2. High power electronics: Stability of SiC in H2 atmosphere

Silicon carbide (SiC) possesses many favorable properties making it interesting for a multitude of applications, from high temperature to high frequency and high power device.

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 201

Among them, its excellent physico-chemical and electronic properties such as wide band gap and high breakdown field, together with the degree of maturity of technology, makes SiC a good candidate for mass production of Schottky diodes [30]. SiC device processing is conditioned to the fabrication of large area single crystal wafers with the lowest defect density associated to deposition of epitaxial thin films which present good structural quality and controlled doping level [31]. The most common processes used to develop SiC wafers and SiC thin films are the seeded sublimation growth technique so called the Modified Lely method and the Chemical Vapor Deposition technique from propane and silane, respectively. Huge improvements for both processes have been observed in the last decades. They come mainly from extensive experimental effort, all over different groups in the world. However, macroscopic modeling has given valuable information to understand the impact of some growth parameters and propose new design of experiment to enlarge wafer size and deposition area. On both processes [32-35], some modeling trends were largely reported combined with experimental results obtained in our researchs groups. Special emphasis is given to chemical related results. To carry out modeling, it was followed the different levels of complexity procedure described in the earlier paragraphs. Owing to the similarity of the two systems, studies on species and material databases have been naturally used for both processes. CVD- grown SiC films can be obtained from a variety of precursors which are generally part of the Si-C-H system. However, to obtain high crystal quality of 4H and 6H SiC layers, which are the most interesting polytypes for the power devices applications, experimental investigations have demonstrated that silane (SiH 4(g)) propane (C3H8(g)) gave the most stable growth, in the typical conditions (temperature higher than 1700K, pressure between 10 kPa to 100kPa, hydrogen as carrier gas) [36]. Operations are separated in two steps, first an in situ etching step to prevent epitaxy-induced defects, then the deposition step. A great body of literature dealing with both theoretical and experimental results has been devoted to understanding chemistries relevant to the separate Si-H and C-H systems. However, it appears that most is unknown about the chemical reactions in which organosilicon species, that include the three elements, can be involved. This is related to the difficulty to measure thermochemical properties of such reactive, short life time, species. Most of the thermodynamic data that have been used for these species come from ab initio electronic structure calculations combined with empiric bond additivity corrections [37, 38]. Mass spectrometry measurements have been carried out to estimate the thermodynamic data of the gaseous species Si2C(g), SiC2(g), SiC(g) and the condensed SiC(s) phase [39, 40].

202 Thermodynamics Fundamentals and Its Application in Science

With a purely thermodynamic approach, it was examined the preliminary operation of in situ etching. It was found that the H2(g) etching of SiC(s) at 1700 K under 100 kPa can lead to the formation of a condensed silicon phase, as shown on Figure 2. Thermodynamic study was made to understand the impact of the temperature, the pressure and the composition of the gas mixture [41]. Heterogeneous thermodynamic calculations show that the mixture (H2(g) + condensed SiC(s)) ends in the formation of gaseous species such as CH4(g) for the C-containing species and SiH2(g), SiH4(g), SiH(g), Si(g) and Si(s) in condensed phase for the Sicontaining species. With the etching, the amount of the gaseous C-species formed (mainly CH4(g)) is three times higher than the gaseous Si-species one. So, there is Si in excess which is condensed at the SiC(s) surface in a solid or liquid phase depending whether the etching temperature is higher or below the Si melting temperature. When the temperature is higher than 1800K, at atmospheric pressure, the quantity of formed gaseous Si-species becomes equal to the quantity of formed gaseous C-species. Consequently, the formation of liquid silicon is avoided.

3.2.1. Conclusions
Thermodynanic simulations have revealed the main phenomena and indicated some solutions. Reducing pressure would provide the same beneficial effect, though the etching rate decreases, as illustrated in Figure 3. To compensate the formation of gaseous CH4(g), the addition of an hydrocarbon species such as propane in the initial gaseous mixture would prevent the formation of condensed silicon. All these effects have been confirmed with experimental studies (Figure 2).

70000 60000

Si SiC-6H

Substrate Si droplet

Intensity (a.u.)

50000 40000 30000 20000 10000 0 400 500 600 700 800 900 1000 1100

SiC-6H

10 m

Raman shift (cm-1)

Figure 2. Optical Micrograph of SiC(s) surface etched with H2(g) at 1700 K under 100 kPa, showing silicon droplets (right). The silicon phase is identified by Raman spectroscopy (left) [41].

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 203

1,6E-05

Partial pressures (105 Pa)

1,4E-05 1,2E-05 1,0E-05 8,0E-06 6,0E-06 4,0E-06 2,0E-06

<SiC>

<SiC >+< Si>

CH4

Siy Hx)
0 0,2

0,0E+00

Pressure (105Pa)

0,4

0,6

0,8

Figure 3. Heterogeneous equilibrium of the SiC(s) - H2(g) system at 1685K. Gaseous species created by the etching are represented as a function of the pressure [41].

3.3. Thermodynamic analysis of plasma etching processes for microelectronics

With the constant downscaling of Complementary Metal-Oxide-Semiconductor (CMOS) devices and the consequent replacement of SiO2 many high-k gate materials such as Al2O3, La2O3, Ta2O5, TiO2, HfO2, ZrO2 and Y2O3 have been investigated. For each high-k material integration, the etch process has to be revisited. In the case of the etching of HfO2, one of the main issues is the low volatility of halogenated based etch by-products [42]. Compared to SiO2 halide based etching process, thermodynamic data shows that, Hf based etch by-products (HfCl4(g), HfBr4(g), HfF4(g)) are less volatile than Si etch by products (SiCl4(g), SiBr4(g), SiF4(g)) [43]. Therefore, for HfO2(s) etching, the choice of the halogenated based chemistry and substrate temperature are crucial parameters. In this work, thermodynamic studies have been carried out in the pressure (0.5 Pa) and temperature range (425 K to 625 K) conditions in order to select the most appropriate gas mixture and temperature leading to the formation of Hf and O based volatile products. Based on thermodynamic calculations in a closed system, the HfO2(s) etching process has been simulated. With this thermodynamic analyses, it is possible to determine an etch chemistry leading to volatile compounds and to estimate an etch rate under pure chemical etching conditions. It should be noted that the thermodynamic approach does not take into account the ion bombardment of the plasma.

3.3.1. Pure thermodynamic calculations of HfO2 etching

For example, lets consider the etching of HfO2(s) in CCl4(g) plasma at 400 K and 0.5Pa. In such case, the thermodynamic system is composed by four elements Hf, O, C, and Cl. The thermodynamic calculation inputs are:each element of CCl4(g) (C and Cl atoms) with

204 Thermodynamics Fundamentals and Its Application in Science

HfO2(s) as a solid phase. The main gaseous species are CO2(g) and HfCl4(g) and the main condensed species are HfCl4(s) on HfO2(s) in a solid phase. There are other gaseous species in very low amount so that they can be neglected as (CO, Cl2, Cl). These results show that carbon and chlorine containing chemistries can lead to the etching of HfO2(s) by forming CO2(g) and HfCl4(g). Similar results have been obtained for the other halide chemistries CCl3F(g), CCl2F2(g), CCl3F(g), CCl4(g).

3.3.2. Thermodynamic analysis coupled to mass transport: evaluation of etching rate

To point out the more promising chemistry among the usually adopted halogens precursors, the etch rate has been estimated from the flow calculations of each gaseous and condensed species under open conditions assuming molecular flow and the validity of the HertzKnudsen relation [44]. For these processes operating at low pressure (<10 Pa), it is possible to associate the incident and emitted flows from a given surface to the equilibrium partial pressures [45]. These calculations are based on the effusion calculations principles from the gas kinetic theory. For a gaseous species e, the total flow e which is emitted from a vaporizing surface can be calculated according to the Hertz-Knudsen relation:
e pe
2 M e RT

mol / s.m2

(25)

Where pe et Me are the partial pressure and molar mass of the species e, respectively. For each etched or deposited element i, there is equality between the incident flow and the emitted or produced from reactions flows: (emitted) (condensed) (incident) i i i on the deposited or etched surface For example, in the case of HfO2(s) etching by CHCl3(g) with Ar(g), the system is Hf, O, C, H, Cl, Ar For the previous thermodynamic calculations (HfO2(s) and CHCl3(g)) the major species at equilibrium are: CO2(g), HCl(g), HfCl4(g), Ar(g) in the gaseous phase C(s), HfO2(s), HfCl4(s) in the solid phase (26)

for a temperature of 300 K and a pressure of 5 Pa. The flow equations are in this case (principle of mass conservation) : Flow of incident C = flow of evaporated C + flow of condensed C:

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 205

1 2 .R.T

PCO

2 2

MCO

F C( s) 3 ( g ) CHCl

(27)

Flow of incident H = flow of evaporated H :

1 2 .R.T

PHCl M HCl

CHCl3 ( g )

(28)

Flow of incident Cl = flow of evaporated Cl + flow of condensed Cl : P PHCl 4. HfCl4 M 2 .R.T M HfCl HCl 4 1 F HfCl ( s) ) 3. CHCl3 ( g 4
0 pCHCl
3 3

(29)

with F(.(s)) the flow in solid phase species and CHCl3 ( g )

0 temperature at the gases inlet and pCHCl the inlet partial pressure).
3

2 .MCHCl .R.T0

(T0 the

So five unknowns are obtained: PCO , F C( s) , PHCl , PHfCl , F HfCl4 ( s)

2 4

To be able to solve this system, five equations are needed. Already, three equations with these ones of flow exist. For the both missing, its enough to consider:

Ptotale The equation of total pressure: PCO PHCl PHfCl PAr

2 4

And the value of the equilibrium constant for the assessment of mass equation of the system, the fifth global equation is supplied by:

1 1 HfO2 ( s) 2.CHCl3 ( g) C( s) .HfCl4 ( s) CO2 ( g) 2.HCl( g) .HfCl4 ( g) 2 2

the equilibrium constant of this equation is :
2 2 PCO .PHfCl .PHCl
2

(30)

Kp

2 PCHCl

(31)

P x 1 CO2 P x HCl 2 with : PHfCl x3 . 4 F C ( s) x 4 F HfCl4 ( s) x5

(32)

206 Thermodynamics Fundamentals and Its Application in Science

The system of five equations and five unknowns is obtained:

x1 1 CHCl3 x4 2 .R.T MCO2 x2 1 CHCl3 2 .R.T M HCl 1 x2 4. x3 x CHCl 3. 5 3 M M HfCl 2 .R.T HCl 4 PTotale x1 x2 x3 PAr 1 x .x 2 .x 2 1 3 2 K p P2 CHCl3

(33)

The partial pressures of the main species are obtained. To determine the etch rate, it is needed to use the calculated values for the pressures of the gases containing the elements of material to etch. In our example, the following gases CO2(g) and HfCl4(g) are considered. The theoretical etch rate ER is given by the lowest value between: ER = flow HfCl4(g).molar volume HfCl4(g) or flow CO2(g).molar volume CO2(g) (in m/s) Where:
FlowCO
2

2 .R.T

PCO

2 2

MCO

(34)

and
FlowHfCl
4

2 .R.T

PHfCl

4 4

M HfCl

in molecules / s.m

(35)

with PCO and PHfCl determined by the resolution of the mathematical system and N the 2 4 Avogadro number, P in Pa and M in kg. Figure 4 shows the evolution of the calculated HfO2(s) etch rate as a function of temperature for different F/Cl ratios in CClxFy(g) based chemistries. The etch rate is lower when the F/Cl ratio increases in the gas mixture at temperature higher than 400 K. The decrease in the etch rate is explained by the non volatility of HfF4(g) in the investigated temperature range.

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 207

3.3.3. Conclusions
From these results, thermodynamic studies predict that a chlorocarbon gas mixture -such as CCl4 -seems to be the most promising chemistry to etch HfO2(s) under pure chemical etching conditions.
110 100 90 80

CClF3 CCl2F2 CCl3F CCl4

Etch rate (a.u.)

70 60 50 40 30 20 10 0 300 K 400 K 500 K 600 K 700 K

Temperature ( K)
Figure 4. Evolution of the thermodynamically calculated HfO2(s) etch rate as a function of F-Cl ratio in CClxFy(g) based chemistries.

3.4. Optics: SiO2 PVD deposition

From optics applications, the example of the evaporation/condensation process to obtain SiO2 films is chosen. In that process, the surface of the evaporating source is heated by electronic bombardment, while the substrate is held at low temperature. The control and the reproducibility of this type of process is based on the following points: Stability of the source with time (chemical composition, morphology of surface of the evaporating zone) Temperature and surface of the evaporated area (what is linked to the parameters of the electronic bombardment).

The object of this study is to simulate the evaporation of a source of glassy silica with the aim of depositing SiO2. The heated zone is about 3-7 cm2, the reactor has a volume about 1 m3, the substrate is located at 1 m from the source. The first paragraph is dedicated to the pure thermodynamic simulations to determine the major species originated from the evaporation. In the second one, the calculations of the

208 Thermodynamics Fundamentals and Its Application in Science

flows of evaporation at equilibrium as well as exchanged flows between source and substrate surfaces are presented.

3.4.1. Pure thermodynamic calculations of SiO2 evaporation

The thermodynamic simulations corresponding to the SiO2(s) evaporation are realized by considering an excess of solid SiO2(s) at a given temperature, in a constant volume. The range of tested temperature is 1600 - 2500 K. The results of the simulation indicate that the only solid present at equilibrium is SiO2(s) and that there is no formation of solid silicon. In the range of selected temperature, the evaporation of the silica is thus congruent (the ratio of the quantity of silicon and oxygen produced in the gaseous form is equal to 2). Figure 5 presents the nature and the partial pressures of the gaseous species formed at equilibrium.

Figure 5. Calculated partial pressures for SiO2 vaporization.

The major species in this range of temperature are SiO(g), O2(g), O(g) and SiO2(g), with trace of Si(g). It can be noted that the mainly evaporated species is not SiO2(g) as it could believed to justify the stoichiometric composition of the deposits. From the results of the molar fractions calculated for various species, the gas phase reaction which takes place is globally the following:

SiO2 s g 0.42 O2 g 0.15 O g SiO

(36)

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 209

These curves show that the evaporated material quantity and consequently the evaporation rate increases with temperature. That explains the best results obtained with sources carried beyond their melting point (besides the higher quality of the surface with regard to a solid source). The calculated total pressure above silica is represented on the figure 5. For the temperatures of evaporation above 1600 K, the total pressure over the silica is superior to 0.1 Pa. If the total pressure is fixed to a lower value, there is then complete consumption of the quantity of silica carried at the evaporation temperature from a thermodynamic point of view.

0.8 0.7

Total pressure (Pa)

0.6 0.5 0.4 0.3 0.2 0.1 0 1600 1800 2000 2200 2400 2600

Temperature (K)
Figure 6. Calculated total pressure for SiO2(s) vaporization

3.4.2. Thermodynamic analysis coupled to mass transport: evaluation of deposition rate

The evaporation flows of the gaseous species originating from the SiO2(s) evaporation should respect the congruent vaporization relation (ratio Si/O in the gaseous phase = 2), demonstrated by the previous approach.

2 * O SiO O 2 * Si O 2 * SiO Si 2 * SiO O 4 * Si O 2 * SiO

2 2 2 2 2 2

(37)

where e is the molecular flow of the species e, according to equation (25). As illustrated by the previous etching case, it is possible to calculate all the species partial pressures (pe) which verify the equation (37).

210 Thermodynamics Fundamentals and Its Application in Science

From the calculated flows from equation (37), the molar volume of SiO2(s), the reactor geometry, and the temperature conditions on the surface, it is possible to estimate the growth rate and the deposition profile (Figure 7). The growth rate on the substrate is given from the exchanged flows between the two surfaces source and substrate, from basic assumptions of molecular flows. With coaxial source and substrate, the exchanged flow between the r0 radius source and r1, radius substrate, separated by a distance h is given by the relation (38).

e pe
2Me RT

* [h2 r02 r12 ( h 2 r02 r12 )2 4 * r02r12 ]mol / s.m2 2

(38)

Figure 7. Deposition profile vs deposition temperature for two evaporation temperatures; Substrate radius r0= 0.5 m; evaporating source surface= 3cm2, h= 1m

The results of the simulations are the same order as the obtained experimental values.

3.4.3. Conclusions
The simulations of the evaporation of SiO2(s) show that it is congruent and that there is thus no evolution of the load in time. The mainly produced gaseous species are SiO(g), O2(g), and O(g). Their proportions remain constant but their quantities increase with the temperature of evaporation. Simulations of the evaporation/condensation process provide good estimations of the deposition rate.

4. Conclusions
This review illustrates the interest to operate a priori an thermodynamic approach to determine the feasibility and optimize a fabrication process, specially gas-solid fabrication

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 211

process. Kinetic approaches will give rise to more realistic simulations but are often difficult to implement, for lack of reliable information. The classic pure thermodynamic can provide useful information. It can be the only approach in the case of complex chemical systems for which few kinetic data are available. To take into account the dynamic character of the processes, the approaches mixing thermodynamics simulations and calculations of exchanged flows are possible. In every case, the methodology has to contain continuous comparisons between experimental results and simulations.

Author details
Elisabeth Blanquet and Ioana Nuta Laboratory Science et Ingnierie des Matriaux et Procds (SIMaP) Grenoble INP/CNRS/UJF, Saint Martin dHres, France

Acknowledgement
This paper was inspired by the collaborative works with the colleagues of the SIMaP (Laboratoire de Science et Ingnierie des Matriaux et Procds): Jean-Nol Barbier, Claude Bernard, Christian Chatillon, Alexander Pisch, Arnaud Mantoux, Raphal Boichot, Michel Pons.

5. References
[1] Cheynet, B., Chevalier, P.-Y. ,Fischer, E. (2002) Thermosuite. Calphad. 26: 167-174. [2] Hack, K. (1996) The SGTE casebook: thermodynamics at work. Scientific Group Thermodata Europe and Institute of Materials. [3] McBride, B. J., Zehe, M. J. ,Gordon, S. (2002) NASA Glenn Coefficients for Calculating Thermodynamic Properties of Individual Species NASA. [4] Miedema, A., De Chatel, P. ,De Boer, F. R. (1980) Cohesion in alloysfundamentals of a semi-empirical model. Physica B+ C. 100: 1-28. [5] Hansen, M. ,Anderko, K. (1958) Constitution of Binary Alloys, Metallurgy and Metallurgical Engineering Series. New York: McGraw-Hill [6] Eliott, R. (1965) Constitution of Binary Alloys, First Supplement. New York: McGrawHill. [7] Massalski, T. B., Okamoto, H., Subramanian, P. R. ,Kacprazac, L. (1990) Binary alloy phase diagrams. Ohio: ASM International, Materials Park. [8] Villars, P., Prince, A. ,Okamoto, H. (1995) Handbook of Ternary Alloy Phase Diagrams. Ohio: ASM International, Materials Park. [9] Chase, M. (1998) NIST-JANAF thermochemical tables. Washington, D.C. and Woodbury, N.Y.: American Chemical Society. [10] Barin, I. (1993) Thermochemical data of pure substances. New York: VCH. [11] Gurvich, L. V., Veyts, I. ,Alcock, C. B. (1990) Thermodynamic Properties of Individual Substances. New York: Hemisphere Pub.

212 Thermodynamics Fundamentals and Its Application in Science

[12] SGTE, S. G. T. E. 38402 Saint Martin d'Heres, France. [13] GTT-Technologies. 52134 Herzogenrath, Germany. [14] Bale, C., Chartrand, P., Degterov, S., Eriksson, G., Hack, K., Ben Mahfoud, R., Melanon, J., Pelton, A. ,Petersen, S. (2002) FactSage thermochemical software and databases. Calphad. 26: 189-228. [15] Belov, G. V., Iorish, V. S. ,Yungman, V. S. (1999) IVTANTHERMO for Windows-database on thermodynamic properties and related software. Calphad. 23: 173-180. [16] Warnatz, J. (1984) Combustion chemistry. New York. [17] (2005) NIST Chemistry WebBook, NIST Standard Reference Database. Gaithersburg MD. [18] Smith, W. R. ,Missen, R. W. (1982) Chemical reaction equilibrium analysis: theory and algorithms. New York: Wiley [19] Barbier, J. N. ,Bernard, C. (1986). In Calphad XV. Fulmer Grange, U.K. [20] Davies, R., Dinsdale, A., Gisby, J., Robinson, J. ,Martin, S. (2002) MTDATAthermodynamic and phase equilibrium software from the National Physical Laboratory. Calphad. 26: 229-271. [21] Sundman, B., Jansson, B. ,Andersson, J. O. (1985) The thermo-calc databank system. Calphad. 9: 153-190. [22] Thomas, N., Suryanarayana, P., Blanquet, E., Vahlas, C., Madar, R. ,Bernard, C. (1993) LPCVD WSi2 Films Using Tungsten Chlorides and Silane. Journal of the Electrochemical Society. 140: 475-484. [23] Bernard, C., Pons, M., Blanquet, E. ,Madar, R. (1999) Computer simulations from thermodynamic data: Materials productions and develeompment-Thermodynamic Calculations as the Basis for CVD Production of Silicide Coatings. MRS BulletinMaterials Research Society. 24: 27-31. [24] Pons, M., Bernard, C., Blanquet, E. ,Madar, R. (2000) Combined thermodynamic and mass transport modeling for material processing from the vapor phase. Thin Solid Films. 365: 264-274. [25] Brize, V., Prieur, T., Violet, P., Artaud, L., Berthome, G., Blanquet, E., Boichot, R., Coindeau, S., Doisneau, B., Farcy, A., Mantoux, A., Nuta, I., Pons, M. ,Volpi, F. (2011) Developments of TaN ALD Process for 3D Conformal Coatings. Chem. Vapor Depos. 17: 284-295. [26] Violet, P., Blanquet, E., Monnier, D., Nuta, I. ,Chatillon, C. (2009) Experimental thermodynamics for the evaluation of ALD growth processes. Surface and Coatings Technology. 204: 882-886. [27] Violet, P., Nuta, I., Chatillon, C. ,Blanquet, E. (2007) Knudsen cell mass spectrometry applied to the investigation of organometallic precursors vapours. Surface and Coatings Technology. 201: 8813-8817. [28] Dinsdale, A. (1991) SGTE data for pure elements. Calphad. 15: 317-425. [29] Violet, P., Nuta, I., Artaud, L., Collas, H., Blanquet, E. ,Chatillon, C. (2009) A special reactor coupled with a high-temperature mass spectrometer for the investigation of the vaporization and cracking of organometallic compounds. Rapid Communications in Mass Spectrometry. 23: 793-800.

Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 213

[30] Di Cioccio, L. ,Billon, T.(2002) Advances in SiC materials and technology for Schottky diode applications. In Silicon Carbide and Related Materials 2001, Pts 1 and 2, Proceedings, eds. Yoshida, S., Nishino, S., Harima, H. & Kimoto, T., 1119-1124. [31] Matsunami, H. (2000) An overview of SiC growth. 125-130. Trans Tech Publ. [32] Pons, M., Blanquet, E., Dedulle, J., Garcon, I., Madar, R. ,Bernard, C. (1996) Thermodynamic heat transfer and mass transport modeling of the sublimation growth of silicon carbide crystals. Journal of the Electrochemical Society. 143: 3727-3735. [33] Pons, M., Anikin, M., Chourou, K., Dedulle, J., Madar, R., Blanquet, E., Pisch, A., Bernard, C., Grosse, P. ,Faure, C. (1999) State of the art in the modelling of SiC sublimation growth. Materials Science and Engineering: B. 61: 18-28. [34] Pons, M., Baillet, F., Blanquet, E., Pernot, E., Madar, R., Chaussende, D., Mermoux, M., Di Coccio, L., Ferret, P., Feuillet, G., Faure, C. ,Billon, T. (2003) Vapor phase techniques for the fabrication of homoepitaxial layers of silicon carbide: process modeling and characterization. Applied Surface Science. 212213: 177-183. [35] Bernard, C., Blanquet, E. ,Pons, M. (2007) Chemical vapor deposition of thin films and coatings: Evaluation and process modeling. Surface and Coatings Technology. 202: 790797. [36] Hallin, C., Ivanov, I.G., Henry, A., Egilsson, T., Kordina, O., and Janzen, E. 1998, J. Crystal Growth, 183, 1-2, 163. [37] Allendorf, M. D. ,Melius, C. F. (1992) Theoretical study of the thermochemistry of molecules in the silicon-carbon-hydrogen system. The Journal of Physical Chemistry. 96: 428-437. [38] Allendorf, M. D. ,Melius, C. F. (1993) Theoretical study of thermochemistry of molecules in the silicon-carbon-chlorine-hydrogn system. The Journal of Physical Chemistry. 97: 720-728. [39] Rocabois, P., Chatillon, C. ,Bernard, C. (1995) Thermodynamics of the Si-C system I. mass spectrometry studies of the condensed phases at high temperature. High Temperatures. High Pressures. 27: 3-23. [40] Rocabois, P., Chatillon, C., Bernard, C. ,Genet, F. (1995) Thermodynamics of the Si-C system II. Mass spectrometric determination of the enthalpies of formation of molecules in the gaseous phase. High Temperatures. High Pressures. 27: 25-39. [41] Neyret, E., Di Cioccio, L., Blanquet, E., Raffy, C., Pudda, C., Billon, T. ,J., C. (2000) SiC in situ pre-growth etching : a thermodynamic study. In Int. Conf. on Silicon Carbide and Related Materials, 1041-1044. Materials Science Forum. [42] Helot, M., Chevolleau, T., Vallier, L., Joubert, O., Blanquet, E., Pisch, A., Mangiagalli, P. ,Lill, T. (2006) Plasma etching of HfO at elevated temperatures in chlorine-based chemistry. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films. 24: 30. [43] Chen, J., Yoo, W. J., Tan, Z. Y. L., Wang, Y. ,Chan, D. S. H. (2004) Investigation of etching properties of HfO based high-K dielectrics using inductively coupled plasma. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films. 22: 15521558.

214 Thermodynamics Fundamentals and Its Application in Science

[44] Dumas, L., Chatillon, C. ,Quesnel, E. (2001) Thermodynamic calculations of congruent vaporization and interactions with residual water during magnesium fluoride vacuum deposition. Journal of Crystal Growth. 222: 215-234. [45] Shen, J.-y. ,Chatillon, C. (1990) Thermodynamic calculations of congruent vaporization in IIIV systems; Applications to the In-As, Ga-As and Ga-In-As systems. Journal of Crystal Growth. 106: 543-552.

Section 4

Material and Products

Chapter 9

Application of Thermodynamics and Kinetics in Materials Engineering

Lin Li
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50335

1. Introduction
1.1. Background
During the last 30 years, there was a surge for coupling thermodynamics and phase diagrams in the field of material science. Many large programmers as well as the exploring of versatile solution models, the description of the magnetism energy of elements and solutions, etc. were developed. Thermo-Calc, as one of the most successful commercial software package for calculation of phase equilibrium from a broad database, offered appropriate guidance for the materials study and reduced the amount of experiments. For example, the slag database in this commercial software package could be used for predicting the composition of oxide and sulphide inclusion formed during the deoxidation and solidification process with a specific multiphase equilibrium calculation. However, there was still far from much work in the field of prediction or estimation based on the principles of thermodynamics and kinetics for the practical processes in mass production or the designing of kinds of materials. This chapter aims at introducing some computational results on the designing of advanced materials.

2. Research and development on Transformation Induced Plasticity (TRIP) steel

2.1. TRIP steel containing Al
Low carbon low alloy TRIP steel receives significant interest in automobile industry since it offers excellent combination of high strength and formability for stretch forming or deep drawing applications. The high formability in this steel is attributed to the transformation induced plasticity of retained austenite. The amount and stability of retained austenite are the key factors, which influences the transformation behavior during straining.
2012 Li, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

218 Thermodynamics Fundamentals and Its Application in Science

As well known high Si content suppresses the formation of cementite during the bainitic transformation and it leads to an increase of the stability and the amount of retained austenite. However, high Si content might cause problems in steel production such as strong oxide layer, poor surface characteristics and low coat-ability. This leads to galvanizing problems. Therefore, efforts are made to improve the composition concept, say, the substitution of Si by other elements which might not spoil surface quality. In the first phase, different amount of Al is added as an alternative to the steel to substitute for Si[1]. In order to understand the complex effects of Al, Si in TRIP steel, many samples of different composition are prepared. As an example, the overall compositions of five samples of them are listed in Table 1[2], where steel no.2, 4, 11 with high Al content are designed as the galvanizing base material with high requirement on elongation, steel no.5 and 10 are compared materials. No. 2 4 5 10 11 C 0.18 0.18 0.21 0.19 0.19 Mn 1.56 1.65 1.41 1.47 1.47 Si 0.02 0.45 1.07 0.87 0.22 Al 1.73 1.01 0.32 0.33 0.94 P 0.017 0.015 0.017 0.024 0.024 Fe Bal. Bal. Bal. Bal. Bal.

Table 1. Compositions of TRIP steels (in wt-%)[2]

Simulation of the inter-critical annealing at 780C of steels is performed with Thermo-calc and its database. The Gibbs free energy of an arbitrary phase is listed as:
O Gm = PI 0 (Y ) GI 0 + RT N S yiS ln yiS + I0 S i

Z 0 IZ

PIZ (Y ) LIZ

(1)

The first summation in equation (1) represented the standard energy, the second the mixing entropy and the third the excess Gibbs energy. The results[2] (see in Table 2) show steel no.2 and 4 must have good plasticity and fairly good strength since both have high volume fraction of phase (ferrite), though the phase (austenite) is less, it can still induce some bainite transformation in the low temperature and raise the strength of the steels. From Table 2[2], it seems steel no.11 may have good combination and highest value of strength and plasticity since it possesses much higher phase than steel no.2 and 4 and also the high phase volume fraction which is favor to ductility. Simulation of the continuous annealing process in the inter-critical temperature is performed with Dictra software package[2]. The concentration profiles in the equilibrium phases are estimated with the number-fixed frame of reference with respect to the substitutional elements as follows:

jk jk 0

(2)

where j is flux and k was substitutional. For crystalline phases of iron based alloys, the vacancy exchange mechanism of diffusion was predominant, thus, in the lattice fixed frame of reference, the diffusion flux of component k could be written as:

Application of Thermodynamics and Kinetics in Materials Engineering 219

J k xk k k

(3)

where xk was the mole fraction of k, k represented mobility and k the gradient of chemical potential of element k. Employing a coupled thermodynamic/kinetic method for the solution of the related equations, the concentration profile of the various elements is obtained. Some of the obtained diffusion data are used to guide the processes in mill. Mechanical properties of the produced TRIP steels are shown in Fig.1[2], where all the steels are inter-critical annealed at 780C for five minutes and then cooled to different temperatures in the bainite transformation zone. steel no. 2 4 5 10 11 phase C 2.66E-4 6.07E-3 1.71E-4 4.65E-3 1.30E-4 4.18E-3 1.20E-4 3.88E-3 1.65E-4 3.99E-3 Mn 1.18E-2 2.61E-2 1.14E-2 2.55E-2 8.57E-3 2.00E-2 9.04E-3 2.10E-2 9.77E-3 2.06E-2 Si 1.96E-4 2.10E-4 4.58E-3 4.36E-3 1.16E-2 9.71E-3 9.40E-3 7.92E-3 2.27E-3 2.12E-3 Al 2.00E-2 9.66E-3 1.24E-2 6.00E-3 4.22E-3 2.12E-3 4.32E-3 2.17E-3 1.21E-2 6.15E-3 P 2.05E-4 7.19E-5 1.98E-4 6.62E-5 2.52E-4 8.32E-5 3.52E-4 1.16E-4 3.38E-4 1.22E-4 % 73.4 63.4 51.1 52.4 54.5 % 26.6 36.6 48.9 47.6 45.5

Table 2. Calculated equilibrium compositions (in wt-%) at 780C and corresponding vol.% of and phases[2]

Figure 1. Mechanical properties of the various TRIP aided steels after different heat treatment[2]

220 Thermodynamics Fundamentals and Its Application in Science

Mechanical properties of steel no.2 and 4 are in accordance with thermodynamic estimation except steel no.11 which does not show high strength and elongation rate as expected. Kinetic calculation results in Fig.2-5 explain that phenomena: after inter-critical annealing, the distribution of C and Mn in steels no.5, 10 and 11 does not exhibit substantial difference. However, high Si concentrates in the phase of steels no.5 and 10 while high Al in steel no.11. It follows from that result Al can substitute for Si to induce TRIP effect but its function is not as strong as Si.

Figure 2. Concentration profile of C at the / interface during inter-critical annealing at 780C of the steel No.5, No.10 and No.11

Figure 3. Concentration profile of Mn at the / interface during inter-critical annealing at 780C of the steel No.5, No.10 and No.11

Figure 4. Concentration profile of Al at the / interface during inter-critical annealing at 780C of the steel No.5, No.10 and No.11

Application of Thermodynamics and Kinetics in Materials Engineering 221

Figure 5. Concentration profile of Si at the / interface during inter-critical annealing at 780C of the steel No.5, No.10 and No.11

Different from steels no.5 and 10, steels no.2, 4 and 11 therefore possess both super coatability and satisfactory mechanical properties due to their high Al content. These three steels mentioned above were adopted and produced in ThyssenKrupp stahl and Voest-Alpine Arcelor and the sheet steels were manufactured as important structural parts, e.g., reinforcement A-pillars and reinforcement B-pillars in FIAT and PORSCHE, which are the pioneers in the organization of ULSAB (Ultra-Light Steel Auto Body).

2.2. TRIP steel containing P

As stated above, in order to replace Si partially and/or totally, efforts were made with Al instead[1,2]. The substitution was successful but only limited at low Al content. Side effect of high Al content in the steel is estimated that it may cause clogging during continuous casting due to precipitation of aluminum oxide[3]. Searching for the other effective element to substitute for Si was then triggered. In the periodic table of elements, Al, Si, and P are located nearby in the same period, these elements have similar electronic structures and may have similar properties. This comes true especially to Si and P since they both are semimetals. It is then natural to consider P as another substitute for Si. P can, on one hand, depress the carbon activity in cementite, prevent cementite precipitation and increase the stability of austenite. On the other hand, this element has a strong tendency to segregate at grain boundary and to induce cold brittleness. Segregation formulation was developed by Guttmann and Mclean in a ternary system (Fe, M, I) [4] based on the sublattice model in melt salts and stoichiometric phases contributed by Hillert et al[5]. Li et al. extended the segregation equation into a five-element system[6], and generalized it into a multicomponent system as[7]:
g g g B B ( yIB / yV )exp{[ 0GI 1 / c g yigiI 1 / c B yiBiI 1 / c g y J Lg : JI yIg / yV A i A i A
JI g B 1 / c g y J Lg : JV 1 / c B y J LB : JI 1 / c B y B LB : JV ] / RT } A A J A JI JI J

(4)

222 Thermodynamics Fundamentals and Its Application in Science

g g g B B ( y M / y A )exp{[ 0GM 1 / a g yIg MI 1 / a B yIBB 1 / a g yM / yA MI

iM

yig Lgi:MV
(5)

1 / a B yiB LB: MV 1 / a B yig Lg :V 1 / a B yiB LB :V ] / RT } i Ai Ai

iM iA i A

where variable y indicates site fraction in sublattice, g grain boundary, B matrix, V vacancy, A base metal, J and I represent impurity, i and M metal element, c and a fraction of sites available in grain boundary or matrix, 0 GI and 0GM are the intrinsic segregation Gibbs free energy of impurity I and metal element M , LB(:g ) stands for the A JI interaction energy between J and I in one sublattice when another sublattice is fully occupied by element A , B( g ) means the interaction energy between elements in different MI sublattices. Following references [7,8], assuming that interaction energy keeps the same on grain boundaries and in matrix and omitting the interaction between impurities and vacancy and between metal element and iron, a series of parameters[7,8] can be listed as g g follows: a c 0.5 , a B 0.75 , c B 0.25 , 0 GP = 47KJ/mol, 0GMn = 8KJ/mol, MnP = 12.5 KJ/mol, LFe :PC = -9KJ/mol. With all the data stated above and the composition of an assumed steel with enough high phosphorus (C = 0.15%, Mn = 1.6%, Si = 0.3%, P = 0.07%), the equilibrium segregation amount of phosphorus on grain boundaries at 400C is calculated as 32%[9], which is a value high enough to cause temper brittleness. The soaking temperature at the over-aging process of cold-rolled TRIP steel is set in the temperature range from 350 to 480C. However, the soaking time is quite short, normally for 3~5 min, being far from equilibrium condition. Thus, the estimated equilibrium segregation amount of phosphorus is not suitable in describing the over-aging process of TRIP steels. Based on Mclean contribution with his kinetic approach for a binary system[10], the amount of segregative element on grain boundaries can be expressed as:
( yi (t ) yi (0)) / ( yi yi (0)) 2( Xi / yid)( Dit / )1/ 2

(6)

where yi (t ) is the grain boundary coverage of element i at time t , yi (0) is its initial value and yi the equilibrium value. Di is the bulk diffusion coefficient of i , d the grain boundary thickness and Xi the mole fraction of i in matrix. Taking d 10-7cm as usual, t 5min 300sec and T 673K according to the actual process condition, X P 1.38710-3 -18[11]. (i.e., wt 0.07%), yi (0) 0; according to Sundman et al, DP 3.5310 The segregated amount of P at grain boundary after soaking at 400C for 300 s is:
y P (300 sec) 2( X P / d)( DPt / )1/ 2 =0.051%[9]

(7)

which is a small amount and would not be of any damage in grain boundary for the TRIP steel. Mechanical properties of the designed steel were measured at low temperatures ( 20C, 60C) and no substantial difference was found between the results obtained at low temperatures and room temperature[9]. Moreover, cold fracture test was taken with the structural part assembles of automobiles and no sign of cold brittleness was detected. The

Application of Thermodynamics and Kinetics in Materials Engineering 223

new type TRIP steel containing P was manufactured according to design stated above in Ansteel company group in China.

2.3. Attractive effect of Al in TRIP steel

Aluminum, however, if the clogging of Al2O3 can be efficiently prohibited through careful control in the continuous casting process, is also a good promoter of TRIP effect. The reason has been studied thermodynamically and the authors found that with the existed database the phase diagram of a steel containing certain a amount of Al can not be described accurately[12] and must be revised. In their work[12], high purity Fe (99.99 wt%, Source), Al (99.97wt%, Source) and C (99.99wt%, Source) are used to prepare different composition FeAl-C alloys. Each alloy composition is checked by wet chemical analysis, as given in Table 3. Additional annealing of encapsulated ingots is carried out at 1100C for 360 h to reach equilibrium states and to obtain a homogeneous element distribution. To check the homogeneity of the annealed alloys, an EDX line scanning of Al and C is applied on the cross-section of the alloys showing the elements are evenly distributed in the Fe matrix. The DIL experiments are carried out in a Formaster-D dilatometer to investigate the ferrite to austenite transformation during the heating and cooling cycles and the results are also listed in Table 3. Alloy C1 C2 C3 C4 C5 C6 C7 C8 Al1 Al2 Al3 Composition (wt%) C 0.15 0.25 0.41 0.54 0.75 0.76 0.91 1.01 0.19 0.20 0.21 Al 1.57 1.51 1.47 1.50 1.53 1.54 1.42 1.54 0.91 1.13 1.30 Fe 98.28 98.24 98.12 97.96 97.72 97.70 97.67 97.45 98.90 98.67 98.49 Experimental T (C) A1 731 708 739 734 732 737 726 734 735 745 745 A3 987 935 892 861 810 788 827 822 900 938 953 Calculated T (C) A1 729 728 727 728 729 729 726 729 726 725 726 A3 1006 918 850 823 796 797 769 793 889 900 920

Table 3. Compositions of the Fe-rich alloys and the transformation temperatures of the alloys obtained by DIL analysis and thermodynamic calculation[12]

With the new set of experimental data, it is possible to optimize the Fe-Al-C system in Ferich corner. The standard element reference (SER) state of Fe (bcc), Al (fcc) and C (graphite) is used as the reference state of the Gibbs energy as usual. The molar Gibbs energy of the ternary liquid phase is described by the Redlich-Kister polynomial [13]:

224 Thermodynamics Fundamentals and Its Application in Science

liquid Gm xi 0Giliquid RT xi ln xi Fe , Al ,C i Fe , Al ,C i

(8)

xFe x Al LFe , Al xFe xC LFe ,C x Al xC LAl ,C xFe x Al xC LFe , Al ,C

Where xi is the mole fraction of element i and 0 Giliquid is the Gibbs energy of liquid Fe, Al and C. The binary parameters Li,j are obtained from the thermodynamic evaluation of the limiting binaries, whereas the LFe,Al,C is a ternary interaction parameter. The Gibbs energy of solid phases, fcc (austenite), bcc (ferrite) and hcp in the Fe-Al-C system is described by a compound energy formalism consisting of substitutional and interstitial sublattices[14]. The Fe and Al substitute each other in the metal sublattice, while C and vacancies in the interstitial sublattice. The crystal structure is therefore modeled as (Fe, Al)a (C, Va)c. Symbols a and c denote the numbers of sites which is dependent on the crystal structure. Here the values of a and c are regarded as a = 1, c = 1, 3, and 0.5 for the fcc, bcc and hcp phases respectively. The molar Gibbs energy is expressed as:
G m

yi ( oGi:C yC oGi:Va yVa ) aRT yi ln yi cRT( yC ln yC yVa ln yVa )

yi y j ( yC Li , j :C yVa Li , j :Va ) yC yVa yi Li :C ,Va yi y j y k ( yC Li , j:C yVa Li , j :Va ) Gmag
i j k i j i i i

(9)

Where i, j = Fe, Al and K = C or Va. In Eq. 9, the variable yi is the site fraction of component i in its sublattice. The components in different sublattices are separated by a colon and in one sublattice by a comma. Gi:Va is the Gibbs energy of pure element i in a relevant nonmagnetic state and Gi:C is the Gibbs energy of a hypothetical non-magnetic state, where all interstitial sites are occupied by carbon. All G values are given relative to the reference state. Gmag is the magnetic part of the Gibbs energy. In the Fe-Al-C system, only one ternary K phase was reported besides the liquid, fcc, bcc and hcp phases. In this optimization, the description of the K phase is after the thermodynamic assessment of Kumar et al [15]. Li et al[12] optimized the Fe-Al-C ternary system based on the previous thermodynamic description of the Fe-C, Fe-Al and Al-C systems[15, 16] as well as the obtained DIL data[12]. Furthermore, Li et al[12] extrapolated the thermodynamic properties of the limiting binary and ternary systems to higher order systems to construct the self-made database, especially for TRIP steels containing Mn, Si, Al, C, Nb and V as alloying elements. A calculated vertical section of the Fe-Mn-Si-Al-C system is presented in Fig.6 for the alloys meeting very well with the experimental results. Phase diagram of a steel with the same composition as in Fig.6 but without Al is calculated with the self-made database and shown in Fig.7. It is obvious that the bcc+fcc field in Fig.6 is much wider than that in Fig.7. As calculated: when at 800, the carbon content in fcc phase in Fe-Mn-Si-Al-C steel is 0.476%, while at 802, the carbon content in fcc phase in Fe-Mn-Si-

Application of Thermodynamics and Kinetics in Materials Engineering 225

C steel is only 0.206%. That means if soaking at the same temperature, the former dissolves much than two times carbon in the fcc phase resulting much higher stability of fcc phase and much better TRIP effect.
1600

liquid
1400
TEMPERATURE_CELSIUS

fcc+liquid
1200

fcc
1000

fcc+graphite fcc+bcc+graphite bcc+graphite

0.5 1.0 1.5 2.0 2.5

800 bcc+fcc 600

400 0

WEIGHT_PERCENT C

Figure 6. Extrapolated vertical section of the Fe-Mn-Si-Al-C steel with 1.60 wt% Mn, 0.37 wt% Si, and 1.31 wt% Al[12].

Figure 7. Phase diagram of the Fe-Mn-Si-Al-C steel with 1.60 wt% Mn, 0.37 wt% Si

This new finding brings substantial improvement for the mechanical properties of TRIP steel. Following this idea, i.e, keeping reasonably high amount Al in the steel and treating it in an ordinary Continuous Annealing Line (CAL), a high performance TRIP steel is manufactured in modern plant, whose strength and ductility product reaches 30,000MPa%. It is actually the property target of a third generation steel[17].

226 Thermodynamics Fundamentals and Its Application in Science

3. Research and development on large-section pre-hardened mold steel for plastic

In large-section pre-hardened plastic mold steel, the inclusion of high alumina content is detrimental to machinability, which is considered as the most important property of mold steel for plastic. It is known that non-metallic inclusion may appear in molten steel at various stages of the refining process or during solidification. One could not analyze in situ the precipitation of inclusions at every period of steel-making by traditional experimental method. However, the effective composition regulation and suitable heat treatment during production could influence inclusion precipitation and improve the quality of the mold steel for plastic. This paragraph is designed to produce a large-section pre-hardened plastic mold steel relying on the step by step thermodynamic calculation[18]. The SLAG database in Thermo-calc software package contributed by Gaye[19] is a useful tool which studied the slag mixture of m oxides ( ( Mi )u Ov , i =1, 2, , m) including two kinds of i i sub-lattice. One is an anionic sub-lattice filled with oxygen ions and the other is cationic sublattice filled with the cations in the decreasing order of their charge (e.g Si4+Ca2+). The structure of the melt is described in term of symmetric (i-O-i ) and asymmetric (i-O-j) cells, in numbers Rii,...2Rij...; the energy parameters consist of parameters for asymmetric cells formation and parameters of interaction between cells. This simplified melt structure greatly and made it possible to describe the multi-component system in terms of only a few binary parameters. Because the formation of melt can be thought as the result of the following bond respond: (i-O-i ) + (j-O-j) = 2(i-O-j) (10)

Then the expression for the mixing free energy of the melt can be derived by statistic thermodynamic method. This paragraph applies the SLAG database of Thermo-calc, to predict a definite range of the composition, with which oxide and sulphide inclusion formed during the deoxidation treatment could be effectively controlled and inhibited. Since Si and Mn in the steel affect the precipitation of alumina, the inter-relation curve of Si and Mn contents is calculated and plotted with a macro file which is input to the software. The calculated result can be used as a guide for the metallurgy engineer to select suitable composition of mold steel for plastic in a broad range. For Al contents of 100 ppm and 300 ppm at a given temperature of 1800K, the calculation results are shown in Fig.8 respectively. The curve in Fig.8 is the calculated critical line of alumina precipitation. When the composition of steel locates at the right side of the curve, alumina does not precipitate and the main inclusion in molten-steel is manganesealuminate. However, if the composition locates at the left side of this curve, the alumina precipitates in molten steel. Thus, the mentioned results are used in the designing of mold steel.

Application of Thermodynamics and Kinetics in Materials Engineering 227

Figure 8. Effect of Si and Mn contents on alumina precipitation under 1800K for (a) Al content of 100ppm (b) Al content of 300ppm[18]

As stated above non-metallic inclusions may appear in molten steel at different stages. Therefore, in addition to the former considerations, the composition of the mold steel is designed in such a way that the oxide inclusion is fixed to be exogenous inclusion, which precipitates before solidification of liquid steel and can be eliminated after slag raking and gas rinsing, or be modified by injecting Ca-Si powder in the ladle. As calculation indicates in Fig.9a, the solidification temperature of the designed steel is 1760K while the lowest precipitation temperature of alumina is 1769K, 9K higher than the solidification point meeting well with the design requirement. The same result is obtained in Fig.9b, where the equilibrium phase diagram is calculated with another database of Thermo-calc, showing the solidification point of the steel is 1760K. Moreover, the composition is carefully designed to let the driving force of the oxide precipitation be the biggest one following closely by the driving force of MnS. Then, when

228 Thermodynamics Fundamentals and Its Application in Science

cooling, the alumina precipitates firstly and MnS precipitates afterwards to form the desired structure of good machinability where hard alumina is set in the core and soft MnS outside. Furthermore, as known, good machining performance connects normally with high homogeneity of microstructures in the steel which is sometimes dependent on annealing process. With Thermo-calc, the main type of carbide which exists in the mold steel but can be dissolved during annealing is designed through the modification of steel composition considerately. The designed carbide is in the type of M7C3, and this prediction is proved by TEM detection. Soaking temperature for dissolving this carbide is estimated as 1220C. Then suitable heat treatment process is taken to ensure the high homogeneity and super machinability of the steel after the annealing treatment in steel production.

Figure 9. (a) Relationship between the precipitation amount of alumina and temperature in the designed mold steel, solidification temperature being shown (b) phase diagram of the same steel[18]

Application of Thermodynamics and Kinetics in Materials Engineering 229

Measurement shows the inclusion number in the designed steel is reduced to be less than one tenth of the steel without composition regulation and its machinability reaches the world highest level of mold steel for plastic. The carefully designed mold steel is successfully put into mass production in Baosteel company.

4. Research and development on the high strength TWIP steel

Recently TWIP (TWin Induced Plasticity) steel, as one of the most promising advanced HSS (High Strength Steel), was developed showing the highest elongation rate (80%) and fairly good strength (600Mpa) due to the effect of TWIP. However, in practical use such as automobile anti-crash parts, the strength seems to be too low but ductility too high. With further consideration of alloy concept, much high strength can be obtained for the steel which comes from hcp martensite transformation. The equilibrium temperature between fcc phase and hcp phase in FeMnSi system and FeMnSiC system has been calculated thermodynamically[20]. It is found that the equilibrium temperature can be adjusted and controlled to be near to the room temperature through rational coordination of Si, Mn and C content in the steel. These results make it possible for realization of strain induced martensite transformation in the steel. However, the (hcp) martensite phase transformation is related to the stacking-fault energy (SFE) in austenite, which is affected by the special characteristics of alloy elements and their interactions and is discussed hereafter[20]. As known, the stacking-fault energy for pure metal can be considered as Gibbs free energy difference between atoms with two layer of fcc and atoms with two layer of hcp. While for alloy, its Gibbs free energy difference between fcc and hcp close-packed structure is not strictly equal to stacking-fault energy, because the element concentration at stacking faults is different from the average composition of alloy, especially the Suzuki Effect caused by C,N , which leads to the obvious difference of concentrations between stacking faults and base material. So according to the work of Olson and Cohen[21], the thermodynamic model of stacking-fault energy can be expressed as:
SF 2A G 2

(11)

Where,
4 1 A 2 3 a N is the bulk density of atomic surface in face-centered cubic, a is the lattice constant of alloy, N is the avogadros constant N =6.021023. is the binding energy of phase interface, according to Allain[22], =(515)mJ/m2. For simplicity, an average, i.e., 10mJ/m2 is taken by Li et al in their calculation[20]. G is the free energy difference between face-centered cubic ( ) and close-packed hexagonal () . Referring to Dumay[23], this part can be expressed as:

230 Thermodynamics Fundamentals and Its Application in Science

G GFeMnSu GFeMnSu/C Gmg

(12)

Where, the first item in the right part of the equation represents the effect of main elements such as Fe, Mn and Si on transformation free energy, denoted as:
GFeMnSu

Gi FeMn [C D(Fe Mn )] FeSi [E F(Fe Si )]

i

(13)

Where Gi is the transformation free energy difference of in pure components i. i is the mole fraction of element i, T is temperature in Kelvin, the last two items in equation (13) represent the interaction between Fe-Mn and Fe-Si, where the interaction between Fe and other elements as well as the mutual action of alloy elements can be neglected. The parameters of C, D, E, F in equation (13) were obtained form the
corresponding curve fitting and listed in Table 4 after Dumaya et al[23]. The GFeMnSu/C in

equation (12) represents effect of interaction between all the substitute elements and carbon on the transformation free energy, which is:
GFeMnSu/C

a bX (1 e C ) cXMn XC

(14)

While in equation (12), Gmg is the mole magnetic free energy difference between phase

and phase, which is:

Gmg Gm Gm

(15)

G , G represents respectively the mole magnetic free energy[24-26] of phase and phase,
m m

which is:
Gm RT ln(

1) f ( ) B

(16)

Where:
f ( ) 1 Or: f ( ) 1 5 15 25 T 518 11692 1 [ ]( 1), butD ( 1) D 10 315 1500 1125 15975 p TC 1 79 1 474 1 3 9 15 T { [ 1][ ]}( 1) D 140 p 497 p 6 135 600 TC

as for fcc and hcp crystal structure, p=0.28, for other structure, p=0.5.

Application of Thermodynamics and Kinetics in Materials Engineering 231

250ln( xMn ) 4750 xC xMn 22 xCu 2.6 xCr 6.2 xSi 720( K ) TN TN 580 xMn ( K )

GFe GMn GFeMn GFeMnx C

-2243.38+4.309T Jmol-1 -1000.00+1.123T Jmol-1 C=1246 Jmol-1, D=-717 Jmol-1 a=1246 Jmol-1, b=24.29 Jmol-1,c=17175 Jmol-1 0.7 xFe 0.62 xMn 0.64 xFe xMn 4 xC Jmol-1 0.62 x Mn 4 xC Jmol-1 2800+5T Jmol-1 -560-8T Jmol-1 E=2850 Jmol-1; F=3520 Jmol-1 -3500 Jmol-1

B B
G Al GSi GFeSi GV

Table 4. Parameters used in calculation of stacking-fault energy in Fe-Mn-X-C system(X=Si, Al, V)[23]

Y.K.Lee et al[27] considered that as for Fe-Mn alloy with 16-24% Mn, the phase transformation driving force of hcp martensite was -68~-120 J/mol. Allain et al[22] thought that for Fe-Mn-C system, if the stacking-fault energy (SFE) was above 12mJ/m2, the austenite was easy to induce twins; if the SFE lower than 18 mJ/m2, austenite easy to induce hcp martensite. The suggestion of Allain et al[22], say, the SFE value between 12~18 mJ/m2 is adopted as the value which induces martensite transformation in the TWIP steel. The calculation result for a steel with 18% Mn but different Si and C is shown in Fig.10 where the composition range suitable for the assigned SFE is pointed. Steels with different Mn,Si and C content but their SFE ranges between 12~18 mJ/m2 is calculated and listed in Table 5 [20]. For designing of the test steel, a value of stacking fault energy in the range of 12~18mJ/m2 is firstly adopted. Besides, the change of carbon content can be used to adjust the size of stacking fault energy while the content of Mn is to be set as low as possible to be favorable to the line process. Based on the above calculation the composition of the high strength high ductility steel is designed as 16~22%Mn, 0.3~0.6%C and 0.2~0.8%Si. The Gibbs free energy difference between fcc matrix phase (austenite) and hcp martensite in the steels is calculated with a self-made database[28] and, as an example, the difference of two phases in a steel of 18%Mn-0.528Si-0.35C is shown in Fig. 11. It can be seen that the T0 temperature(at which the Gibbs energy of fcc phase equals to hcp phase) is 330K, if adding -68 J/mol as driving force[27]

232 Thermodynamics Fundamentals and Its Application in Science

to the difference, the corresponding temperature is 293K, which means hcp martenisite can be obtained in room temperature.
30 28 26 24 22 20 18 16 14 12 10 8 6 4 2 0

(a)

0.45

0.63

0.2

0.4

0.6

0.8

1.0

30 28 26 24 22 20 18 16 14 12 10 8 6 4 2 0

(b)

SFE,mJ/m

SFE,mJ/m

0.44

0.2

Mass fraction of C,%

0.4 0.6 0.8 Mass fraction of C,%

1.0

32 30 28 26 24 22 20 18 16 14 12 10 8 6 4 2 0

(c)

0.365

0.52

0.2

0.4 0.6 0.8 Mass fraction of C,%

1.0

30 28 (d) 26 24 22 20 18 16 14 12 10 8 6 4 2 0 0.0

SFE,mJ/m

SFE,mJ/m

0.32

0.47

0.2

0.4 0.6 0.8 Mass fraction of C,%

1.0

Figure 10. Estimated stacking fault energy(SFE) in Fe-18Mn-YSi-C alloys with Y = 0(a),Y= 0.3(b),Y= 2(c) and Y = 5(d) [20]

Fe-Mn Fe-22Mn Fe-22Mn Fe-22Mn Fe-22Mn Fe-18Mn Fe-18Mn Fe-18Mn Fe-18Mn Fe-15Mn Fe-15Mn Fe-15Mn Fe-15Mn

Si 0 0.3 2 5 0 0.3 2 5 0 0.3 2 5

C(SFE=12) 0.282 0.28 0.24 0.23 0.45 0.44 0.365 0.32 0.55 0.53 0.44 0.37

C(SFE=18) 0.44 0.43 0.38 0.37 0.63 0.6 0.52 0.47 0.73 0.7 0.6 0.52

Table 5. Chemical compositions with different SFE(mass fraction, %)

Application of Thermodynamics and Kinetics in Materials Engineering 233

Figure 11. Gibbs free energy difference of two phases G %)steel

in Fe-18Mn-0.528Si-0.35C(mass fraction,

The test steel is melt in the 35kg vacuum melting furnace and the measured stacking fault energy is 20mJ/m2. The ingot is heated up to 1200C and then forged into the stocks with a thickness of 25mm. The stocks are heated at 1100C for 30min, finally hot rolled into the plates with a thickness of about 1.5mm and then quenched in oil. The final specimens are conducted with XRD, metallographic and SEM analyses. XRD spectrum shows weak martensite peak in the steel. Optical metallography confirms there exists -martensite in the steel when the sample is chemical polished and the effect of mechanical grinding is removed. SEM topography also indicates thin strips with different orientations which is regarded primarily as -martensite. Therefore, as revealed by calculation, -martensite is formed in this high-Mn TWIP steels after oil quenching. In order to raise the mechanical property of the steel, different heat treatment after hot rolling is applied. Table 6 shows different final rolling temperatures and cooling methods after hot rolling.

234 Thermodynamics Fundamentals and Its Application in Science

Steel No. Mn18_1 Mn18_2 Mn18_3

Final hot rolling temp./ C 850 750 850

Cooling medium water water air

Table 6. Final rolling temperatures and cooling methods after hot rolling

Figure 12 shows the XRD spectrum of the test steels treated with different heat treatment methods after hot rolling processes. It can be seen that the microstructure is the combination of austenite and -martensite after hot rolling at 850C and water quenching, but the microstructures are austenite alone after treatment by other processes. Figure 13 shows the strain-stress curves of the test steels treated with different processes. It can be seen that air cooling after hot rolling (as Mn18_3 steel) can lead to the best property such as strength above 1GPa and elongation rate above 60%. To examine the effect of structure on property, the fracture of the steels is analyzed with XRD as shown in Fig. 14. It can be found that martensite peak is displayed in the fracture of three specimens. Among this peaks, martensite peak in Mn18_3 specimen is the weakest. Thus, according to the XRD results before and after drawing and the result of tensile test, it can be concluded that -martensite existed before tensile test as well as a great amount of -martensite induced during tensile test may both raise the strength of the steel, while only a bit of induced -martensite during tension improves the property much effectively. All those steels exhibit strength higher than 800 MPa caused by martensite transformation.
800 700 600
XRD
(111)

500 400 300 200 100 0 20 30 40 50 60 2 theta 70 80 90

(100) (102) (103) (101) (200) (220) (311)

Mn18_3 Mn18_2 Mn18_1 100

Figure 12. XRD spectra of hot rolling steel

Application of Thermodynamics and Kinetics in Materials Engineering 235

1.2 1 0.8
/GPa

0.6 0.4 0.2 0 0 0.1 0.2

Mn18_1

Mn18_2

Mn18_3

0.3

0.4

0.5

0.6

0.7

Figure 13. Stress-strain curves of hot rolling steels

300 250 200
XRD
(111)

150 100 50 0 20 30 40
(100)

(101) (200) (102)

(220) (311) (103)

Mn18_3 Mn18_2 Mn18_1 50 60 2 theta 70 80 90 100

Figure 14. XRD spectra of hot rolling steel after deformation

Combining with the calculation results and experimental process stated above, new type of high strength and ductility TWIP steel is successfully produced in Ansteel group.

5. Research on high-tech ceramics

Ceria-doped zirconia ceramics found profound use in automobile emission system recently. When this ceramics is exposed to an inert atmosphere or low oxygen partial pressure at elevated temperature, the Ce+4 will be reduced to Ce+3, a nonstoichiometric phase Zr1-zCezO2x is then formed and the ZrO2-CeO2 system will convert to a quasi-ternary ZrO2-CeO2-CeO1.5 system. It is therefore very useful to study the effect of oxygen partial pressure on the stability of the nonstoichiometric fluorite phase Zr1-zCezO2-x in the ZrO2-CeO2-CeO1.5 system, which is directly connected to the ability to accumulate or release oxygen of a system, proved to be a guide in producing the high-tech ceramics in the modern industry especially in automobile manufacturing factory.

236 Thermodynamics Fundamentals and Its Application in Science

In this paragraph, the three limiting binary systems ZrO2-CeO2, ZrO2-CeO1.5 and CeO1.5-CeO2 are evaluated with compound energy model[29-31] and substitutional model[32]respectively and the calculation results met well with each other proving the substitutional model is still available to the complex oxide system[33,34]. In ZrO2-CeO1.5 system[33], compound energy model with structure (Zr+4, Ce+3)1(O-2, Va0)2 is used for css phase. The Gibbs energy of one mole of formula unit can be expressed as follows:
css yZr 4 yO2 oGZr 4 :O2 yZr 4 yVa0 oGZr 4 :Va0 Gm

yCe 3 yO2 oGCe 3 :O2 yCe 3 yVa0 oGCe 3 :Va0 RT[( yZr 4 ln yZr 4 yCe 3 ln yCe 3 ) 2( yO2 ln yO2 yVa0 ln yVa0 )] EGm The excess term EGm is given by an equation of the form:
E

(17)

Gm yZr 4 yCe 3 [ L0 4 ,Ce 3 :O2 Zr ( yZr 4 yCe 3 ) L1 4 ,Ce 3 :O2 ] Zr

(18)

In the CeO1.5-CeO2 system[33], the nonstoichiometric phase <CeO2-y> is described with structure (Ce+4, Ce+3)1 (O-2, Va0)2. The Gibbs energy of one mole of formula unit can be expressed as follows:
css yCe 4 yO2 oGCe 4 :O2 yCe 4 yVa0 oGCe 4 :Va0 Gm

yCe 3 yO2 oGCe 3 :O2 yCe 3 yVa0 oGCe 3 :Va0 RT[( yCe 4 ln yCe 4 yCe 3 ln yCe 3 ) 2( yO2 ln yO2 yVa0 ln yVa0 )] EGm The excess term EGm is given as follows:
E

(19)

Gm yCe 4 yCe 3 [ L0 4 ,Ce 3 :O2 Ce ( yCe 4 yCe 3 ) L1 4 ,Ce 3 :O2 ] Ce

(20)

In the ZrO2-CeO2 system[33], the css phase is modeled with two sublattices, (Zr+4, Ce+4)1(O-2)2. Because the valence of cations and anions can fit the condition of electroneutrality without the addition of any defects. All the limiting binaries are optimized and all the parameters are obtained[33]. When ZrO2-CeO2 system exposed in reduced atmosphere at high temperature, part of CeO2 changes to CeO1.5 in css phase. A new nonstoichiometric phase <Zr1-zCezO2-x> is considered under the conditions. To describe the ionic characteristics of this phase, the compound

Application of Thermodynamics and Kinetics in Materials Engineering 237

energy model, i.e., (Zr+4, Ce+3, Ce+4)1(O-2, Va0)2 is also applied to this phase. Based on the parameters of phase css in the three sub-binary oxides system, The Gibbs free energy of one mole phase is[33]:
css yZr 4 yO2 oGZr 4 :O 2 yZr 4 yVa0 oGZr 4 :Va0 Gm

yCe 3 yO2 oGCe 3 :O2 yCe 3 yVa0 oGCe 3 :Va0 yCe 4 yO 2 oGCe 4 :O 2 yCe 4 yVa0 oGCe 4 :Va0 RT[( yZr 4 ln yZr 4 yCe 3 ln yCe 3 yCe 4 ln yCe 4 ) 2( yO2 ln yO2 yVa0 ln yVa0 )] EGm The excess term EGm is represented by:
E yZr 4 yCe 3 [ L0 4 ,Ce 3 :O2 ( yZr 4 yCe 3 ) Gm Zr

(21)

L1 4 ,Ce 3 :O2 ] yCe 4 yCe 3 [ L0 4 ,Ce 3 :O2 Zr Ce ( yCe 4 yCe 3 ) L1 4 ,Ce 3 :O2 ] yZr 4 yCe 4 Ce [ L0 4 ,Zr 4 :O2 ( yCe 4 yZr 4 ) L1 4 ,Zr 4 :O2 ] Ce Ce

(22)

The calculated phase diagrams and corresponding experimental information of ZrO2-CeO2, ZrO2-CeO1.5 and CeO1.5-CeO2 systems are shown in Fig.15-17[33], where the little circles denote experimental data. In Fig.17, only the miscibility gap is considered in CeO1.5-CeO2 system. The calculated results met very well with experiments and keep consistent with each other.

Figure 15. Calculated and experimental phase diagram of ZrO2-CeO1.5 system, circles showing the experimental result[33]

238 Thermodynamics Fundamentals and Its Application in Science

Figure 16. Calculated and experimental phase diagram of ZrO2-CeO2 system, cycles showing the experimental result[33]

Figure 17. Calculated and experimental miscibility gap in CeO1.5-CeO2 system, circles showing the experimental result[33]

In order to understand thermodynamically the degasing of CeO2, additional deduction is necessary as follows: The chemical potential of oxygen in phase <CeO2-y> depends on the two mass variables, undefected species CeO2 and defected CeO1.5. In CeO1.5-CeO2 system, it would be natural to list the formula 4CeO1.5 O2 2 4CeO (23)

Application of Thermodynamics and Kinetics in Materials Engineering 239

With the evaluated model parameters of phase <CeO2-y> and Thermo-Calc, The authors[33] get the chemical potential of component CeO2 and CeO1.5 respectively. Therefore, the chemical potential of oxygen in this phase can be listed as:

O o O RT ln( PO2 ) 4CeO 4CeO

2 2 2

1.5

(24)

Under reduced atmosphere, phase css in ZrO2-CeO2 system changes to <Zr1-zCezO2-x>. Since no defects have been introduced in phase css in ZrO2-CeO2 system, The authors[33] also get oxygen potential for phase <Zr1-z CezO2-x> from Eq. 24. To get the relation between nonstoichiometry y in <CeO2-y> and oxygen potential in phase <Zr1-zCezO2-x> in the ternary system at different temperatures, some manipulation has been made. It is supposed that phase <Zr1-z CezO2-x> is composed of (1-z) mole ZrO2 and z mole <CeO2-y>. <CeO2-y> is composed of m2 mole CeO2 and m1 mole CeO1.5. Then the O/Ce ratio is calculated from the ratio O/(Ce+Zr)

2 y [2 x 2(1 z)] / z

(25)

To obtain the ln(y)-T-ln(PO2) relation, one first need to determine the moles, mi, of each components. These are calculated from the mass-balance for cerium and oxygen, which is m2 m1 and z(2 y) 2 m2 1.5m1 z

(26)

Which lead to m1 2 zy , m2 z(1 2 y ) Where z =1 mole represents a system without component ZrO2. With the thermodynamic parameters of the three sub-binary systems[33] and Eq. 24, the relation ln(y)-ln(PO2) in CeO1.5-CeO2 system, as well as in ZrO2-CeO1.5-CeO2 system are calculated by Thermo-Calc[33]. Fig. 18-20 shows the calculated results. Fig. 18 represents the experiment data and the calculated relation ln(y)-ln(PO2) at 1773K, 1573K, 1473K, where the little circles denote experiment data from Lindemer et al.[35]. It is obvious that the assessed parameters from CeO2-CeO1.5 system with compound energy model can represent the relations very well. Fig. 19 reveals the relation between CeO1.5 and ln(PO2) in a system without component ZrO2 (z=1) at different temperatures, showing temperature has great effect on oxygen partial pressure. In Fig. 20, different solid lines represent different z values (0.1, 0.2, 0.3, 1.0) corresponding to different mole fraction of ZrO2 (0.9, 0.8, 0.7, 0 respectively) in the ternary system at 1473K. It is obvious that the same nonstoichiometry y corresponds to different oxygen partial pressure at different z. Also can be found is the significant effect of z value (the content of ZrO2) on the relation between oxygen partial pressure and nonstoichiometry value. (27)

240 Thermodynamics Fundamentals and Its Application in Science

Figure 18. Calculated and experimental relationship ln(y)-ln(PO2), circles showing the experimental result[33]

Figure 19. Relations between the different amounts of CeO1.5 and oxygen partial pressure at different temperatures[33]

Application of Thermodynamics and Kinetics in Materials Engineering 241

Figure 20. Predicted relations ln(y)-ln(PO2) at 1473K with different z values [33]

A substitutional model was used to describe the quasibinary systems, which estimates the mixing entropy of complex ceramic systems in a very simple way. Kaufman et al[32] Du et al,[36] and Li et al.[37-39] already successfully evaluated oxide phase diagrams in this way. Li et al[40] pointed: When calculating oxide systems, if there do not exist any short range ordering, shortage of elements or molecular-like associate in sublattice, the substitutional model is an effective alternative of sublattice model. Furthermore, if the valence of the cations are the same, the application of substitutional model can obtain the same formalism of Gibbs free energy and the same calculated result as that can be obtained by the subblatice model, though the former is more simple and easy to be extened into higher order symtems. Then, the Gibbs free energy of one mole solution phase, is described as: G ( x , T ) m

n0

i 1 1

xi .G i (T ) RT xi ln xi x1x2 f
n 3

(28)

( x1 x2 )

The first term on the right side accounts for the mechanical mixture of the pure components. oG i (T ) is the standard Gibbs free energy , i.e., the formation energy of mass parameter f i from the elements in their standard states. The second term refers to an ideal solution, and the third term is the excess Gibbs free energy function, which is a Redlich-Kister polynomial. The K n factor in Eq. (29) is a temperature-related polynomial and is expressed as:

242 Thermodynamics Fundamentals and Its Application in Science

K n An BnT C nT ln T DnT 2 En / T F nT 3

(29)

Gibbs free energy of one mole (cation) stoichiometric compound phase with pyrochlore structure is described as:

G(1 / 4)Zr2Ce (1 / 2)Gcss Zr 02 (1 / 2)Gcss CeO1.5 A B*T f f 2O7

(30)

Also with the relationship deduced in Eqs.(23-27), one can find in a system without ZrO2 component i.e., z=1 (mole), the mole fraction of CeO1.5 is N1=m1/(m1+m2) and the mole fraction of CeO2 is N2=m2/(m1+m2). Moreover, y=0.50.5N2. Based on the thermodynamic information of the limiting quasi-binary systems, which is evaluated in reference [34,41] the molar Gibbs free energy of the nonstoichiometric phase Zr1 zCe zO2 x can be written according to Maggianu[42] as: GZr1 zCezO2 x / ( m1 m2 m3 ) N1G css ZrO2 N 2 G css CeO2 f f N 3 G css ZrO2 N1RT ln( N1 ) N2 RT ln( N 2 ) f
3 4 N 3RT ln( N 3 ) K1,2 N1N 2 K1,2 N1N 2 ( N1 N 2 ) 3 4 3 K1,3 N1N 3 K1,3 N1N 3 ( N1 N 3 ) K2,3 N 2 N 3 4 K2,3 N 2 N 3 ( N 2 N 3 )

(31)

Where oG css i is the standard Gibbs free energy of formation of mass parameter i from f the elements in their standard states. oG css ZrO2 is after the compilation of Pankratz, f whereas oG css CeO1.5 is retrieved from the quasi-binary phase diagrams f
[41] [43]

. Kin, j is the

interaction coefficient, where n is the order of the RedlichKister polynomial and the subscripts i,j represent the components, i.e., CeO1.5=1, CeO2=2, ZrO2=3. Ni(i=1,2,3) is the molar fraction of CeO1.5, CeO2 and ZrO2 respectively. The partial molar free energy for mass parameter i equals to,
[G' Zr1 zCe zO2 x ] / mi Gi

(32)

With the equation similar to Eq. 24,

RT ln( Po2 ) 4 GCeO2 4 GCeO1.5

(33)

The relationship between ln(y) and ln(PO2) at 1473K is calculated and shown in Fig. 21, which is exactly the same as shown in Fig. 20 calculated by CEM.

Application of Thermodynamics and Kinetics in Materials Engineering 243

Figure 21. Predicted relationship between ln(y) and ln(PO2) at 1473 K at different CeO2 y molar fractions in the ZrO2CeO2CeO1.5 system[34]

The research staff members in Exhaust System of MERCEDES CAR GROUP checked independently the work stated above over years, they followed each of the published papers and calculated their system with the equations and model parameters in the publications. They were convinced that the calculation stated above predicted the mechanism in the automobile emission system and met very well with their detected data in all the gasoline engines of Mercedes Car.

6. Conclusion
An aspiration of engineers in materials field is to have the possibility to estimate in advance the composition, properties, processing parameters, etc., while they are planning to develop a new material. This chapter offers a basic sketch where one could find how thermodynamics, coupled with accurate experiment results, constructs the entrance for mass production. In order to limit the chapter length, only less examples were listed and most of them are stressed at steels, which include developing new type steel, improving the quality of existed steel and discussing the factors mainly influencing steel property. Calculation is applied in the light of the existed commercial software package though, in some cases, suitable derivation to reveal the relationship between thermodynamic properties of substances and self-made database exhibit also extreme importance in the designing of materials. Moreover, both compound energy model and substitutional model are used to describe the complex degassing behavior in the ZrO2-CeO2 system which reveals how and why the simple model could be successfully applied in complex systems.

244 Thermodynamics Fundamentals and Its Application in Science

Author details
Lin Li School of Materials, Shanghai University, Shanghai, P.R.China

Acknowledgement
This work is financially supported by National Key Basic Research Development Project of China (973 Programme, No.2010CB630802), NSFC(No.50934011 and No.50971137) and School of Materials, Shanghai University.

7. References
[1] Meyer M.D., Vanderschueren D., De Cooman B.C., ISIJ Inter., 1999, 39(8), 813. [2] Lin Li, B.C. De Cooman, P. Wollants, Yanlin He and Xiaodong Zhou, J Mat. Sci. & Technol., vol.20,No.2, 135-138, 2004. [3] Li Lin, Liu Rendong, Shi Wen, Zhang Mei, He Yanlin, Liu Huachu, Fu Renyu, Development of a new type TRIP steel with good weldability and galvanizing property, Proc. 2009 Inter. Symp. automobile steel, Dalian, China, 2009, 332-336. [4] Guttmann M., Mclean D., Grain Boundary Segregation in Multicomponent Systems, [A] eds. Johnson W.C., Blakely J.M., Interfacial Segregation[M]. Ohio: ASM, Metals Park, 1979. 261-348. [5] M. Hillert, L.I. Staffansson, Acta Chemica, Scandinavica, 1970, 24, 3618 [6] Li L., Delaey L., Wollants P., O.Van Der Biest, Thermodynamic analysis of the segregation of multicomponent steels[J]. J.Chim. Phys., 1993, 90, 305-312. [7] Li L., Delaey L., Wollants P., O.Van Der Biest, Thermodynamic Calculation of Segregation in Multicomponent Steels[J]. J.Mater.Sci.& Technol., 1996, 12(3), 238-240. [8] Guttmann M., Dumoulin Ph., Wayman M., The thermodynamics of interactive cosegregation of phosphorus and alloying elements in iron and temper-brittle steels[J]. Metall. Trans., 1982, 13A, 1693-1711. [9] Lin Li, Microstructure and property control of advanced high strength automotive steel, eds., Y.Q.Weng, H.Dong, Y.Gan, Metalluygical Industry Press and Springer, Beijing, 2010, 265 [10] Mclean D., Grain Boundaries in Metals, [M]Oxford: Clarendon Press, 1957. [11] Sundman B., Jansson B., Andersson J., The thermo-calc databank system[J]. CALPHAD, 1985, 9(2), 153-190. [12] L. Li, S.G. Huang, L. Wang, Y.L. He, J. Vleugels, O. Van der Biest, Thermodynamic reassessment of the Fe-Al-C system based on the Fe-rich experimental data, Front. Mater. Sci., China, 3(1), 33-37, 2009. [13] O. Redlich and A.T. Kister, Algebraic Representation of Thermodynamic Properties and the Classification of Solutions, Ind. Eng. Chem. 40 (1948), 345-348.

Application of Thermodynamics and Kinetics in Materials Engineering 245

[14] Bo Sundman and John gren, A regular solution model for phases with several components and sublattices, suitable for computer applications, Journal of Physics and Chemistry of Solids, 42 (4) 1981, 297-301. [15] K.C.H. Kumar and V. Raghavan, a thermodynamic analysis of the Al-C-Fe system, Journal of Phase Equilibria, 12 (3) (1991), 275-286. [16] P. Gustafson, A thermodynamic evaluation of the Fe-C system, Scandinavian Journal of Metallurgy, 14 (1985), 259 [17] David K. Matlock, John G. Speer, Third Generation of AHSS, Microstructure Design Concepts,A. Haldar, S. Suwas, and D. Bhattacharjee (eds.), Microstructure and Texture in Steels, Springer 2009,185-205 [18] Yanlin He, Lin Li, Xiaochun Wu, P. Wollants, J Mat. Sci. & Technol., vol.20, No.1, 71-74, 2004. [19] H. Gaye, J. Welfringer,Proc.2nd Inter. Conf. Metallurgical Slags & Fluxes, Lake Tahoe, Nevada, Nov. 1984, 357 [20] Li Lin, Gao Yi, Shi Wen, Liu Rendong, He Yanlin, Fu Renyu, Zhang Mei, Martensite Transformation in High Mn Steels, HMnS2011, Soeal, Korea, A19 [21] G.B. Olson, M. Cohen: Metall. Trans. A, 7A (1976) p. 1897. [22] S. Allain, J.-P. Chateau, O. Bouaziz, S. Migot, N. Guelton: Materials Science and Engineering A 387389 (2004) p. 158. [23] A. Dumaya, J.-P. Chateau, S. Allain, S. Migot, O. Bouaziz: Materials Science and Engineering A 483484 (2008) p. 184. [24] Inden G, Metallkde Z. 1977; 68: 529 [25] Hillert M, Jarl M. CALPHAD, 1978; 2: 227 [26] Dinsdale A T. CALPHAD, 1991; 15: 317 [27] Y.K. Lee, C.S.Choi: Metall. Mater. Trans., 31A(2000) p. 355. [28] LIU Ren-dong, Shi Wen,He Yanlin,Li Lin, ZHANG Xiao-gang, WANG Fu,Designing and Investigating on the Hot Rolling TWIP Steel with TRIP Effect,Acta Metall. Sinica (in Chinese), 2012 [29] T.I. Barry, A.T. Dinsdale, J.A. Gisby, B. Hallstedt, M. Hillert, B. Jansson, S. Jonsson, B. Sundman and J.R. Taylor, J. Phase Equil., 1992, 13,459 [30] M. Hillert, J. Alloys Comp., 2001,320, 161 [31] B. Sundman, J. Alloys Comp., 1991, 12(1), 127 [32] Kaufman, L. and Nesor, H., Calculation of quasi-binary and quasi-ternary oxide systems I. CALPHAD, 1978, 2, 3553. [33] Shuigen Huang, Lin Li, O. V. D. Biest, J. Vleugels, Peiling Wang, J Mat. Sci. & Technol., vol.18, No.5, 422-426, 2002. [34] Shuigen Huang, Lin Li, Jef Vleugels, Peiling Wang, Omer Van der Biest, Thermodynamic prediction of the nonstoichiometric phase Zr1-zCezO2-x in the ZrO2 CeO1.5CeO2 system, J. Eur. Ceram. Soc., 23 (2003) 99106 [35] T.B. Lindemer,J. Brynestad,J. Am. Ceram. Soc., 1986, 69 (12), 867 [36] Du, Y., Yashima, M., Koura, T., Kakihana, M. and Yoshimura,M., Thermodynamic evaluation of the ZrO2-CeO2 system. Scripta Metall. Mater., 1994, 31, 327332.

246 Thermodynamics Fundamentals and Its Application in Science

[37] Li, L., Xu, Z. Y. and Ao, Q., Optimization of the phase diagram of CeO2-ZrO2 system. J. Mater Sci. Tech., 1996, 12, 159160. [38] Li L., Van Der Biest O., Wang P. L., Vleugels J., Chen W. W. and Huang S. G., Estimation of the phase diagram in the ZrO2-Y2O3-CeO2 system. J. Eur. Ceram. Soc., 2001, 21(16), 29032910. [39] Li L., Van Der Biest O., Xu L. P., Vleugels J. and Huang S. G., Prediction of the isothermal sections of the ZrO2-Y2O3-CeO2 system. J. Mater. Sci. Tech., 2001, 17(5), 529 534. [40] Lin Li,O. Van Der Biest,Peiling Wang,Application of Substitutional Model in Oxide System, J.Mater. Sci. Technol., 19(1), 2003, 66 [41] Shuigen Huang, Lin Li, O.V.D. Biest, J. Vleugels, Peiling Wang, Thermodynamic Assessment of the ZrO2CeO2 and ZrO2CeO1.5 Binary System, J.Mater. Sci. Technol., 18(4), 2002, 325 [42] Muggianu, Y. M., Gambino, M. and Bros, J. P., Enthalpies de formation des alliages liquides bismuth-etain-gallium a 723 K. J. Chim. Phys., 1975, 22, 8388. [43] Pankratz, L. B., Thermodynamic Properties of the Elements and Oxides. US Dept. Interior, Bureau of Mines Bulletin 672, US Govt Printing office, Washington, DC, 1982.

Chapter 10

Thermodynamics of Wool Dyeing

Rza Atav
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51618

1. Introduction
The pleasure derived from imparting color to clothing has existed since the time of the earliest civilizations; a world of fashion without color is impossible to imagine. Coloration processes produce the most visible results of all the finishing operations carried out during preparation of textile goods [1]. Dyes are synthetic aromatic compounds which can bring bright and firm color to other materials. It is reported that over 100,000 commercially available dyes exist and more than 7x105 metric tons of dyes are produced worldwide annually [2]. When a textile fiber is immersed in a solution of dye under suitable conditions, the fiber becomes colored, the color of the solution decreases and dyeing has occurred [3]. The wool fiber is the hair of the sheep and forms the protecting covering of the animal [4]. Structurally, a wool fiber is an assembly of cuticle and cortical cells held together by the cell membrane complex (See Figure 1). The dyeing and diffusion properties of fibers are known as governed by this membranous structure, which is formed predominantly by internal wool lipids [5].

Figure 1. Cross-section diagram of a merino wool fiber [6]

2012 Atav, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

248 Thermodynamics Fundamentals and Its Application in Science

Wool cuticle cells (overlapping cells that surround the cortex) are subdivided into two main layers, namely the exocuticle and endocuticle [7]. The outer surface of the scale of the cuticle is covered by a very thin membrane called the epicuticle. Below this hydrophobic epicuticle is the exocuticle, a cystine-rich part forming about two-thirds of the scale structure. The exocuticle just below the epicuticle is referred to as the A layer, having a distinctly higher cystine part than the rest of the exocuticle (known as the B layer). Below the exocuticle, forming the rest of the scale structure is the endocuticle and then a thin layer of intercellular cement [6]. For wool, its complexity is illustrated by the different important chemical groups it has and the intermolecular forces of attraction that are formed. First, there are the polar peptide groups (i.e., -CO-NH-). Second, the oxygen of the carbonyl groups (-CO-)is slightly negatively charged and, as a result, will form hydrogen bonds with the slightly positively charged hydrogen of the imino groups (-NH-) of other peptide groups. Third, cystine, the sulfur-containing amino acid capable of forming disulfide crosslinking tends towards greater chemical stability, resulting in less dye absorption [8]. Wool dyeing is a process involving high temperature for long periods in acidic to neutral pH medium to do good penetration, optimum fastness, and dyebath exhaustion. The shape of the conventional dye uptake curve is consistent with an initial dwell time (20 to 40C) when dye is transported 1 through the medium, a primary exhaustion stage (40 to 60C) when dye levels at the fiber surface and diffuses within, and a secondary stage (60 to 90C and above) during which time the dye disperses and immobilizes within the fiber. There is much resistance to dye penetration from the epicuticle layer of the cuticle cell of the wool [9]. The surface of the cuticle cells is highly hydrophobic due to covalently bound fatty acids. The covalently bound fatty acids and the high amount of disulphide bridges make the outer wool surface highly hydrophobic. Especially in the printing and dyeing of wool, the hydrophobic character of the wool surface is disturbing. Diffusion of the hydrophilic dyes into the fibers is hindered [10]. Earlier workers identified the epicuticle with the barrier to dye penetration, thinking that this part forms a continuous membrane around the fiber. The barrier has also been ascribed to the cuticle and to the highly crosslinked A-layer of the exocuticle. All these suggestions on the nature of the barrier were based on a common belief that dyes must diffuse through the cuticle cells to reach the fiber cortex (i.e. the transcellular route shown in Figure 2) [11]. A continuous phase of membrane cells, the cell membrane complex underneath the cuticle, forms a network of penetrating canals to help mediate the impedance of the lipid barrier to dye diffusion, thereby facilitating dye penetration into the fiber interior [9]. In the manufacture of the almost infinite variety of wool textures, the dyeing of the wool itself is one of the series of many operations involved; and whilst of cardinal importance, the dyeing process must be subordinated to the particular final texture devised by the manufacturer [13]. For dyeing of wool fibers acid, metal complex 1:1 and 1:2, chrome

Thermodynamics of Wool Dyeing 249

Figure 2. Diffusion pathways for dyes into wool [12]

and reactive dyes can be used [14]. In this chapter knowledge related to the thermodynamics of wool dyeing will be given.

2. Thermodynamics of wool dyeing

Dyeing systems can be classified as follows; 1. a. b. 2. a. b. Non-ionic dyes applied to substrates which are non-ionic or ionic Disperse dyes on essentially non-ionic substrates, such as the hydrophobic fibers produced from polyester, secondary cellulose acetate and cellulose triacetate, and Disperse dyes on ionic substrates such as nylon. Ionic dyes applied to substrates which themselves carry a charge Ionic dyes applied to substrates which carry the same charge as the dye, as exemplified by anionic dyes on cellulose, and Ionic dyes applied to substrates which carry the opposite charge as the dye, such as anionic dyes on wool and nylon and cationic dyes on acrylic fibers [3].

From above classification, it can be understood that the wool dyeing is a good example for dyeing systems described in 2b. In general, wool dyeing process occurs in four basic steps; Wetting and swelling of fibers in dyeing liquor Adsorption of dye molecules on the fibers Diffusion of dye molecules into the fibers Fixation of dye molecules in fibers via various physical and chemical forces [15]

Knowledge in detail related to the thermodynamics of wool dyeing such as aggregation and adsorption of dyes, rate, standard affinity, enthalpy and entropy of dyeing exc. is given below.

2.1. Aggregation of dyes

The nature of the dyeing process requires a complete understanding of the state of the dye in the dyebath, and many of the problems associated with the dyeing of wool can be

250 Thermodynamics Fundamentals and Its Application in Science

explained in terms of the colloidal or aggregated nature of the dye [16]. Aggregation can be defined as Clustering of each particle of a substance to give it colloidal properties [1]. A number of organic dyes form aggregates in solution via weak non-covalent interactions. The color, physical properties such as the solubility and photophysical behavior of dyes are affected due to aggregate formation [17]. In dyes, the aggregation principally forms dimers except at high concentrations in solvents with a high dielectric constant. For coloration of materials, it is the monomer adsorbed on the surface. There may be next build up of dye units through aggregation but the first layer must be composed of monomers [18]. Many studies have been carried out on the aggregation of dyes molecules or ions in aqueous and non aqueous solutions. The interactions between dye molecules and other molecular entities are of paramount importance in many industrial processes. The forces of attraction responsible for such interactions are also capable of causing physical interaction between dye molecules to produce molecular species ranging in size from dimmers to aggregates containing hundreds of molecules [19]. The dye aggregation is a function of temperature, electrolyte concentration, surfactant type, and dye concentration [20]. Aggregation is promoted by increasing the concentration of dye in solution [3]. The addition of electrolyte to a dyebath can increase the degree of aggregation, but fortunately the aggregation process is reversible and may be decreased by a rise in temperature. A certain degree of aggregation can be beneficial since it tends to increase the attraction of the dye for the fiber, but the large size of the dye aggregates can lead to a drastic reduction in the rate of fiber penetration, or in some cases to the precipitation (separation) of a dye from solution after prolonged storage [1]. Also chemical structure of dye molecule has an important effect on aggregation. For example; the tetrasulphonated dye C.I. Acid Red 41 has been shown to be monodisperse in aqueous solution by both diffusion-based and light scattering techniques. This result is to be expected, since the four sulphonate groups confer upon this molecule a high degree of hydrophilicity. When the number of sulphonate groups is reduced to one, as in C.I. Acid Red 88, then aggregation is expected to increase. The aggregation of C.I. Acid Red 88 has been determined by diffusion and by polarography at 25C, and was found to range between 2 and 5 [16]. So far the changes in absorption spectra have been described qualitatively, yet the aggregation of dyes in aqueous and non-aqueous solutions may be studied quantitatively. The Maximum Slope has proved to be the simplest and the most convenient method to apply for such quantitative study. This method is based on the assumption that a simple equilibrium model between a monomer (m) and polymer (m)n is operative [19]: n(m)(m)n First the following equation is used to estimate the values for degree of aggregation and aggregation constant: logC (1- ) = n logC (- n) + log n Kn (1- n)1-n (1)

Thermodynamics of Wool Dyeing 251

where n = n / n 1 = molar absorbativity of monomer = experimentally measured molar absorptivities n = molar absorbativity of polymer C = concentration of dye solution in mol/L n = aggregation number Kn = aggregation constant By plotting logC (1- ) against logC (- n), the points should lie on a straight line; the slope of which gives the degree of aggregation (n), and the aggregation constant (Kn) can be calculated from the intercept. Reliable results are very difficult to be obtained due to the assumption one has to make for 1 and n. The above equation is then rearranged in the form [19]: 1/(n-1) logC (1- ) n/(n-1) n logC (- n) = log C = X where = (nk)1/(n-1)(1- n)-1 The Maximum Slope Method consists of correlating the curves of vs. logC and vs. X for different values of n and n until a value of n is reached which gives the best fit between the experimental results and the theoretical curve [19]. (2)

2.2. Adsorption of dyes

Adsorption is a process that occurs when a gas or liquid solute accumulates on the surface of a solid or a liquid (adsorbent), forming a molecular or atomic film (the adsorbate). It is different from absorption, in which a substance diffuses into a liquid or solid to form a solution. The term sorption encompasses both processes, while desorption is the reverse process [21]. The strength of the adsorption depends on the kind of interactions taking place between the fiber surface and the dye molecules. Clearly, the highest strength results when a chemical interaction occurs. Unfortunately, in many fiber/dye systems such surface interaction cannot be realized. In the case of physical adsorption process, the strength is determined by the Lifshitz - van der Waals, hydrogen bonding, and electrostatic interactions. The nature of the process can be evaluated from the thermodynamic functions of the process [22]. As a result of its chemical structure, wool contains a considerable number of both acidic and basic groups and hence, it was natural to consider that the adsorption of ions by wool was directly concerned with the presence of these groups; this is in turn led to the idea that ions are adsorbed by wool on specific sites in the fiber [3]. Adsorption is usually described through isotherms, that is, functions which connect the amount of adsorbate on the adsorbent, with its pressure (if gas) or concentration (if liquid)

252 Thermodynamics Fundamentals and Its Application in Science

[21]. The Langmuir isotherm, the Freundlich isotherm, and the Nernst isotherm are all commonly used to classify dyeing isotherms even though they more correctly apply to the adsorption of gases on metal surfaces [16]. Their shapes are shown in Figure 3 [23].

Figure 3. Specific isotherms of dye-fiber systems (Ds: Dye concentration in the dyebath, Df: Dye concentration in the fiber) [23]

The simplest physically plausible isotherm is based on three assumptions: 1. 2. 3. Adsorption cannot proceed beyond monolayer coverage. All sites are equivalent and the surface is uniform There are no interactions between adsorbed molecules, so the ability of a molecule to adsorb at a given site is independent of the occupation of neighboring sites [24].

The Langmuir isotherm is well suited to describe dye adsorption by certain textile fibers. Considered in terms of dyeing, the basic postulate is that adsorption of dye takes place on specific sites in the fiber and that when a dye molecule occupies a site that site is saturated and incapable of further adsorption [3]. The Langmuir model is valid for monolayer sorption onto a surface with a finite number of identical sites. Langmuir isotherm theory is based on the assumption that adsorption on a homogeneous surface [25]. On the bases of these assumptions Equation 3 can be written [16]: Cf,a= KCs,m / (1 + KCs,m) Cf,a: concentration of adsorbed dye molecules on the fiber Cs,m: concentration of mobile dye molecules in the bath K: Adsorption constant In the case of the Freundlich model (Equation 4) the dye is considered as being contained in an internal phase of volume V of the fiber. (3)

Thermodynamics of Wool Dyeing 253

ln[C]f = ln KF + x ln[C]s

(4)

where: [C]f represents the dye concentration in the fiber at equilibrium, in mol/kg dry fiber, and [C]s represents the dye concentration in solution at equilibrium, in mol/L; KF is the equilibrium constant, and x is a sub-unitary power [26]. The Freundlich isotherm is commonly used to describe adsorption characteristics for heterogeneous surface [27]. The Freundlich model assumes a heterogeneous multilayer adsorption surface with sites that have different energies of adsorption which are not equally available [28]. The Nernst adsorption isotherm (Equation 5) is considered as a limit case of Freundlich and Langmuir adsorption isotherms [26]. [C]f = KP [C]s (5)

Nernst isotherm equation is a mathematical representation of the distribution law, which states that a dissolved substance, irrespective of its total amount, distributes itself between two layers or phases in a constant concentration ratio, at constant temperature; the ratio, equal to the constant in Equation 5, is referred to as the distribution or partition ratio. Theoretically the law is limited to describing the behavior of dilute solutions [3].

2.3. Rate of dyeing

Four steps can be envisaged in the process of dye uptake: a. b. c. d. diffusion to the fiber surface, transfer across that surface, diffusion within the fiber to appropriate sites, and binding at those sites.

In principle, any of these could be the slowest-and hence the rate determining-step. The theory of the kinetics of wool dyeing has generally been based on the premise that (c) is the rate determining step (diffusion control). Various algebraic expressions have been derived from Ficks laws of diffusion in an attempt to describe experimental dyeing rates. The most common treatment is the parabolic, rate law, which was originally derived by Hill to explain the diffusion of phosphate and lactate in muscles. If a semi-infinite solid is brought into contact with a liquid containing a diffusible substance at concentration y0, then the total amount diffused across a unit area (A) at time t is given by the following equation: A = 2.y0.(Dt/)1/2 (6)

where D is the diffusion coefficient of the substance in the solid [29]. The calculated diffusion coefficient appears to be exceedingly small when compared with values for other simpler ions and molecules. This may, of course, be due merely to the size of the dye anion, as diffusion within the solid is subject to greater restriction than aqueous diffusion, which suggests that the diffusing unit must force a path through more or less rigidly held molecules, so that a high activation energy is required. The apparently very low mobility of the dye ions may be due to interaction of ions with the fiber in such a way that the majority

254 Thermodynamics Fundamentals and Its Application in Science

of ions within the fibers are held on specific sites; diffusion proceeds by way of a small fraction of mobile dye ions, thus giving an apparently very low value for diffusion coefficient [30]. The rate of diffusion of a dye in a fiber increases with increase in dyeing temperature. The effect of temperature on the rate of diffusion is given numerically by the activation energy of diffusion (E) according to the relationship shown in Equation 7: DT=D0e-E/RT (7)

Where DT is the observed diffusion coefficient at absolute temperature T, D0 is a constant and R is gas constant. Hence, if the logarithm of the observed diffusion coefficient is plotted against the reciprocal of T, a straight line of slope E/R should be obtained; from which E can be calculated [23]. Time of half-dyeing (t1/2) is the time taken for a fiber to adsorb 50% of the dye it would adsorb at equilibrium. It provides an indirect measure of rate of diffusion and is useful for comparing the behavior of dyes applied under identical conditions. Because of the very gradual approach to equilibrium, the time taken to reach equilibrium cannot be measured accurately. However, equilibrium adsorption, C can be estimated readily by dyeing for a prolonged period and t1/2 is then determined using a graph of exhaustion versus time of dyeing at Ct=0.5C (Figure 4). In certain cases, it is preferable to plot exhaustion against logt since then the relevant portion tends to be a straight line and a more accurate estimate of t1/2 can be obtained [23].

Figure 4. Exhaustion of dyes (%C) with time [23]

In practice, the experimental conditions must be chosen with care. If the conditions are such that the bulk of the dye is adsorbed on to the surface of the fibers quickly this will musk the effect of diffusion into the fiber [23, 31]. The conditions should be so chosen that the dyefiber attraction is low and the final exhaustion is not very high (<80%). The time of half dyeing is also very dependent on the amount of dye used [23]. If the time of half dyeing is known for two different temperature activation energy of diffusion (E) can be calculated from the equation given below [31]; log(t1/2)323 log(t1/2)363 = [E/2.3*R] * [(363-323)/(363*323)] (8)

Thermodynamics of Wool Dyeing 255

2.4. The standard affinity of dyeing

Thermal activation is only the first stage in the dyeing process. The driving force in the transfer of dyes from solution to the fiber is the difference in free energy between the two phases. In other words, the energy needed to compress the dye molecules from their freedom of movement in the solution to the restricted volume within the fiber. This is more conveniently expressed in the form of the chemical potential () which is defined as the difference in free energy between two phases when a very small quantity of dye is added to the solution, all other variables kept constant. The standard potential is derived from the basic equation, applicable to ideal solution, namely Equation 9: = A + RT lnC where A is a constant, and C is the molar concentration [23]. A numerical parameter is needed to describe the behavior of individual dyes at equilibrium (thermodynamics) which is independent of variations in the dyeing conditions. Such a parameter would be standard affinity of the dye. Standard affinity of dyes has been defined as the difference between the chemical potential of the dye in its standard state on the fiber and the corresponding chemical potential in its standard state in the dyebath [32]. Affinity (-) is measurable according to the principles of thermodynamics and may be expressed in energy unit (kjoules/mole). It is the most basic thermodynamic parameter of the dye in dyeing solution towards fiber substrate. The greater the degree of exhaustion at equilibrium the greater is the affinity [33]. The standard affinity for the distribution of dye between the fiber and dyebath is proportional to the logarithm of the ratio of the absolute activities of the dye in the fiber and dyebath. Since the activity of the dye is assumed to be directly related to its concentration, one can write equation as follows [16]; (9)

0 RT[ In([C ]F / [C ]L )]
: standard affinity (J mol-1) R: gas constant (8.317 J K-1 mol-1) T: absolute temperature (K) [C]F: concentration of dye on the fiber at equilibrium (g/l) [C]L: concentration of dye remaining in the dyebath at equilibrium (g/l)

(10)

It was this point, where values had to be assigned to activities of the ions in the fiber, that a difference of opinion arose and this led to two different approaches being formulated, namely the Langmuir or Gilbert-Rideal method and the Donnan method. The differences between the two are described pictorially in Figure 5 for a simple, monobasic strong acid HX [3].

256 Thermodynamics Fundamentals and Its Application in Science

Figure 5. Pictorial representation of two approaches to wool dyeing theory: (a) Gilbert-Rideal, (b) Donnan [3]

a) Gilbert - Rideal theory: In that explanation, the activity coefficients of ions sorbed into the wool phase are reduced due to specific binding with sites on the wool, that is, the formation of ion pairs. Wool dyeing generally occurs in the presence of an acid as well as the dye (the acid is usually applied in a preliminary step). Gilbert and Rideal proposed that dye uptake is an anion exchange process, in which the dye molecules displace smaller anions [29]. b) Donnan theory: In this theory, the dye was considered to partition between the external solution and an internal solution phase in the wool. The latter phase is believed to contain a high concentration of fixed ionic groups, and hence solute molecules have reduced activity coefficients in that phase due to Coulombic interactions [29]. Derbyshire and Peters, proposed a unified interaction theory for all dye-fiber systems, postulating that the principal contribution to the standard affinity of the dyes, of all classical types, to all kinds of fibers arises from the nonpolar Van der Waals forces. They postulated that non-polar forces are mainly responsible for dye-fiber attachment and that in aqueous solution they occur between hydrophobic surfaces. The dyeing behavior of each type of fiber is predicted from the postulate that dye substantivity is due to non-polar forces. They suggested that the hydrophobic parts of the dye molecules have adequate affinity for the hydrophobic parts of the fiber. Accordingly the less hydrophobic dye molecules also have sufficient affinities for the more hydrophobic synthetic fibers, whereas dye molecules with larger hydrophobic parts will be required to dye a hydrophilic fiber such as wool [34]. Zollinger considered hydrophobic bonding in addition to the two well-known types of dyefiber interaction in the adsorption of anionic dyes by wool such as coulombic attraction of dye anions to cationic groups on the fibers and Van der Waals (London) forces. The thermodynamic parameters such as standard enthalpies and standard entropies were measured for the adsorption of three suitable acid dyes on wool, and it was concluded that aliphatic side-chains contributed to the dye-fiber hydrophobic interaction. However, the

Thermodynamics of Wool Dyeing 257

detection of this contribution was difficult, because of the additional effect of dye-dye aggregation equilibria in solution [35]. Iyer et al. carried out a study using three different related acid dyes (Table 1); they calculated the heats and entropies of dyeing. They showed that with increasing hydrocarbon chain length, the affinity of the dye was increased, while the effect of a phenyl group was greater than that of a straight chain of four carbon atoms. It is surprising that the heat evolved on dyeing is decreased as the affinity increases. This is unusual, since higher affinity generally corresponds to larger heat of dyeing [36]. R -CH3 -C4H10 -C6H6 - (kCal mol-1) 5.3 5.8 6.0 - H0 (kCal mol-1) 7.6 7.1 5.6 S0 (Cal k-1 mol-1) -7.2 -4.1 +1.2

Table 1. Thermodynamic parameters of acid dyes on wool (at 50C and pH 4.6) [36]

The results of the study carried out by Ferrini et al. (Table 2) was also indicated that the phenyl group is more effective in reducing H0 than is the butyl chain [37]. Asquith et al. claimed that the reason of the effect of a phenyl group to be greater than that of a straight chain was the effect of the phenyl group on dye aggregation to be greater than that of the butyl chain [38]. Temp. (C) 41-51 70-79 41-51 70-79 41-51 70-79
Table 2. Heats of dyeing and entropies of acid dyes on wool [37]

- H0 (kCal mol-1) 4.8 7.2 7.0 11.3 5.7 8.9

S0 (Cal k-1 mol-1) -2.2 -9.3 -4.9 -17.7 -0.8 -10.5

2.5. The enthalpy of dyeing

The second thermodynamic quantity which is important in describing a dyeing process is the heat of dyeing or the change in enthalpy of the system when adsorption takes place [3]. As a result of dye molecules to be adsorbed on the fiber surface, free movement of these molecules gets restricted. So that entropy decreases when dye molecule is adsorbed. Adsorption also causes free energy to decrease.

258 Thermodynamics Fundamentals and Its Application in Science

G0 = H0 T.S0

(11)

According to the Equation 11, enthalpy change should be negative, in other words adsorption is exothermic. For this reason adsorption amount will increase, when temperature is decreased [15]. Also the affinity of a dye is dependent on temperature. It decreases as the temperature rises, i.e. the equilibrium shifts in favor of the external phase. When -/T is plotted against 1/T (T is the absolute temperature for a particular affinity value), the slope of the straight line obtained gives H0, the heat of dyeing [39]. However, the numerical value of , obtained from dye absorption, cannot be verified, and S0 is impossible to measure, while H0 is solely dependent on . Hence, using Equation 5, any error in will accumulate in H0 and S0. One of the errors in determining may be due to aggregation of the dye in solution under some conditions. Such an aggregation equilibrium could explain why a linear plot of - /T against 1/T cannot always be obtained. In an attempt to clarify the latter point, Asquith et al. carried out a study on two dyes (C.I. Acid Orange 7 and 10), one known to be non-aggregating under the selected conditions of dyeing studied. Figure 6 shows the plots of - /T against 1/T for these two dyes [38].

Figure 6. The relationship between - /T and 1/T for various acid dyes [38]

According to these experimental results Asquith et al. denoted that for Orange 7, the plots each consist of two straight lines, intersecting at 60C, which clearly indicates that this dye has two H0 values, corresponding to two temperature ranges-viz, below and above 60C. The deviation from linearity in the above plots immediately leads to the speculation that the and H0 values obtained from dyeing with Orange 7 has been influenced by dye aggregation equilibria in solution [38]. If the values of are available for two absolute temperatures T1 and T2, it is more convenient to use the Equation 12 [39]: H0= (T21-T12) / (T2-T1) (12)

where T1 is the initial dyeing temperature in Kelvin; T2, the final dyeing temperature in Kelvin, 1, the affinity at T1 K, and 2, the affinity at T2 K [40]. The value of H0

Thermodynamics of Wool Dyeing 259

represents the difference in heat content between that needed to free one mole of dye from the solvent, and that required to free the same quantity of adsorbed molecules from the surface or from the interior of the solid by thermal agitation. It is thus the heat of sorption, i.e. the increase in heat content (enthalpy) of the system when the dye is sorbed. Large negative values of H0, therefore, correspond to high potential affinity [23].

2.6. The entropy of dyeing

The third thermodynamic parameter is the standard change in the entropy of the system (S0) [3]. The standard entropy of dyeing, S0, can be calculated from the Gibbs equation [26]: = H0 T.S0 (13)

Because there is no direct experimental means of measuring the entropy change, it is necessary to calculate its value from measurements of and H0 [3]. According to Boltzmans conception, the entropy is proportional to the probability of the system [26]. The change in entropy (S0) represents (on a logarithmic scale) the ratio of probability of sorption (1) to that of desorption (2) as shown in Equation 14: S0 = Rln1 - Rln2 = Rln(1/2) (14)

This entropy of sorption is the gain in entropy or disorder of the system when dye is adsorbed [3]. From the dyeing point of view the entropy change is of practical importance especially in two cases, in which either two dyes are compared on a common fiber or one dye is compared on two fibers. Therefore, dyeing entropy can almost be identified with dye/fiber orientation [26]. The entropy changes due to the dye sorption can be evaluated in a similar way to the enthalpies from the sorption isotherms determined at different temperatures via the free energy of adsorption G0. S0ad=R(T1 lnC1 - T2 lnC2) / (T2 - T1) (15)

The change in entropy upon the sorption process consists of two parts, one of which results from the dehydration of dye molecules before their adsorption (and dilution of the solution) and the other is connected with the actual interaction of the molecules with the solid surface. While the latter part is negative (loss of the molecular freedom), the former is positive. During a spontaneous adsorption process, the total entropy change is always positive [22].

3. Conclusion
Wool fibers have the most widely usage in the textile sector among the animal fibers and these fibers are dyed with acid, metal complex 1:1 and 1:2, chrome and reactive dyes. In order to understand the dyeing mechanism of these fibers better, it is needed to know thermodynamic and kinetic aspects of the dyeing such as aggregation and adsorption of dyes, rate, standard affinity of dye, enthalpy (standard heat) and entropy of dyeing exc.

260 Thermodynamics Fundamentals and Its Application in Science

Author details
Rza Atav Namk Kemal University, Textile Engineering Department, Tekirda, Turkey

4. References
[1] Ingamells W. Colour for Textiles a Users Handbook Society of Dyers and Colourists ISBN 0 901956 56 2 1993 [2] Gong R., Liu Y., Jiang Y., Li C. Isothermal, Kinetic and Thermodynamic Studies on Basic Dye Sorption onto Tartaric Acid Esterified Wheat Straw African Journal of Biotechnology 2009;8(24) 7138-7147. [3] Johnson A. The Theory of Coloration of Textiles Second Edition Society of Dyers and Colorists 1989 [4] Von Bergen W., Krauss W. Textile Fiber Atlas: A Collextion of Photomicrographs of Common Textile Fibers American Wool Handbook Company New York 1942 [5] Marti M., Barsukov L.I., Fonollosa J., Parra J.L., Sukhanov S.V., Coderch L. Physicochemical Aspects of the Liposome-Wool Interaction in Wool Dyeing Langmuir 2004;20 3068-3073. [6] Feughelman M. Introduction to the Physical Properties of Wool, Hair and Other Keratin Fibers in: Mechanical Properties and Structure Of Alpha-Keratin Fibers: Wool, Human Hair and Related Fibers UNSW Press 1997; 1-14. [7] Silva C.J.S.M., Prabaharan M., Gubitz G., Cavaco-Paulo A. Treatment of wool fibers with subtilisin and subtilisin-PEG Enzyme and Microbial Technology 2005;36 917-922. [8] Micheal M.N., El-Zaher N.A. Efficiency of Ultraviolet/Ozone Treatments in the Improvement of the Dyeability and Light Fastness of Wool Journal of Applied Polymer Science 2003;90 3668-3675. [9] Cardamone J.M., Damert W.C. Low-temperature Dyeing of Wool Processed for Shrinkage Control Textile Research Journal 2006;76(1) 7885. [10] Onar N., Sark M. Use of Enzymes and Chitosan Biopolymer in Wool Dyeing Fibers & Textiles in Eastern Europe 2005;13(1) 54-59. [11] Marti M., Parra J.L., Coderch L. Natural Dyes: Chapter 5: Lipid Role in Wool Dyeing Ed. by Akcakoca Kumbasar E.P. InTech ISBN 978-953-307-783-3 2011. [12] Simmonds D.H. The Amino Acid Composition of Keratins Australian Journal of Biological Sciences 1955;8(4) 537-540. [13] Horsfall R.S., Lawrie L.G. The Dyeing of Textile Fibers Chapman&Hall LTD London 1946; 229. [14] Yurdakul A., Atav R. Principles of Dyeing and Printing Ege University Engineering Faculty Department of Textile Engineering Bornova-Izmir 2006. [15] Tarakoglu I., Textile Dyeing-I Notes, Ege University Engineering Faculty Press Izmir 1979-1980. [16] Lewis D.M. Wool Dyeing Society of Dyers and Colourists 1992.

Thermodynamics of Wool Dyeing 261

[17] Saha S.K. Dye-aggregation in Solution: Molecular Exciton Model 2010. http://www.scitopics.com/Dye_aggregation_in_solution_Molecular_exciton_model.htm l (accessed 22 April 2012) [18] Walmsley F. Aggregation in Dyes: A Spectrophotemetric Study 1992;69(7) 583. [19] Alarfaj N.A., El Khiate Z.M., Moussa E.A., Spectrophotometric Studies on Aggregation of Some Acid Dyes in Different Media Journal of King AbdulAziz University Science 2008; 99-110. [20] Gabriela M.S., Elena G.M., Szabaday Z. Aggregation of Two Direct Dye Derived from 4,4-Diaminostilbene-2,2-Disulphonic Acid. Spectroscopic and Mathematical Studies, 14th International Electronic Conference on Synthetic Organic Chemistry, 1-30 November 2010. [21] http://www.fpharm.uniba.sk/fileadmin/user_upload/english/Physical_Chemistry/5Adsorption.pdf (accessed 25 April 2012) [22] Espnosa-Jmnez M., Padlla-Wegand R., Ontveros-Ortega A., Perea-Carpio R., Ramos-Tejada M. M., Chbowsk E. Investigation of the Polyamide 6,6 Dyeing Process with Acid Blue 45 dye. Part I. Thermodynamics of Acid Blue 45 Adsorption J. Adhesion Sci. Technol. 2002;16(3) 285-301. [23] Kumar A., Choudhury R. Textile Preparation and Dyeing Science Publishers-USA ISBN 1-57808-402-4 2006 [24] Atkins P., Paula J. Elements of Physical Chemistry Oxford University Press Fourth edition ISBN: 0199271836 2005 [25] Tan L.S., Jain K., Rozaini C.A. Adsorption of Textile Dye From Aqueous Solution on Pretreated Mangrove Bark An Agricultural Waste: Equilibrium and Kinetic Studies 2010;5(3) 283-294. [26] Simu G.M., Funar-Timofei S., Kurunczi L. Influence of Temperature and of the Electrolyte Concentration in the Dyeing Process of a Cellulosic Fiber with a Disazo Direct Dye Buletinul Stiinific al Universitii Politehnica din Timisoara ROMANIA 2008;53(67) 153-155. [27] Zawani Z, Luqman Chuah A, Thomas S.Y. Choong Equilibrium, Kinetics and Thermodynamic Studies: Adsorption of Remazol Black 5 on the Palm Kernel Shell Activated Carbon (PKS-AC) European Journal of Scientific Research 2009;37(1) 63-71. [28] Narayanachar K., Puttaswamya V., Gowdab K.N., Sudhakar R. Extraction of Natural Color Component from The Bark of Belleric Myrobalan (Terminalia Bellerica): Kinetic and Adsorption Studies European Journal of Chemistry 2010:1(3) 206-210. [29] Bruce R.L., Broadwood N.V., King D.G. Kinetics of Wool Dyeing with Acid Dyes Textile Research Journal 2000; 70(6) 525-531. [30] Alexander P., Hudson R.F. The Kinetics of Wool Dyeing: Part I: Simple Acid Dyes Textile Research Journal 1950:20 481-491. [31] Dugg D.G., Sinclair S. Giless Laboratory Course in Dyeing (Fourth Edition) ISBN-13: 978 0 901956 49 1 December 1989. [32] Aspland J.R. Textile Dyeing and Coloration American Association of Textile Chemists and Colorists ISBN 0-9613350-1-7 1997.

262 Thermodynamics Fundamentals and Its Application in Science

[33] Adebayo G.B, Adekola F.A, Olatunji G.A, Bello I.A. Some Thermodynamic Parameters of Two Indigenous Mineral Dyes Applied on Wool Material Bulletin of Pure and Applied Sciences 2010:29C (2) 77-95. [34] Derbyshire A.N., Peters R.H. An Explanation of Dyeing Mechanisms in Terms of Nonpolar Bonding J. Soc. Dyers Colour. 1955:71 530-536. [35] Zollinger H. The Dye and the Substrate: The Role of Hydrophobic Bonding in Dyeing Processes J. Soc. Dyers Colour. 1965;81 345-350. [36] Iyer S.R.S., Ghanekar A.S., Singh G.S. The Chemistry of Synthetic Dyes Vol. VII Ed. by Venkataraman K. Academic Press New York 1974; 236 [37] Ferrini B., Kimura Y., Zollinger H. A Contribution to the Dyeing Mechanism of Acid Dyes on Wool Proc. Int. Wool Textile Res. Conf. Paris 1965; 291-300. [38] Asquith R.S., Kwok W.F., Otterburn M.S. An Assessment of Some Thermodynamic Treatments of Wool Dyeing Systems Textile Research Journal 1980;50 333-336. [39] Kumar A., Choudhury R. Textile Preparation and Dyeing Science Publishers ISBN 157808-402-4 2006. [40] Samanta A.K., Agarwal P., Datta S., Physico-chemical Studies on Dyeing of Jute and Cotton Fabrics Using Jackfruit Wood Extract: Part II Dyeing Kinetics and Thermodynamic Studies Indian Journal of Fiber&Textile Research 2008;33 66-72.

Chapter 11

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones
L.E. Panin
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51515

1. Introduction
Biological membranes are liquid heterocrystals with low shear stability. The main structureforming bonds in biological membranes are covalent and hydrogen bonds, and hydrophobic and weak electrostatic interactions. These bonds are responsible for high membrane elasticity a property of particularly importance to erythrocytes, which have to pass through blood capillaries of diameter equal to the erythrocyte one. Any structural changes that increase the erythrocyte membrane viscosity hamper the motion of erythrocytes through capillaries and may result in diffuse hypoxia. In this context, of great interest is the effect of stress hormones (cortisol, adrenaline, noradrenaline) on the behavior of erythrocyte membranes. The nonspecific binding of stress hormones with erythrocyte membranes was studied earlier in [1]. It was shown that excess of these hormones in blood are capable for nonspecific binding with blood cells, primarily with erythrocytes, producing changes in rheological properties of the blood. It was found that CO, OH, and NH active groups incorporated in the structure of hormones can form hydrogen bonds with similar groups of proteins and phospholipids of erythrocyte membranes. Hydrophobic rings of hormones can participate in hydrophobic interactions with residues of phospholipid fatty acids, as a result of which complex domains arise in the membrane structure, the membrane microviscosity increases, and the motion of erythrocytes through capillaries becomes difficult. This effect is particularly dangerous to heart because it can leads to coronary syndrome [2, 3]. Physicians still fail to understand the nature of this phenomenon, which shows up as
2012 Panin, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

264 Thermodynamics Fundamentals and Its Application in Science

exertional angina and ischemic ST segment depression on electrocardiograms with a normally functioning left ventricle. Anabolic steroid hormones have been used for many decades, finding their most extensive use in sports medicine. Nowadays, it is impossible to train as an international class athlete without anabolic hormones. A coachs aspiration for high sporting results prompts that coach to use an ever increasing amount of anabolic steroids. Lacking a profound knowledge of sports medicine, such a coach cannot imagine all of the negative effects of anabolics on the body of an athlete. Moreover, sports medicine itself has no comprehensive information on the subject. As a consequence, the number of sudden and unexpected deaths of atheletes during the competitions has drastically increased in recent years [4]. Physicochemical analysis of the behavior of erythrocyte membranes as liquid heterocrystals makes it possible to disclose a link between structural changes in erythrocyte membranes and erythrocyte function. Of particular interest is activity of the Na+, K+-ATPhase that supports the transmembrane potential of cells and precludes their aggregation. It was previously supposed that the regulatory action of different ligands can be based on certain conformational changes of the Na+, K+-Phase [5]; however, the mechanism by which steroid hormones affect the activity of the Na+, K+-Pase is poorly known. In this work, the mechanism of testosterone, androsterone, dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate (DHEAS) and cortisol interaction with structural components of erythrocyte membranes (mesomechanics and termodinamics of nanostructural transition) changes in their microviscosity and functional characteristics during the interaction have been studied. The results obtained could also shed light on the causes of cardiovascular catastrophes, which are often observed in sportsmen taking anabolic steroid hormones for a long time [6].

2. Materials and methods

The action of five hormones: testosterone, androsterone, dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate (DHEAS) and cortisol (Amersham) is analyzed in the work (Fig. 1). For this purpose, the following methods were used.

2.1. Atomic force microscopy (AFM) of erythrocytes

Erythrocytes were obtained from fresh blood after decapitation of Wistar rats under light nembutal narcosis. Blood was diluted twofold by isotonic phosphate buffer ( 7.35) containing 0.043 M of 24 and 0.136 M of Na24. After precipitation of cells by centrifuging at 330 g for 10 min, supernatant liquor was decanted, and the washing procedure was repeated twice more. All the procedures were performed at 4 C [1]. The resulting erythrocyte suspension of 20 mcl volume was deposited onto a glass slide as a thin smear. The smear was predried for

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 265

10 min in air at 24 C and humidity of 40%. After evaporation of excessive surface moisture, the smear was observed under a Solver Bio atomic force microscope (NT-MDT, Russia) at 24 C using a semi-contact mode. An analogous procedure of obtaining red blood cells for the AFM examination was employed earlier by other authors [7]. In each experiment first a control specimen without hormones, and then the experimental one have been tested. Silicon cantilevers NSG11 (NT-MDT, Russia) with a resonant frequency between 120 and 180 kHz and spring constant ~ 6 N/m were used (all of these probe parameters were offered by manufacturer). Images of the surface relief of erythrocyte membrane after absorption of hormones were obtained with the scan size 11 m2 and 1.31.3 m2.

Figure 1. Chemical structure of steroid hormones.

266 Thermodynamics Fundamentals and Its Application in Science

2.2. IR spectroscopy of erythrocyte shadows

Erythrocyte shadows were obtained after their hemolysis in hypotonic phosphate buffer ( 7.35) containing 2.75 mM of KH24 and 8.5 mM of Na24. Shadows were precipitated by centrifuging at 5500 g, supernatant liquor was decanted. The washing procedure was repeated four more times [8]. All operations and further storage of shadows were performed at 4 C. A film for taking the IR spectra of erythrocyte shadows was prepared in a cuvette with fluorite backing via slow evaporation of water under weak vacuum at a pressure of ca. 0.1 atm (ca. 0.5104 Pa) and temperature 41 C [8]. Drying lasted 180 min. A suspension of erythrocyte shadows in a 0.001 M phosphate buffer with pH 7.35 and volume 60 mcl was introduced into a cuvette. This was supplemented with 30 mcl of the same buffer and 1.0 mcl of the hormone solution with concentration 106 M. Stirring and incubation lasted 10 min at 16-17 C. The cuvette was placed horizontally on a special table of a vacuum unit. When the film was prepared, the cuvette was transferred into an optical chamber and blown with dry air for 30 min, then the scanning unit was switched on. IR spectra were taken on a Specord-M80 spectrometer (Germany, Leipzig), sequentially experiment and control against the fluorite backing, or experiment and control to obtain a difference spectrum. Integration, determination of the spectrum band frequency, and mathematical processing were performed with special programs enclosed to the spectrometer. Erythrocyte suspensions were examined upon addition of cortisol using UV (Evolution 300, Thermo Scientific, USA). Merk or Sigma reagents were used in the work.

2.3. Fluorescence analysis of erythrocyte shadows

Fluorescence measurements were performed with a Shimadzu spectrofluorophotometer RF5301(PC)SCE. 4 ml of hypotonic phosphate buffer containing 2.75 mM of 24 and 8.5 mM of Na2HP4 ( 7.35), and erythrocyte shadows were poured into a quartz cuvette of size 1 1 4 cm3. The concentration of shadow proteins was determined by the Warburg Christian method from changes in the optical density of suspension [9]. On the average, it varied in the range of 0.100-0.250 mg/ml. A cuvette with the shadow suspension was placed into a spectrofluorimeter thermostat for 1 hour. Getting a stationary temperature regime in the cuvette was controlled by an electronic thermometer. In all the experiments, temperature in the cuvette was 36 C. After establishing a stationary temperature in the cuvette, intensity of the intrinsic fluorescence of tryptophan residues in protein membranes was measured. The tryptophan emission spectrum was taken in the range of 300 nm 400 nm at the excitation wavelength 281 nm, with the maximum of emission intensity observed at 332 nm. The average value of maximum emission intensity was obtained graphically after its continuous measuring for 4 minutes. Intensity of tryptophan fluorescence fluctuated within 1%. The possible reasons include variation of temperature in the cuvette with suspension, instrumental error in determination of fluorescence intensity, and photochemical reactions occurring in the

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 267

system. Spectral width of the slits was 1.5/10. The tryptophan absorption spectrum was recorded in the range of 220 nm 300 nm at the emission wavelength = 332 nm. Testosterone, androsterone, dehydroepiandrosterone (DHEA) and dehydroepiandrosterone sulfate (DHEAS) were dissolved in a mixture of dimethyl sulfoxide (DMS) and ethanol (1 : 1, V/V). Concentration of the hormone in the initial mother liquor was 103 M. If necessary, the solution was diluted with hypotonic phosphate buffer to obtain a desired concentration. A solution of hormones with the concentration 106 M was prepared in hypotonic phosphate buffer. The time of hormone incubation with shadows was one hour. Absorption and emission spectra were taken, the average value of emission and absorption intensity was measured. For each hormone (testosterone, androsterone, dehydroepiandrosterone (DHEA) and dehydroepiandrosterone sulfate (DHEAS)), the binding constant Kb was calculated by the method [10] as well as the stoichiometric concentration of a bound hormone Bmax and a change in free energy of the system G . The interaction of hormone and erythrocyte membrane is described by the equation
B nS , Sn B

(1)

where B is a membrane protein, S is the hormone, and n is the number of moles of hormone per a mole of proteins. The binding constant Kb was calculated by the formula
S B Kc n , S B

(2)

where Sn B is the concentration of bound protein, B is the concentration of free protein, and S is the concentration of free hormone. It is supposed that hormone, upon binding to protein, completely quenches its fluorescence. Thus, the fluorescence intensity F will be proportional to the concentration of free protein. Lets write C for total concentration of protein in the cuvette, and x for concentration of the bound protein. Then,
C x , F Fmax C

(3)

where F is the intensity of tryptophan fluorescence at = 332 nm (the excitation wavelength = 228 nm), Fmax is the intensity of tryptophan fluorescence in the absence of hormone (when the entire protein is free), is the proportionality factor, and AS is the stoichiometric concentration of hormone. When concentration of hormone exceeds AS , the fluorescence quenching does not increase. Dividing the first equation of set (2) by the second one gives
Fmax F x Q Q C , where Fmax

(4)

268 Thermodynamics Fundamentals and Its Application in Science

A S A n x A n Q C , where A is the total concentration of hormone; n S ; C

B C x C(1 Q) . Substitution of (2) and (3) into expression for binding constant (1) gives

Kc

Q (1 Q)( A nQC )

(5)

In our case, molar mass of membrane proteins is unknown, so the concentration of proteins in cuvette C is determined in mg/ml, and concentration of hormones A in mol/l. The constant n is expressed in moles of molecules of hormone per milligram of protein (M/mg) and is a ratio of the maximum concentration of bound hormone to the concentration of membrane proteins. This can be written as

BMAX

AS mole mg protein C

(6)

Changes in Gibbs free energy G of the system upon transition of hormone from aqueous medium to erythrocyte membrane are calculated by the formula
G RT ln( Kc ) J mole ,

(7)

where R 8.314

J , and T is the absolute thermodynamic temperature. K mole

The measurement errors appeared due to inaccuracy in volumetric dosing of the shadow suspension specimens and their titration against hormones. Specimens were dosed using pipette dispensers DPAOF-1000 and DPAOF-50, their relative error at (202)C being 1% and 2%, respectively. 4 ml of the buffer was taken once with a DPAOF-1000 pipette, and suspension of erythrocytes and hormones was dosed twice using a DPAOF-50 pipette. The fluorescence intensity of erythrocyte shadows F is directly proportional to the concentrations of proteins C and hormones A in the specimen. Relative error EF in measuring the F value can be estimated by the formula
EF

1% 2% 2%

3%.

(8)

Relative measurement errors for Kb and BMAX can be obtained in the same way. They are equal to 10%. In calculation, the values of fluorescence intensity F were corrected for dilution of suspension after the introduction of solution with hormone, for quenching of tryptophan emission by the solvent (a mixture of DMS and ethanol), for proper fluorescence of hormones, and evaporation of water from the cuvette.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 269

2.4. Measurement of erythrocyte membrane microviscosity

Membrane microviscosity for translational diffusion of pyrene probe was calculated as a ratio of fluorescence intensity of the pyrene dimer to fluorescence intensity of the pyrene monomer. Microviscosity of erythrocyte membranes was measured also on a Shimadzu RF-5301(PC)SCE spectrofluorimeter. The experimental specimen was prepared as follows: 4 ml of hypotonic phosphate buffer containing 2.75 mM of KH24 and 8.5 mM of Na24 ( 7.35), a fluorescent pyrene probe, erythrocyte shadows and a specified amount of hormone were placed in a quartz cuvette of size 1 1 4 cm3. Before use, all the components were stored at 4 C. The concentration of shadow protein in the cuvette was 0.100-0.250 mg/ml; that of pyrene, 7.76106 M. Pyrene was diluted in ethanol, its initial concentration being 1.5103 M. The cuvette was placed into the spectrofluorimeter thermostat for 10 min, then the fluorescence measurements were performed at 36 C. Before placing the specimen into the spectrofluorimeter thermostat, it was shaken vigorously for 1 min. For fluorescence measurements of shadows upon their loading with a different amount of hormones, each time a new specimen was prepared by the same procedure. Such a procedure is necessary because pyrene favors fast degradation of erythrocyte membranes. To measure microviscosity of a lipid bilayer near proteins (the region of protein-lipid interaction), we used the excitation wavelength = 281 nm and spectral slit width 1.5/5. Microviscosity of a lipid bilayer far from proteins (the region of lipid-lipid interaction) was measured with the excitation wavelength = 337 nm and spectral slit width 1.5/3. At that, the maxima of emission intensity were observed at = 374 nm and = 393 nm (the vibronic emission peaks of excited pyrene monomers), and = 468 nm (the emission maximum of excited pyrene dimer). The relative microviscosity of membranes was determined as a ratio ( A) / 0 , where ( A) and (0) are microviscosities of membranes, respectively, with and without hormone added to the shadow suspension. For the region of lipid-lipid interaction, relative microviscosity was calculated by the formula

A F (0) F393 ( A) 468 0 F468 ( A) F393 (0)

(9)

where F468 ( A) is the fluorescence intensity of pyrene at wavelength = 468 nm in a specimen at the hormone concentration A in suspension; F468 (0) is the fluorescence intensity of pyrene at wavelength = 468 nm in a specimen with no hormone in suspension. F393 ( A) and F393 (0) are the fluorescence intensities of pyrene at wavelength = 393 nm at the hormone concentration A in suspension and without hormone in suspension, respectively. The excitation wavelength is 337 nm. For the region of protein-lipid interaction, relative microviscosity was calculated by the formula

270 Thermodynamics Fundamentals and Its Application in Science

A F (0) I 468 F393 ( A) I 393 468 0 F468 ( A) I 468 F393 (0) I 393

(10)

where I 393 and I 468 are the fluorescence intensities of tryptophan at wavelength = 393 nm and = 468 nm, respectively. The excitation wavelength is = 281 nm. A relative measurement error for relative microviscosity was equal to 6%.

2.5. Change of the Na+, K+-Pase activity

Erythrocytes were extracted from fresh blood of rats. Erythrocyte suspensions with hormones of differing concentration were analyzed to activity of the Na+, K+-Phase. The experimental procedures used in these investigations are described in [5].

3. Results
3.1. Atomic force microscopy
Under atomic force microscope, erythrocytes of healthy animals looked as large biconcave discs ca. 6 m in diameter, which agrees with the results obtained by other authors [7]. At a higher magnification, their surface showed a slight nonuniformity caused most likely by the presence of membrane proteins. When the erythrocyte suspension was supplemented with DMS and ethanol (0.25% of the mixture volume), the surface nonuniformity increased, probably due to denaturating effect of solvent on the surface structural proteins (Fig. 2). Domains with the length 200-250 nm and height 2 nm are seen. The pattern changed upon addition of testosterone to erythrocyte suspension with the final concentration 10-7 M (Fig. 3). The interaction of testosterone with erythrocyte membranes leads to their restructuring. The surface is tuberous, there are domains of size 400 400 nm and height 20-25 nm, with smaller domains on the surface of large ones: size 50 50 m2 and height 10 nm. Between them, there are regions of loosened substance that form hollows. In this case, there are pronounced distortions in the primary structure of erythrocyte membranes. Other structural changes of erythrocyte membranes were obtained in our study upon interaction with androsterone (Fig. 4) with the final concentration 106 M. The surface is flat, there are domains of size 100 100 nm and height 6-8 nm. In comparison with control specimens, domains decreased in area, but increased in height. The surface of rat erythrocyte after adsorption of DHEA is depicted in Fig. 5. Concentration of the hormone is 107 M. The surface is tuberous, there are domains of size 220 220 nm and height 20 -25 nm. However, they are not separated into subdomains, as in the case of testosterone. Of the four hormones, DHEAS has the weakest effect on the membrane morphology. The surface of rat erythrocyte after adsorption of DHEAS is shown in Fig. 6. Concentration of the hormone is 107 M. The surface is flat, there are domains of size 100 100 nm and height 3 - 4 nm. Changes are insignificant in comparison with control. It can be suggested that DHEA

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 271

and DHEAS did not affect deep layers of the membranes, so the effect was much less pronounced. IR spectroscopy allowed us to reveal the nature of these structural transformations.

Figure 2. Control surface of rat erythrocyte. The erythrocyte suspension was supplemented with DMS and ethanol (0.25% of the mixture volume): (a) scan size 1 1 m2; (b) center section of the surface.

272 Thermodynamics Fundamentals and Its Application in Science

Figure 3. Surface of rat erythrocyte after adsorption of testosterone. Concentration of the hormone is 10-7 M: (a) scan size 1.5 1.5 m2; (b) center section of the surface.

3.2. IR spectroscopy of erythrocyte shadows

Analysis of IR spectra of erythrocyte shadows obtained from rats with no hormone loading (Fig. 7) revealed in membrane-bound proteins not only a disordered structure,

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 273

but also -helix at 1650 and 1656 cm1, and -structure at 1686 and 1520 cm1. Besides, we recorded NH stretching vibrations in proteins (3308 cm1), CH stretching vibrations in proteins and phospholipids (2948, 2930 and 2848 cm1), and a set of bands corresponding to phospholipids, in particular, C=O bond (1748 cm1), P=O bond (1236 cm1), 2 deformation vibrations (1460 and 1386 cm1), 44-55 bond (1048 cm1) and C-C bond of deformation vibrations (978 cm1). It should be noted that = band (1736 cm1) is quite narrow, which gives grounds to suggest that phospholipids in membranes of normal erythrocytes are well ordered at a level of ester bonds of higher carboxylic acids and glycerol.

3.2.1. Effect of testosterone

Under the action of testosterone, intensity of absorption bands 1544, 1656 and 3292 cm1 increased by 30% and more (Fig. 8, Table 1). Absorption band of N bond showed a 3272 cm1 shift ( = 36 cm1). The bands 2852 and 2932 cm1 increased in intensity; 3308 the ratio of band intensities 2852/2932 cm1 changed. The enhancement of integral intensity of the indicated absorption bands indicates an increased ordering of membrane proteins and, in particular, an increased fraction of -helices. The fraction of -helices grows due to structural transition tangle -helix. A 3308 3272 cm band shift of NH bond ( = 36 cm1) is caused by the formation of hydrogen bond between keto group (C3=O) in testosterone A-ring and NH bond of peptide group in membrane protein or indole ring in tryptophan. An increased intensity of the 2932 and 2852 cm1 bands together with a growing intensity ratio 2852/2932 cm1 confirm the rising orderliness of the entire membrane. Absorption band 1740 cm1 (= bond of the ester group in phospholipids) increased in intensity and shifted to the short-wave region. The enhanced intensity of = bond reflects an increased ordering of phospholipids within domains and an increased interdomain ordering. The short-wave shift of this band is caused by the formation of hydrogen bond between OH group at 17 carbon atom in testosterone Dring and = bond in phospholipids. Similar to segnetoelectrics a hysteresis phenomenon was observed in erythrocyte membranes [11, 12]. The spectrin-actin-ankyrin meshwork, which is connected both with membrane proteins and phospholipids, also contributes to 1098 and 1236 1248 cm1 shifts of absorption bands the ordering of phospholipids. The 1088 to the short-wave region result from dehydration of phospholipids due to increase in their orderliness, since the hydration process shifts these bands to the long-wave region [13] An increased intensity of bands 1098 and 1247 cm1 (-- and = bonds of phospholipids, respectively) in comparison with control specimens confirms an enhanced ordering of phospholipids under the action of the hormone.
1

Thus, the formation of complex domains in erythrocyte membranes upon their interaction with testosterone is caused by simultaneous interaction of and OH groups of the hormone with and N groups both of proteins and phospholipids. In the process, water is displaced to adjacent regions, which is accompanied by membrane loosening.

274 Thermodynamics Fundamentals and Its Application in Science

Figure 4. Surface of rat erythrocyte after adsorption of androsterone. Concentration of the hormone is 10-6 M: (a) scan size 1.5 1.5 m2; (b) center section of the surface.

3.2.2. Effect of androsterone

Incubation of rat erythrocyte shadows with androsterone (CC = 2.76 x 108 M) results in shifting the frequency of NH bonds (stretching vibrations of amide A) to the long-wave

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 275

region by 38 cm1 as well as shifting of N bond of amide II ( = 2 cm1) (Table 1). Integral intensity of absorption bands of (1654 cm1) and N groups (3280 cm1) increased by 30% and more. There appeared a band at 1635 cm1 corresponding to the -structure. An increase in intensity of stretching vibrations of CH bonds at 2848 and 2930 cm1 was observed. The frequency shift of NH bond is related with the formation of hydrogen bond with 17= group of the hormone D-ring. Androsterone has a more flexible structure as compared to cholesterol: its , and -rings can take a more favorable conformation during the interaction with membrane proteins. Only D-ring has a flat structure, due to the presence of carbon 17 with s2 hybridization. Hydrophobic interaction with the membrane surface should also be taken into account. High conformational mobility of the molecule creates more advantageous steric conditions for hydrophobic interaction both with tryptophan, which fluorescence quenching was observed in our study, and hydrophobic regions on the membrane surface. This increases the constant of their binding to hormone and leads to more pronounced structural changes in the membranes. An increase in intensity of -peptide bond is related with the growing fraction of -helices due to transition tangle -helix. An increase in intensity of absorption band 1620-1635 cm1 is caused by structural transition tangle -structure. Of interest is a hypothesis stating that the indicated transitions may take place in contractile proteins, since their removal from the membrane results in a decrease or disappearance of transitions [12-13].

3.2.3. Effect of dehydroepiandrosterone

Incubation of DHEA with erythrocyte shadows showed that the frequency of stretching 3288 cm1), vibrations of N peptide bond shifted by 20 cm1 to the long-wave region (3308 whereas halfwidth of amide A decreased. An increase in the integral intensity of absorption bands at 1546, 1654.9 and 3288 cm1 was observed (Table 1). 1247.6 cm1 band shift points to dehydration of phosphate groups in phospholipids. A 1236 Shifting of the frequency of = bond in phospholipids (1748 1732 cm1) was observed; 2925.8 and 2848 2851 cm1 shifts ( intensity of this band also increased. The 2930 stretching vibrations) took place, intensity of the bands increased. The intensity ratio 2852/2924 cm1 changed.

3.2.4. Effect of dehydroepiandrosterone sulfate

Incubation of DHEAS with erythrocyte shadows resulted in the band shift 3308 3286 cm1 (N peptide bond) by 22 cm1 (Table 1). Bands at 1548, 1656 and 3298 cm1 increased in intensity with respect to control specimen; however, this was more pronounced upon addition of DHEA as compared to DHEAS. Absorption bands 1632 and 1684 cm1 attributed 2928 and 2848 2852 cm1, to -structure were observed. The band shift was recorded: 2930 which was accompanied by a change in the 2852/2928 cm1 ratio. The band at 1236 cm1 (= bond) showed a strong splitting and had 3-4 bands in the region of 1236-1256 cm1. Bands at 1084 and 1100 cm1 (P-O- bond) were observed. A 1748-1738 cm1 shift was detected; however, it was less pronounced than in the case of DHEA addition. The DHEAS hormone

276 Thermodynamics Fundamentals and Its Application in Science

has a stronger binding with hydrophilic heads of phospholipids as compared to DHEA, and a weaker binding with membrane proteins. This suggests that DHEAS molecules cannot penetrate deep into the membrane due to their higher hydrophilicity with respect to DHEA.

Figure 5. Surface of rat erythrocyte after adsorption of DHEA. Concentration of the hormone is 10-7 M; (a) scan size 1 1 m2; (b) center section of the surface.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 277

Figure 6. Surface of rat erythrocyte after adsorption of DHEAS. Concentration of the hormone is 10-7 M; (a) scan size 1 1 m2; (b) center section of the surface.

Overall, it can be concluded that the interaction of DHEA and DHEAS with erythrocyte membranes is accompanied by the formation of hydrogen bonds between keto group (17=) and N group of proteins as well as between group at 3 in the A-ring of the hormones and C=O group in biomembrane phospholipids. The formation of indicated

278 Thermodynamics Fundamentals and Its Application in Science

hydrogen bonds leads to ordering of membrane proteins (transition tangle -helix) and phospholipids. Hydrophobic interactions of hormone with the surface of erythrocyte membranes also contribute to their structural rearrangement; however, they are much less pronounced for DHEAS as compared to DHEA. The reason is that substitution of group by SO3 strongly diminishes the energy of hydrogen bond, since in group the unshared pair of electrons is located on the oxygen atom, whereas in SO3 group it is delocalized over the entire -conjugated bond.

4. Fluorescence analysis
In the study, absorption intensity (D) and emission intensity (F) of tryptophan were estimated at different wavelengths. Corrections were made for dilution of erythrocyte shadow suspension after the introduction of a hormone solution, for tryptophan emission quenching by a solvent (DMS : ethanol), intrinsic fluorescence of hormones, and evaporation of water from a cuvette. To obtain a correction for solvent, the erythrocyte shadow suspension was titrated with solvent. It was shown that solvent decreases the intensity of tryptophan absorption at = 227.8 nm by 33% and results in its long-wave shift to = 230.2 nm. Absorption intensity at = 281 nm changed only by 1.3% without a long-wave shifting. A maximum of emission intensity differed from control specimen also at = 332 nm. It did not shift upon addition of solvent, but its intensity decreased by 1.3%. Upon addition of testosterone with the final concentration 3106 M to erythrocyte shadows, the absorption intensity at 227 nm diminished by 19 a.u. or by 2.8%; this was accompanied by an upward shift of to 230.4 nm. As the hormone concentration increased to 6.05106 M, the absorption intensity at 227 nm decreased by 25 a.u., or 5.0%, which was accompanied by shifting the absorption maximum to 232 nm. In the region of 280 nm, addition of hormone caused only minor changes in fluorescence. Considerable changes in the spectrum were obtained upon addition of androsterone to the shadows. Even at a concentration of 6.92 10 8 M, which is two orders of magnitude lower compared to the case of testosterone, the absorption intensity at 227 nm decreased by 90 a.u., or 122%. It means that this hormone penetrates deeper into erythrocyte membranes than testosterone and enhances the tangle -helix transition in proteins, thus increasing their ordering. When erythrocyte shadows were supplemented with DHEA or DHEAS, the hypochromic effect was weak or entirely absent. A decrease in absorption intensity and a long-wave shift observed in our study can be attributed to the effect of solvent. Analysis of the tryptophan fluorescence quenching spectra testifies that all four hormones interact with membrane-bound proteins, although a degree of this interaction differs (Figs. 9-12). The most pronounced quenching was observed in the case of androsterone (Fig. 9). The maximum fluorescence quenching was observed at a concentration of 2.2108 M. Testosterone showed a lower fluorescence quenching (Fig. 10). The maximum quenching was observed at a concentration of 1.2107 M, which is 5.5 times higher as compared to

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 279

androsterone. Fluorescence quenching was even less pronounced with DHEA (Fig. 11). In this case, the maximum quenching occurred at a concentration of 2.4106 M. And finally, the lowest fluorescence quenching was observed for DHEAS (Fig. 12). The maximum quenching took place at a concentration of 5.3106 M, which is 2.2 times higher as compared to DHEA.

Figure 7. IR spectra of rat erythrocyte membranes (control) (Cphosph.buff. = 0.01 M, pH 7.35, relative humidity 0%): (a) = 900-1800 cm-1, (b) = 2600-3700 cm-1.

280 Thermodynamics Fundamentals and Its Application in Science

Figure 8. IR spectra of rat erythrocyte membranes incubated with testosterone (CC = 2.7 10-8 M, Cphosph.buff. = 0.001 M, pH 7.35, relative humidity 0%): (a) = 900-1800 cm-1, (b) = 2600-3700 cm-1.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 281

According to the results obtained, testosterone and androsterone penetrate deeper into erythrocyte membrane and have a stronger effect on the structure of membrane-bound proteins toward their increased ordering. DHEA and DHEAS have some effect on erythrocyte membranes; these hormones adsorb on the membrane surface, but do not penetrate deep into hydrophobic layer of the membranes. These hormones have a weaker binding with proteins via hydrogen bonds. This conclusion is confirmed by the calculated values of hormone binding constant (b), total amount of bound hormone (max), and changes in free energy (G) upon hormone transition from free state to the membrane-bound one (Table 2). The highest values of b were obtained in our study for testosterone and androsterone, b for androsterone being higher by a factor of 4. Amount of the bound hormone (max) obeyed an inverse relationship: it was 2.4 times higher in the case of testosterone as compared to androsterone. Changes in free energy upon interaction of hormones with erythrocyte membranes were most pronounced Compound Shadows (control) Shadows + androsterone (A = 2.76 108 ) Shadows + testosterone (A = 2.7 10 8 ) Shadows + DHEA (A = 2.64 108 ) Shadows + DHEAS ( = 1.63 108 ) CO 1655.4 1686 1656 1635 1620 1657 1684 1632 1654.9 NH
stretch.

C=O 1748

P=O 1236

P-O-C 1080

O545O4

CH
stretch.

A 1.2150 10

3308

1056

2948 2930 2848 2958 2928 2848

3270 329 2 3272 3298 3309 3288.0 1739.4

1260 1240

1098 1088

1247 1236

1098 1088

1065 1076

2956.4 2924 2850 2956.3 2925.8 2851.8 2952.0 2926.4 2852.0

2.2433 10

1732

1247.6

1088

1070.7

2.1266 10

1656.0 1680 1632.0

3286 3300 3312

1738

1248.0

1084

1070 1052.7

1.2598 10

Table 1. IR spectroscopy. Frequency parameters of rat erythrocyte shadows after their interaction with hormones

282 Thermodynamics Fundamentals and Its Application in Science

Figure 9. Q = (Fmax - F)/Fmax versus the concentration A of androsterone hormone introduced into a cuvette. Concentration of membrane protein C = 0.203 mg/mL.

Figure 10. Q = (Fmax- F)/Fmax versus the concentration A of testosterone hormone introduced into a cuvette. Concentration of membrane protein C = 0.101 mg/mL.

Figure 11. Q = (Fmax _ F)/Fmax versus the concentration A of dehydroepiandrosterone hormone introduced into a cuvette. Concentration of membrane protein C = 0.139 mg/mL.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 283

All values for DHEA and DHEAS strongly differed from those listed above. Binding constants were nearly two orders of magnitude lower. Amount of the bound hormone (max) was much greater, indicating a low specificity of interaction with the membranes. Changes in free energy (G) were low for both hormones (Table 2). Thus, a comparison of two pairs of hormones demonstrated their considerable difference from each other. The higher is b, the greater is the binding specificity and the lower is the amount of bound hormone (max). Large negative values of G for testosterone and androsterone testify that their interaction with erythrocyte membranes increases their ordering (negentropy). DHEA and DHEAS are characterized by a low specificity of binding to membranes.

Figure 12. Q = (Fmax - F)/Fmax versus the concentration A of dehydroepiandrosterone sulfate hormone introduced into a cuvette. Concentration of membrane protein C = 0.139 mg/mL.

It shows up even when hormones are compared with each other. In DHEA, substitution of group by S3 in the 3rd position of A-ring decreases b by a factor of 3.8 and increases max by a factor of 2.2. A decrease in G is also pronounced. The reason is that the presence of group and additionally of two keto groups and an S atom enhances the interaction of DHEAS with hydrophilic and N groups of the surface proteins. DHEA and DHEAS cannot bind to the proteins residing in hydrophobic layer of the membrane. These two hormones do not change the conformational state of spectrin-actin-ankyrin meshwork and have only a slight effect on the morphology of membrane surface. DHEAS, being most hydrophilic among the four hormones, has the weakest effect. As hormone hydrophilicity increases, the amount of membrane-bound hormone rises and b decreases. During the interaction of testosterone and androsterone with erythrocyte membranes, both hydrogen bonds and hydrophobic interactions may strongly contribute to the growth of b. This is explained by a deeper penetration of hormones into hydrophobic layer of erythrocyte membrane, which increases the specificity of their interaction. The accompanying structural -structure -helix, increase ordering of these transitions in membrane proteins, tangle proteins and substantially raise the G value. Results obtained in the study agree well with changes in microviscosity of erythrocyte membranes.

284 Thermodynamics Fundamentals and Its Application in Science

Steroid hormone testosterone androsterone DHEA DHEAS

Binding constant b (1) (2.240.22)x106 (3.20.32)x10

6

Amount of bound hormone Bmax (mol/mg protein) (1.090.11)x109 (4.460.45)x10

10

Changes in free energy G (kJ/mol) -37.6 -38.5 -28.3 -24.8

(5.990.60)x104 (1.560.16)x10
4

(1.800.18)x108 (4.030.40)x10
8

Table 2. Parameters of steroid binding to erythrocyte membrane based on tryptophan fluorescence quenching of membrane proteins

5. Changes in microviscosity
In erythrocyte membrane, a fluorescent pyrene probe is distributed in the lipid phase and can be a source of information on the state of its deeper layers. The rate of its migration and the ability to form excimers upon interaction with each other are estimated. This is the way to determine changes in microviscosity of the membranes. In our study, an increase in microviscosity was most pronounced at the addition of androsterone to erythrocyte membranes. Microviscosity started to grow at a hormone concentration of 108 M, the growth proceeding up to 2.5108 M with subsequent saturation (Fig. 13). The S-shaped curve points to high cooperativity in changing the conformational state of the membrane. A microviscosity increment attained 50% with respect to the initial state. In the region of protein-lipid interactions it appeared earlier and reached a higher value as compared to the region of lipid-lipid interactions. The absorption intensity (D) and emission intensity (F) of tryptophan in membrane proteins started to decrease at the same concentrations and attained a maximum also at the same concentrations (Fig. 9). Thus, our results revealed a cooperative nature of changes in erythrocyte membranes under the action of androsterone. Addition of testosterone produced similar changes in membrane microviscosity. In the region of protein-lipid interactions, microviscosity increased at lower concentrations of hormone and attained higher values as compared to the region of lipid-lipid interactions (Fig. 14). In both cases, the revealed structural changes were initiated in proteins and carried over to lipids by virtue of cooperativity. The effect of DHEA and especially DHEAS on erythrocyte membranes is much less pronounced as compared to testosterone (Figs. 15, 16). DHEA and DHEAS increased microviscosity by 10% with respect to initial values. In these experiments, the concentration of DHEAS reached 8106 M. For DHEA, the growth started at a hormone concentration of 5107 M and attained its maximum at 1.5106 M (Fig. 15). Alteration of viscosity was described by S-curve and correlated with a decrease in fluorescence and absorption of tryptophan (Fig. 11). The latter processes started at the same hormone concentrations and

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 285

reached their minima also at the same concentrations. Microviscosity in the region of protein-lipid interactions increased earlier, at lower concentrations of hormone, and was more pronounced than in the region of lipid-lipid interactions. Structural changes were initiated in proteins and involved lipids due to cooperativity.

Figure 13. Changes in the relative microviscosity of membranes (A)/(0) of erythrocyte shadows at the concentration A of androsterone hormone. Concentration of shadows C = 0.133 mg protein/mL. Line 1 shows changes of the region of lipid-lipid interaction; line 2 the region of protein-lipid interaction.

Figure 14. Changes in the relative microviscosity of membranes (A)/(0) of erythrocyte shadows at the concentration A of testosterone hormone. Concentration of shadows C = 0.117 mg protein/mL. 1 - the region of lipid-lipid interaction; 2 the region of protein-lipid interaction.

The mechanism of changes in membrane microviscosity under the action of a more hydrophilic hormone DHEAS is quite different. Microviscosity goes to a constant value at a higher concentration of DHEAS in suspension as compared to that of DHEA (5106 M versus 1.5106 M for DHEA). First changes of microviscosity appeared in the region of lipid-

286 Thermodynamics Fundamentals and Its Application in Science

lipid interactions (Fig. 16), which was followed by an increase of microviscosity in the region of protein-lipid interactions. DHEAS interacted with polar heads of phospholipids, then structural changes carried over to proteins due to cooperativity. Hydrophilic molecules of DHEAS cannot penetrate deep into hydrophobic layer of the membranes. There are only minor structural changes in the spectrin-actin-ankyrin meshwork and weak changes in membrane microviscosity.

Figure 15. Changes in the relative microviscosity of membranes (A)/(0) of erythrocyte shadows at the concentration A of hormone DHEA. Concentration of shadows C = 0.113 mg protein/mL. 1 - the region of lipid-lipid interaction; 2 the region of protein-lipid interaction.

Figure 16. Changes in the relative microviscosity of membranes (A)/(0) of erythrocyte shadows at the concentration A of DHEAS hormone. Concentration of shadows C = 0.290 mg protein/mL. 1 - the region of lipid-lipid interaction; 2 the region of protein-lipid interaction

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 287

6. Change of the membrane microviscosity, and Na+, K+-ATPase activity

Erythrocyte suspensions from fresh blood of rats with hormones of differing concentration were analyzed. For this purpose cortisol and adrenalin were used. Under the action of hormones, the microviscosity of erythrocyte membranes increases following a saturation curve (Fig. 17). This increase depends on the hormone type and differs greatly for protein-lipid and lipid-lipid interactions. As can be seen from Fig. 17, protein-lipid interaction makes a decisive contribution to the increase in membrane microviscosity under the action of hormones. It is due to this contribution that the system of compaction domains is formed in the membrane, resulting in an increase in erythrocyte rigidity. The effect depends strongly on the hormone type. Adrenaline, which penetrates the entire erythrocyte bulk, rapidly increases the erythrocyte microviscosity, and the latter comes to saturation even at small hormone concentrations of 1710-9 M. Cortisol acts on an erythrocyte surface layer alone; hence, the microviscosity reaches saturation only at a cortisol concentration of 60 10-9 M, and the increase in viscosity with cortisol is half as much as that with adrenaline. The most important result concerns the influence of hormones on the activity of the Na+, K+Pase (Fig. 18). For both hormones analyzed, increasing the hormone concentration causes the quantity first to increase, reach its maximum, and then to decrease. The maximum of activity corresponds to the hormone concentration at which the microviscosity reaches saturation. A good correlation is found between the stages of variation in activity and in microviscosity with an increase in the concentration of different types of hormones. Adrenaline, which is responsible for the rapid increase in erythrocyte microviscosity, is responsible as well for the rapid increase in the Na+, K+-Pase activity and for its subsequent fast decline following the maximum (Fig. 18a). Increasing the cortisol concentration (Fig. 18b) causes a slow increase in microviscosity and Na+, K+-Pase activity (), and then a slow decrease in whose value does remain high at a very high hormone concentration. At a 20 10-9 hormone concentration, the activity is 0.05 and 0.03 mol/hmg protein for adrenaline and cortisol, respectively. At the stage of decline in at 60 10-9 hormone concentration, ~ 0.02 and 0.035 mol/hmg protein for adrenaline and cortisol, respectively. The maximum activity in the series of adrenaline and cortisol is observed at their respective concentrations of 3 108 and 5 108 M. Important information on the nature of structural changes produced in erythrocytes by the analyzed hormones was obtained with infrared spectroscopy [14]. The increase in the absorption band intensity of CO- (1655.2 cm1) and NH-bonds (1548 and 3290 cm1) by about 20 % with cortisol points to enhanced ordering of membrane proteins due to the tangle helix structural transition [15]. The shift 3308 3280 in stretching vibrations of the peptide NH-bond and the increase in its intensity owes to the formation of a hydrogen bond between cortisol and NH-bond of proteins. The increase in the absorption band intensity of

288 Thermodynamics Fundamentals and Its Application in Science

the =-bond of phospholipids and its shift 1748 1740 points to enhancement of ordering of higher carboxylic acids and to a decrease in phospholipid entropy.

Figure 17. Changes in the relative microviscosity of membranes (L) of erythrocyte shadows at the concentration A for adrenaline (a) and cortisol (b) hormones added to the shadows suspension. Concentration of shadows C = 0.128 mg protein/ml. Concentration of pyrene in the suspension is 7.710-6 M, temperature of the specimens 309.10.1 K (36C), pH of the suspension 7.35. The measured value of L(A) exhibit an error of 6%. 1 - the region of lipid-lipid interaction; 2 the region of protein-lipid interaction

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 289

Figure 18. Changes in the activity of Na+, K+-ATPase of erythrocyte membranes as a function of a hormone concentration in suspension: a adrenaline; b cortisol.

290 Thermodynamics Fundamentals and Its Application in Science

The concurrent hormone interaction with protein and phospholipids enhances the proteinlipid interactions resulting in a complex domain structure in erythrocytes. The frequency shift of the =-bond toward the short-wave range and the increase in its intensity is associated with dehydration of membranes due to its hormone-induced compressive deformation. It is the loss of bound water that increases the frequency of the P = O-bond [16]. The displacement of water dipoles from protein-lipid domains to adjacent regions leads to the development of mesobands of localized deformation and discontinuities in them. The obtained experimental results suggest that an important role in the action of hormones on erythrocytes belongs to two factors:
-

collective effect of the increase in erythrocyte elastic modulus due to the formation of the domain structure in the region of protein-lipid and lipid-lipid interaction (macroscale); hindered structural transitions in mass transfer processes through a membrane (microscale).

The first factor causes an increase in energy quanta h (phonone) required for structural transitions in mass transfer through erythrocyte membranes. This factor increases the activity of the Na+, K+-Pase at the first stage of growth of hormone concentrations. The second factor retards microscale structural transitions. Once the microviscosity ceases to increase (the formation of the domain structure is completed), the contribution of the first factor no longer grows, the contribution of the second factor continues to escalate, and the activity of the Na+, K+-Pase decreases.

7. Effect of cortisol
Here we try to go beyond the influence of cortisol on the red cell membrane, and consider the action of the hormone on erythrocyte as a multi-layered liquid crystal system. The mechanism of erythrocyte deformation and structural transformation of membranes and hemoglobin by the action of cortisol is still scantily investigated. The interaction of hemoglobin with contraction proteins and band 3 protein of erythrocytes is reported by Discher, D.E., Mohandas, N. & Evans, E.A [17]. These works imply that the disturbance and deformation of erythrocyte membrane caused by cortisol or other external factors can be transferred to hemoglobin by means of band 3 integral protein or contraction proteins. According to modern ideas, contraction proteins reside as at the inner as outside of membrane. Within this concept, a reverse response is also possible, i.e., the disturbance can be transferred from hemoglobin to the cell membrane. The addition of cortisol to erythrocyte suspension with the hormone concentration of 108 to 6108 M produced a set of UV spectral curves. A maximum of absorption band at 418 nm was shown to decrease with increasing the hormone concentration. A decrease in the optical density was 22% as compared to erythrocyte suspension without hormone (control) (Fig. 19). The resulting set of curves was used to plot the dependences of optical density for band 418 nm on the concentration of hormones.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 291

Figure 19. Changes in the optical density of absorption band 418 nm at the addition of cortisol to human erythrocyte suspensions (C = 10-8 6 10-8 M).

An increase in the optical density in the regions of 600-700 and 310 nm, which points to increasing diffusion of light has been also observed. In these regions, optical density changed by ~5.5%, which considerably exceeds the measurement error (0.5%) (Fig. 19). It should be noted that absorption band at 418 nm may shift spontaneously by 2-3 nm in different runs, generally to the short-wave region. Shifting of this band occurs either due to fluctuations in the structure of hemoglobin itself [18] or by the action of fluctuations in the structure of membrane and cell as a whole [19, 20]. The analysis of IR spectra of rat erythrocyte ghosts not loaded with hormone (control, Fig. 7) revealed not only a disordered structure, but also the presence of -helix 1650-1656 cm1 and structure (1686 and 1520 cm1) in the proteins of rat erythrocyte ghosts [1]. N stretching vibrations of proteins (3308 cm1), CH stretching vibrations of hydrocarbon chains in proteins and phospholipids (2948, 2930 and 2848 cm1) as well as some bands typical of phospholipids, in particular, C=O bond (1748 cm1), = bond (1236 cm1), 2 deformation vibrations (1460 and 1386 cm1) of hydrocarbon chains, 4-4-5-5 bond (1048 cm1) of monosaccharides in glycolipids and glycoproteins, and - deformation vibrations (978 cm1) have been recorded. Note that the = band (1736 cm1) is quite narrow; hence it follows that phospholipids are well ordered at the level of ester bonds in higher carboxylic acids and glycerol. Analysis of the IR spectra of rat erythrocyte ghosts upon incubation with cortisol at its concentration of 4.4 . 108 M revealed a ca. 20% increase in intensity of the absorption bands

292 Thermodynamics Fundamentals and Its Application in Science

of CO (1655.2 cm1) and NH bonds (1548 and 3290 cm1), the effect building up with an increase in the hormone concentration (Table 3, Fig. 20). A growing intensity of the band 1655.2 cm1 testifies an increase in the fraction of -helix [8]. The increasing fraction of helices in membrane proteins is related with the structural transition tangle -helix. A shift of N bond (stretching vibrations of peptide bond, 3308 3280 cm1, = 28 cm1) was accompanied by a growth of its intensity, which is related with the formation of hydrogen bond between cortisol and N group. Hydrogen bond is likely to form between keto group of A-ring (C3=) and N group of the membrane protein. Meanwhile, keto group (C20=) of D-ring and OH group at 11 in C-ring could also be involved in the formation of hydrogen bonds. The presence of several hydrophilic groups strongly changes the biological activity of cortisol and other steroid hormones, in distinction to cholesterol. Cholesterol binds to phospholipids mainly due to hydrophobic interaction (Van der Waals forces) with fatty acid residues [19]. Shifting of CH bond stretching vibrations 2848 2852 cm-1 ( = 4 cm-1) and 2930 2925 cm-1 ( = 5 cm-1) were observed. The latter increased in intensity under the action of hormone. Changes in intensity of this band confirm the presence of structural transition, but cannot differentiate the place where the transition occurs in membrane proteins or in phospholipids, as CH bond is present both in proteins and phospholipids. However, as seen from our experimental data, this band reflects mainly the changes in phospholipid orderliness. An increase in intensity of the absorption band of phospholipid C=O bond and its shift 1748 1740 cm1 were observed. This increase of the band intensity indicates a growing orderliness of higher carboxylic acids and a decreasing entropy in phospholipids. Shift of the band is related with the formation of hydrogen bond between hormone, for example OH group at C21, and CO bond of phospholipids. Such interaction of the hormone simultaneously with protein and phospholipids can occur at the interface between protein and phospholipids, i.e., in a near-boundary or annular layer of the band 3 integral protein, glycophorin and other proteins. P=O bond shifted in frequency by 3 cm1 to the short-wave region and increased in intensity. Shifting of P=O bond to the short-wave region is attributed to dehydration of membranes during their deformation under the action of hormone. A loss of bound water increases the frequency of P=O bond [1]. Deformation (contraction) occurs due to spectrin-actin and spectrin-ankyrin networks [19], since the extraction of spectrin from membrane relieves the deformation caused by hormones. It should be noted that 30% of membrane proteins is represented by spectrin. Overall, contraction proteins constitute 55-60% of all membrane proteins [21]. Steroids can attack either the spectrin-actin-ankyrin network located both on internal and external surfaces of the membrane or the integral proteins associated with contraction proteins [22]. Our FTIR spectroscopy study of the hormone effect on intact erythrocytes revealed considerable changes of the spectra in absorption regions both of proteins and phospholipids. In particular, cortisol gave rise to absorption band 1636 cm1 corresponding to -structure of membrane proteins, which indicates a transformation in the secondary

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 293

structure of membrane proteins (tangle -structure transition) involving also the contraction proteins. Shifting of some other absorption bands attributed both to proteins and phospholipids was observed too (Fig. 21). Noteworthy are the shift of absorption band 2870 cm1 corresponding to stretching vibrations of CH bond in hemoglobin [23], and a more pronounced splitting in the region of stretching and deformation vibrations of phospholipid CH orderliness in and between the domains. A stronger splitting of CH bonds testifies the formation of new lipid-protein clusters as a result of intermolecular interaction, due to compaction of membrane elements caused by structural transformation of the contraction proteins network. In our earlier studies of high density lipoproteins (HDL), when calculating the enthalpy of structural transitions from experimental data, the occurrence of smectic A smectic C transition in HDL phospholipids [8] has been suggested. Such a transitions may occur here, since it has a low enthalpy [8, 24]. Of interest is the appearance of the absorption band 2851.8 cm1, which is assigned to stretching vibrations of CH bond in phospholipids [8]. This band results from structural transition in membrane phospholipids. No. The object of CO measurement Ghosts 1655,4 (control) 1686 2 Ghosts + cortisol (C= 4,410-8 M) Ghosts + cortisol (C= 10-7 M) Erythrocytes (control) 1655,2

NH val.
3308

C=O
1748

P=O
1236

P-O-C
1080

05C4-C504 CH val.
1056 2948 2930 2848 2924,2 2848,9 2962 2925 2852 2956,8 2935,8 2871,7 3030,2 2956,6 2937,5 2872,3 3028,4 3052,4

ACO 1,2150E + 01 1,5169E + 01 1,5640E + 01

3290,4 3308.0 3280 3300 3282,1 3272,0

1743 1740

1236

1080

1051,2

1656,0 1630 1649,9

1239

1083,7

1245,7

1106,2

Erythrocytes + 1642,7 cortisol 1627,5 (C= 10-8 M)

3285,3 3270,2 3247,3

1741,1 1707,5

1239,4 1201,3

1100,0 1089,5

1060,2

Note. ACO is the integral intensity of absorption band CO of the peptide bond in semilogarithmic form.

Table 3. Frequency characteristics of human erythrocytes and rat erythrocyte ghosts before and after their interaction with hormones

294 Thermodynamics Fundamentals and Its Application in Science

Figure 20. IR spectraof rat erythrocyte ghosts at the addition of cortisol (C = 4.4 10-8 M): a. - = 1000 1800 cm-1, b. - = 2600 3400 cm-1.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 295

Figure 21. FTIR spectra of human erythrocytes at th addition of cortisol (C = 3 10-8 M): a. - = 1000 1800 cm-1, b. - = 2600 3400 cm-1.

Splitting in the region of 1088 ( bond) and 3282 cm1 (NH bond) was observed. Splitting of these bands indicates an increasing orderliness in phospholipids and membrane proteins,

296 Thermodynamics Fundamentals and Its Application in Science

respectively. An increase in the fraction of -structure points to the tangle -structure transitions; however, in this case more pronounced is the -helix -structure transition, due to redistribution of intensity between absorption bands at 1650 and 1638 cm1. The first band corresponds to -helices, the second one to -structure [19]. Using the fourth derivative of the absorption band 1600-1700 cm-1 the maintenance of elements of the secondary structure in the erythrocyte membranes has been calculated. The results are given in Table 4. This table shows the considerable increase of -structure under the action of adrenaline. In this case we observe the structural transition tangle -structure. However, the increase of -helices and decrease of tangle under the action of cortisol has been seen. So it can be concluded the structural transition tangle -helix took place. A comparison of IR spectra obtained from ghosts and intact erythrocytes revealed some general regularities: 1) splitting of absorption bands of NH peptide bonds, 2) an increased intensity of absorption bands corresponding to -structure, 3) splitting of absorption bands corresponding to CH bonds of phospholipids, 4) a frequency shift of some bands (Table 4). However, there is also a distinction related with the appearance of absorption bands at 2870 and 1108 cm1 corresponding to hemoglobin [23]. These bands are shifting when erythrocytes are subjected to the action of hormones. Conformation Erythrocyte (control) 25% 25% 25% Erythrocyte + cortisol Ccortis = 3 10-8 M 48% 30% 22%

-helical -structure Random coil

Table 4. The quantitative definition of the elements of secondary structure in membrane proteins

Thus, these results suggest that the erythrocyte react to the effect of steroid hormones as a complex liquid-crystalline co-operative system in which nanostructured transitions are irreversible and are closely associated with the functional activity of cells.

8. Thermodynamics of nanostructural transitions in erythrocyte as a liquid crystal system, a relation with the cell function
The application of IR and UV spectroscopy showed that the interaction of steroid hormones with erythrocytes increases the ordering of both the membranes and hemoglobin, which means an increase in negentropy. E. Schrodinger defined it as S = k lg (1/D), (11)

where S is the negative entropy, or negentropy; k is the Boltzmanns constant equal to 3.2983 1024 cal/deg; D is the quantitative measure of disorderliness of atoms in the system, lg (1/D) is the negative logarithm of D, and 1/D is the measure of orderliness.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 297

However, of prime importance for us is that increasing negentropy is always supported by increasing amount of structural information. This can be expressed by the following equation: -S = k lg(1/D) + pi log pi (12)

where pi is the probability of individual events in the system. Thus, the informational component in this equation determines an increase of negentropy in the system and is related with acquisition of new properties. Developing the concept about a correspondence between negentropy and structural information, we can present the following equality: -S = k lg(1/D) = pi log pi Hence, lg (1/D) = (pi log pi)/k, and
1 / D 10 D 10 ( p log p ) / k i i , then

(13)

(14) (15) (16)

( p log p ) / k ( p log p ) / k i i i i or 1 / 10

If in the Helmholtz equation for free energy entropy is replaced by D, this gives the following expression:

F U

T p log p / k i 10 i

(17)

Thus, F can be considered as a function of the amount of structural information in a system. This equation is essential for understanding the self-organization processes in living systems, so as the cell. An increase in the amount of structural information determines the transition from liquid crystal to crystal. This may incapacitate a cell from its functioning. It has been already shown that the interaction of steroid hormones increases microviscosity of erythrocyte membranes in the regions of lipid-lipid and protein-lipid interactions. At low concentrations of hormones in the incubation medium, the activity of erythrocyte Na+,K+Pase even increases, probably due to growing elasticity of the lipid microenvironment of the enzyme, which facilitates structural transitions in the enzyme itself. At high concentrations of hormones (the saturation phase), an increase in microviscosity in the region of lipid-protein interactions makes impossible structural transitions in the enzyme; so, its activity rapidly drops. This determines a dome shape of the enzyme activity curve. Since erythrocyte is a liquid crystal cooperative system, changes occur not only in the activity of Na+,K+-Pase of erythrocyte membranes, but also in the state of cell hemoglobin, its ordering and ability to bind oxygen.

298 Thermodynamics Fundamentals and Its Application in Science

It seems interesting to compare changes in liquid crystals with those occurring in solid crystals in the fields of external action. Destruction of solid and liquid crystals increases the molar volume [24, 25]. A dependence of the Gibbs thermodynamic potential F() on the molar volume taking into account local zones of different scale stress concentrators is described by the equation: F() = U TS + p - iCi, where i chemical potential, Ci concentration (Fig. 22, [26]) . At critical values of molar volume i = (1,26), the thermodynamic potential F() has local minima. They reflect local nonequilibrium potentials in the zones of different scale hydrostatic tension. Critical values of i correspond to different levels of homeostasis in a deformable solid: 0 is an equilibrium crystal; the initial level of homeostasis; 1 are the zones of stress microconcentrators where dislocation cores are generated; the next level of homeostasis; 2, 3 are the zones of stress meso- and macroconcentrators where local structural-phase transitions with the formation of meso- and macrostripes of local plastic deformation take place; the next levels of homeostasis; 4 corresponds to intersection of curve F() with the abscissa. At a further increase of the local molar volume, changes of the Gibbs thermodynamic potential proceed under the conditions of F() 0, and the system becomes unstable. Various forms of material failure appear; solid crystal starts to behave as a liquid one. 6 the existence of two phases is possible: at = 5 the vacancy phase atom, at 6 different thermodynamic levels of the crystal lattice in a deformable solid, different levels of its homeostasis. Thus, plastic deformation of solid and liquid heterocrystals in the fields of external action is a multilevel process of their destruction, with the corresponding levels of crystal lattice selforganization and levels of its homeostasis, i.e., the destruction via different phases of strengthening (self-organization). On solid crystals this decreases the orderliness and amount of structural information. In liquid crystals this increases the orderliness and amount of structural information i.e. liquid crystal crystal transition. Dependence of Gibbs thermodynamic potential on the molar volume and changes in the structural information (I), taking into account local zones of stress concentrators is determined by the expression: (18)

F( , I ) U T / 10

( p log p ) / k i i p C i i

(19)

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 299

These quantitative interrelations underlie transition of the system to a new structural level of homeostasis.

Figure 22. The dependence of the Gibbs thermodynamic potential F (v) from the molar volume v in the light of local zones of stress concentrators of different scales [26].

In biological membranes as liquid crystals, destruction is related with structural transitions and is generally accompanied by increasing structural orderliness (the order order transition). Earlier [1], it was shown that the action of steroid hormones on erythrocyte membranes disturbs the mechanisms of self-organization that operate in the cells in normal functional condition. The active CO, NH and OH groups of stress hormones interact with CO and NH groups both of proteins and phospholipids in biological membranes. This leads to the formation of complex protein-lipid clusters, where compressive hydrophobic interactions are reinforced. Molecularly bound water is displaced to adjacent regions. Here, hydrostatic forces increase the tensile tangential stresses. Mobile nanostructural boundaries are formed, along which the biological membranes are destructed. This results in the formation of numerous pores and mesostrips of plastic deformation. In terms of physical mesomechanics, these transformations resemble those developing in solid crystals in the fields of external action (Fig. 23). However, in biological membranes such selforganization may be related even with increasing order and decreasing entropy, but this is incompatible with conditions that determine cell viability. Structural transitions cover the membrane-bound enzymes, transmembrane carriers and hormone receptors. It is reasonable to say that cell membranes go to a new level of homeostasis (self-organization) which is incompatible with life. The nature of life implies dynamics. The cell dies. Here, one can tell about thermodynamic features related with changes in the structure and function (properties) of solid crystals and biological membranes in the fields of external action.

300 Thermodynamics Fundamentals and Its Application in Science

Various structural transitions (phase transitions, nanostructural, etc.) strongly contribute to the functional activity of a cell. These are the transitions like smectic A smectic C, smectic cholesteric, and nematic isotropic state; in proteins, the transitions tangle structure and tangle -helix. They all affect the vital characteristics of a cell. I. Prigogine believed that there is a wonderful analogy between instability of nonequilibrium origin and phase transitions [27]. This problem is of great interest and deserves special examination. Thus, on the curve of thermodynamic Gibbs potential versus molar volume F(), solid crystals fall in the region of strongly negative values, whereas liquid crystals are located near zero. Structural transformations taking place in the fields of external action draw together the positions of liquid and solid crystals on the functional curve. Morphologically, the destruction patterns of crystals are quite similar (Fig. 9a and b). Thermodynamically, cells as hierarchic multilevel liquid crystal systems can function only near a zero value of thermodynamic Gibbs potential, i.e. in the region where reversible nanostructural transitions underlying life processes can occur.

Figure 23. a Atomic force microscopy. The surface of rat erythrocytes after adsorption of cortisol. Concentration of the hormone is 10-6M. Deep meso-bands with bifurcation are seen; b Formation of micropore chains along localized-deformation shear-bands. Plate of high-pure aluminum 180 nm thick glued on flat specimen of commercial Al. Alternative bending, = 293 ; cycle number N = 17.55106 [26].

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 301

Biomembranes are of vital importance in the processes of self-organization of cell metabolism. These processes are transport of organic compounds through cell (plasma) membranes with delivery of nutrients to the cell and removal of their decay products (metabolism); diffusion of gases (O2, CO2) through a cell membrane; passive and active ion transport and production of electrochemical potential on the outer and inner surfaces of plasma membranes, and many others. All membranes are liquid crystals. Their behavior in an organism obeys physicochemical laws. The mechanism of their self-organization is the same as that of multilevel systems. Multilevel systems mean the hierarchy of scales of shear stability loss of the internal structure of a loaded material in local regions at the nano-, micro-, meso- and macrolevels [26]. In liquid crystals, this is associated with lipid-lipid, protein-lipid, and protein-protein interactions, i.e. with cooperative behavior of a liquid crystal as a system. The ordering of these crystals as well as the nature of their components is determined by covalent and hydrogen bonds, weak electrostatic and hydrophobic interactions. Shear stability loss of natural liquid crystals depends on structural phase transitions such as the formation of smectic, cholesteric, nematic and isotropic structures and transitions between them. For membrane-bound proteins, states like - helix, -structure and chaotic coil are of significance. Structural transitions can be reversible and irreversible. In the latter case, defects are accumulated in liquid crystals, making some functions of the cell membranes unrealizable. The cell dies. These transitions, as a rule, arise on the surfaces of cell membranes and, because of cooperativeness, go deep into their lower levels. They can be also initiated at the inner membrane or particle interfaces and can be related to lipids and proteins. Thus, the case in point is different thermodynamic states of liquid crystals. The low transition enthalpy suggests that the transitions involve low-energy bonds, mainly hydrogen bonds, weak electrostatic and hydrophobic interactions. The external factors capable of changing (disrupting) the interactions are also physicochemical in nature. Among these factors are variations in temperature, pH, electrolyte content, etc. However, they are all of no fundamental character, and the behavior of liquid crystals under external actions fit in the same concept as the behavior of solid crystal does. It is very important for medicine. As indicated in the report of World Health Organization, cardiovascular pathology, infections and oncological diseases are three main causes of human mortality all over the world [28]. Cardiovascular diseases stand first in this short list. In 2005 they killed 17.5 million people, which constitutes 30% of all deaths in the world. WHO predicts that in 2015 these diseases may take away the lives of 20 millions people. This will be caused mainly by infarctions and strokes, i.e. acute tissue hypoxia.

9. Conclusion
Especially dangerous is myocardial ischemia, which is related with the formation of atherosclerotic plaques within the coronary arteries and a considerable decrease in the blood flow rate. Such mechanism of tissue hypoxia development is typical of the older age groups. However, this pathology may develop also by a different mechanism. Nowadays acute

302 Thermodynamics Fundamentals and Its Application in Science

myocardial ischemia and coronary deficiency are often observed in young people. There are many cases of sudden death that occur in young sportsmen during the competitions [29]. Coronary arteries of sportsmen are free of plaques, nevertheless, acute coronary deficiency develops somehow. Stress hormones and steroid anabolics may be a possible reason. Today the world is changing very rapidly, and not everybody can adjust to these changes. Chronic stress becomes a wide-spread phenomenon [18]. Such reaction may be very pronounced in anxious persons. This is why cardiac syndrome X is often diagnosed now. Its clinical characteristics include angina chest pain with exertion and ischemic type ST segment depression on electrocardiogram, without angiographic signs of coronary artery stenosis and with normal left ventricle function. It means that acute coronary deficiency of obscure etiology occurs not only in sportsmen, but also among people at large [30]. Cortisol is the main stress hormone. It is a cholesterol derivative, and cholesterol is the essential component of all cell membranes. Of special interest is the erythrocyte membrane. Erythrocyte is a specialized cell that transfers oxygen from lungs to tissues by means of hemoglobin (b). In capillaries, oxyhemoglobin bO2 decomposes, and O2 diffuses to the organ and tissue cells. The first obstacle to such diffusion is erythrocyte membrane. Changes in the properties of erythrocyte membrane determine the rate of oxygen diffusion across the membrane. Besides, capillary and erythrocyte may have comparable diameters. Sometimes the erythrocyte diameter happens to be even larger. To go through so small capillary, erythrocyte should have a high plasticity. Structural transformations in erythrocyte membrane under the action of stress hormones may be reflected not only in its plasticity, but also in the mechanism of gas exchange. In this work, an attempt to elucidate the effect of steroid hormones on the structure of erythrocyte membranes and their physicochemical properties, i.e. the introduction of principles and regularities of physical mesomechanics in biology and medicine provides a deep insight into the mechanism interrelating structure and function of biological membranes, both in the norm and at systemic membrane pathology (upon variation of hormone concentration, temperature, pH, electrochemical potential, etc. has been made. Thus, from a thermodynamic standpoint, life is the ability of cells to undergo reversible nanostructural transitions near a zero value of thermodynamic Gibbs potential. A loss of this ability leads to cell death and development of pathology.

Author details
L.E. Panin Scientific Research Institute of Biochemistry SB RAMS, Russia

Acknowledgement
The author is grateful to Dr. Sci. (med.) V.G. Kunitsyn and Ph. D. (phys.-math.) P.V. Mokrushnikov for participation in the preparation of experimental material.

Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 303

10. References
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304 Thermodynamics Fundamentals and Its Application in Science

[17] Discher, D.E., Mohandas, N. & Evans, E.A. (1994). Molecular maps of red cell deformation: hidden elasticity and in situ connectivity. Science. Vol. 266. No. 5187, (Nov. 1994) pp. 1032-1035. ISSN 0036-8075. [18] Shnol, S.E. (1979) Physicochemical factors of biological evolution, Nauka, Moscow (Rus.) ISBN 978-91-85917-06-8. [19] Kunitsyn, V.G. (2002). Structural phase transitions in erythrocyte membranes, lipoproteins and macromolecules. Thesis, Dr. Sci. (biol.), Novosibirsk. (Rus.) [20] Park, Y.; Best, C.A.; Badizadegan, K., Dasari, R.R.; Feld, M.S.; Kuriabova, T.; Henle, M.L.; Levine, A.J. & Popescu, G. (2010). Measurement of red blood cell mechanics during morphological changes. Proc. Natl. Acad. Sci. U S A. Vol. 107. No. 15, (Apr. 2010) pp. 6731- 6736. ISSN 0027-8424 [21] Bennett, V. (1984) In: Cell Membranes: Methods and Reviews, eds. Elson, E., Frazier, W. & Glaser, L. Vol. 2, Plenum, New York, pp. 149-195. [22] Storozhok, S. A.; Sannikov, A. G. & Zakharov, Yu. M. (1997) Molecular Structure of Erythrocyte Membranes and Their Mechanical Properties, Tyumen Gos. University: Tyumen. [23] Wolkers, W.F.; Crowe, L.M.; Tsvetkova, N.M.; Tablin, F. & Crowe, J.H. (2002). In situ assessment of erythrocyte membrane properties during cold storage. Mol. Membr. Biol. Vol. 19. No. 1, (Jan-Mar 2002) pp. 59-65. ISSN 0968-7688 [24] Panin, L.E. & Kunitsyn, V.G. (2009). Mechanism and thermodynamics of multilevel structural transitions in liquid crystals under external actions. Physical Mesomechanics, Vol. 12. No. 1-2, (Jan. Apr. 2009) pp. 78-84. ISSN 1029-9599 [25] Panin, L.E. (2011). Thermodynamics and mesomechanics of nanostructural transitions in biological membranes under the action of male sex hormones. 13-th International conference on mesomechanics. Vicenza, Italy, 6-8 July 2011. Eds. G.Sih, P. Lazzarin, F. Berto. p. 48-51. [26] Panin, V.E. & Egorushkin, V.E. (2008). Nonequilibrium thermodynamics of a deformed solid as a multiscale system. Corpuscular-wave dualism of plastic shear. Physical Mesomechanics. Vol. 11. No. 3-4, (May - August 2008) pp. 105 123. ISSN 1029-9599. [27] Nicolis, G. & Prigogine, I. (1979). Self-Organization in Non-Equilibrium Systems. From Dissipative structures to Order through Fluctuations, Mir, Moscow, Russia. [28] Vermel', A.E. (2006). Cardiac syndrome X. Klin Med (Mosk). Vol. 84. No. 6 (Nov.Dec. 206) pp. 5-9. ISSN 0023-2149. Russian. [29] Montagnana, M.; Lippi, G.; Franchini, M.; Banfi, G. & Guidi, G.C. (2008). Sudden cardiac death in young athletes. Intern Med. Vol. 47, No. 15, (Aug. 2008) pp. 1373-1378, ISSN 0918-2918 [30] Panin, L.E. & Usenko, G.A. (2004). Anxiety, adaptation and prenosological clinical examination. SB RAMS, Novosibirsk, ISBN 5-93239-050-6 (Rus.)

Chapter 12

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts

Yu Liu and Kui Wang
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51406

1. Introduction
Cyclodextrins (CDs), a class of macrocyclic oligosaccharides consisting of six, seven, or eight glucose units linked by -1,4-glucose bonds, have been widely used as receptors in molecular recognition in the field of supramolecular chemistry because they are able to form inclusion complexes with hydrophobic guests in aqueous solution owing to their hydrophilic outer surface and their lipophilic cavity [13]. Therefore, much effort has been devoted to the design and synthesis of a wide variety of cyclodextrin (CD) derivatives to explore their binding behaviors for model substrates [4]. In order to further explore their inclusion complexation mechanism, most of these studies have been focused on the binding modes and complexation thermodynamics based on CDs and their derivatives in recent years [5]. Among the numerous guests researched, bile salts attracted much more attention because they are one kind of important surfactant-like biological amphipathic compounds possessing a steroid skeleton, which have distinctive detergent properties and play an important role in the metabolism and excretion of cholesterol in mammals [6]. For example: the thermodynamics and structure of inclusion compounds of glyco- and tauro-conjugated bile salts with CDs and their derivatives have been studied by Holm et al. during the last years [711]; the interactions of different kinds of bile salts with -CD dimers linked through their secondary faces have been investigated by Reinhoudt and Vargas-Berenguel et al. [12 14]. It has been demonstrated that the formation of inclusion complexes between CDs and guest molecules is cooperatively governed by several weak forces, such as van der Waals interactions, hydrophobic interactions, hydrogen bonding, electrostatic interactions, and every weak force does its contribution to the complexation. In this chapter, the related investigations concerned on the binding modes, binding abilities, molecular selectivities and their thermodynamic origins of CDs and their derivatives with four typical bile salts (Cholate (CA), Deoxycholate (DCA), Glycocholate (GCA), and Taurocholate (TCA)) (Figure
2012 Liu and Wang, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

306 Thermodynamics Fundamentals and Its Application in Science

1) have been summarized, which will be discussed from the aspect of the types of host molecules: (1) natural CD series; (2) modified CD series; (3) bridged CD series. This summary is helpful to improve understanding of the correlation between the structural features and molecular-recognition mechanism from thermodynamic viewpoints, and further guide its biological, medicinal and pharmaceutical applications in the future.

Guests Cholate (CA) Deoxycholate (DCA) Glycocholate (GCA) Taurocholate (TCA)

R1 OH H OH OH

R2 COONa COONa CONHCH2COONa CONHCH2CH2SO3Na

Figure 1. Molecular structures of four typical bile salts

2. Natural CD series
2.1. Binding modes for bile salts and natural CD series
Since two protons located closely in space (the corresponding internuclear distance is smaller than 34 ) can produce NOE (Nuclear Overhauser Effect) cross-peaks between the relevant protons in NOESY (Nuclear Overhauser Effect Spectroscopy) or ROESY (Rotating Frame Overhauser Effect Spectroscopy) spectra, 2D NMR spectroscopy has become an important method for the investigation of the interaction between different kinds of CDs and guest molecules. It is well-known that only H3, H5, and H6 of CDs can give cross-peaks for analyzing hostguest interactions, as H2 and H4 are not facing to the inner cavity and H1 is affected by D2O. For example, the ROESY study on the resulting complex of natural -CD 1 (Figure 2) with CA has been reported by Tato et al. [15,16]. The results successfully indicated that in the 1:1 complex between 1 and CA the steroid body entered forward into the inner cavity of 1 by the side of the secondary hydroxyl groups, with the side chain folded toward the steroid body, i.e., rings D and C are totally and partially included, respectively. Therefore, the binding modes of bile salts with different kinds of CDs have been widely deduced by 2D NMR spectroscopy during the last years.

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 307

Figure 2. Structure of natural -CD

2.2. Complexation thermodynamics for bile salts and natural CD series

The microcalorimetric titrations can be used to simultaneously determine the enthalpy and equilibrium constant from a single titration curve. Titrations were performed below the critical micelle concentration of bile salts. In each run, a solution of the host (guest) molecules in syringe was sequentially injected into the calorimeter sample cell containing a solution of guests (hosts). Each addition of hosts (guests) into the sample cell gave rise to a heat of reaction, caused by the formation of inclusion complexes between hosts and guests. The heats of reaction decrease after each injection because less and less molecules in cell are available to form inclusion complexes. A control experiment was performed to determine the heat of dilution by injecting a host (guest) solution into a pure solution containing no guest (host) molecules. The dilution enthalpy was subtracted from the apparent enthalpy obtained in each titration run, and the net reaction enthalpy was analyzed by using the one set of binding sites model. This model will work for any number of sites N if all sites have the same Ks and H. In this case, the total heat Q was fitted via a nonlinear least-squares minimization method to the total host concentration in cell (Mt) using the following equation: Q = (NXtHVo/2){1 + Mt/(NXt) + 1/(NKSXt) {[1 + Mt/(NXt) + 1/(NKSXt)]2 4Mt/(NXt)}1/2} (1) where N is the number of binding sites of host, Xt is the total concentration of guests in cell and Vo is the cell volume. The value of Q above can be calculated (for any designated values of N, K, and H) at the end of the ith injection and designated Q(i). Then the correct expression for the heat released, Q(i), from the ith injection is Q(i) = Q(i) + dVi/(<ital> Vo){[Q(i) + Q(i 1)]/2} Q(i 1) (2)

where dVi is the volume of titrant added to the solution. Along with obtaining of Ks and H in this fitting program, the N value in eq 1 can also be obtained, which represents the numbers of guests bound to one host molecule. The ORIGIN software (Microcal), used for the calculation of the binding constant (Ks) and standard molar reaction enthalpy (H) from the titration curve, gave the relevant standard derivation on the basis of the scatter of data points in a single titration experiment. The binding

308 Thermodynamics Fundamentals and Its Application in Science

stoichiometry was also given as a parameter when fitting the binding isotherm. Knowledge of the binding constant (Ks) and molar reaction enthalpy (H) enabled the calculation of the standard free energy of binding (G) and entropy change (S) according to G = RT lnKS = H TS where R is the gas constant and T is the absolute temperature. The microcalorimetric experiments of natural -CD 1 with bile salts (CA, DCA, GCA, and TCA) showed typical titration curves of 1:1 complex formation [17]. The stoichiometric ratios observed from curve-fitting results of the binding isotherm fell within the range of 0.91.1. This clearly indicated that the majority of the inclusion complexes had a 1:1 stoichiometry of bile salts and 1. Thermodynamically, the binding behaviors of bile salts by 1 were entirely driven by favorable enthalpy changes accompanied by small unfavorable entropy changes, which are attributed to the predominant contribution of the van der Waals interactions arising from the size/shape fit and geometrical complement between host and guest and to the accompanying decreases in translational and structural freedoms upon complexation. As can be seen from Table 1, the enthalpy change for the complexation of 1 with DCA is more favorable than that with CA, which directly contributes to the increased complex stability. It is reasonable that DCA possesses a more hydrophobic structure due to the absence of C-7 hydroxyl group as compared with CA, as a result, it is easier to bind into the cavity of 1, which leads to more favorable hydrophobic and van der Waals interactions and gives larger enthalpy and entropy changes. However, the enhanced favorable entropy gain by the desolvation effect may be canceled by the unfavorable entropy change caused by the structural freezing of the resulting complexes of 1 and DCA. Therefore, the stronger interaction between 1 and DCA only shows the larger negative enthalpy change, directly contributing the relatively larger complex stability constant. Meanwhile, 1 shows a lower binding ability upon complexation with GCA and TCA. Compared with 1 and CA, the complexation of 1 with GCA and TCA exhibit similar enthalpy changes but much more unfavorable entropy changes. The more polar side chains of GCA and TCA may be the reason for it. (3)

3. Modified CD series
3.1. Binding modes for bile salts and modified CD series 3.1.1. Aminated -CDs
The ROESY study on the resulting complex of 2 (Figure 3) with CA has been reported by Tato et al. [15]. The results exhibited different interactions of the side chain of CA with H5 and H6 of 2 from natural -CD 1. The facts indicated that the side chain was unfolded, with the negative carboxylate group moving toward the positive protonated amino group, and the side-chain elongation produced a deeper penetration of the steroid body in the inner cavity of 2.

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 309

The ROESY experiments of modified -CD 3 in the presence of CA or DCA have been performed in D2O by Liu et al. [17]. The results indicate that the D-ring of CA is accommodated shallowly in the cavity and CA enters 3 from the second side of CD with the side chain and D-ring. At the same time, the side chain with the negative carboxylate group of CA moves toward the positive protonated amino group of 3. For the resulting complex of DCA3, the ROESY spectrum exhibits entirely different NOE cross-peaks and the D-ring of DCA is included within the cavity of CD from the primary side of CD. Meanwhile, the ethide protons of chiral tether interact with H6 of CD. 2D ROESY NMR experiment of 5 and CA has also been performed by Liu et al. in D2O to investigate the binding mode between bile salt and CD [18]. The results show that steroid body enters the CD cavity from the second side with its tail and D-ring parts.

3.1.2. Nucleobase-modified -CDs

In host 8, the adenine group is deeply inserted into the -CD cavity with an orientation parallel to the C7 axis of -CD while the thymine and uracil groups are shallowly inserted in the -CD cavity with an orientation perpendicular to the C7 axis of -CD [19]. As a result, upon complexation with DCA guest, the deeply included adenine group in host 8 should be expelled from the cavity upon complexation with DCA guest, however, the shallowly included thymine and uracil groups in hosts 9 and 10 are hardly influenced by the inclusion of DCA guest.

3.1.3. Tryptophan- and Tyrosine-modified -CDs

The binding modes of L/D-Trp--CD (11 and 12) with bile salts have been examined by Liu et al. by 2D ROESY NMR experiments [20]. For L-Trp--CD (11), the results show that in the absence of guest, L-Trp residue is only shallowly included or perching on the rim of the CD cavity. However, in the presence of DCA, the D-ring of DCA is close to the wide end of CD cavity, and the D-ring of DCA and the side chain is co-included in the same cavity from the primary side of 11. For D-Trp--CD (12), the 2D NMR results indicate that the D-Trp residue attached to -CD is more deeply self-included than the corresponding L-Trp residue in the absence of guest. However, in the presence of DCA, the carboxylate side chain and D-ring of DCA penetrate into the CD cavity from the secondary side shallowly. The binding modes of L/D-Tyr--CD (13 and 14) with bile salts have further been examined by Liu et al. by 2D ROESY NMR experiments [21]. The results show that the L-tyrosine moiety was self-included in the -CD cavity from the narrow opening. The DCA guest entered the CD cavity from the wide opening with the tail and the D ring and coexisted with the Ltyrosine substituent in the -CD cavity to form a cooperative inclusion manner. For Dtyrosine-modified -CD (14), the D-tyrosine substituent was deeply self-included in the -CD cavity and might be located in the center of the -CD cavity. Upon complexation with DCA, the D-tyrosine substituent of 14 would partially move out of the -CD cavity. Compared with DCA + 13 complex, DCA penetrated into the -CD cavity of 14 more deeply (Figure 4).

310 Thermodynamics Fundamentals and Its Application in Science

Figure 3. Structures of mono-modified -CD derivatives

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 311

Figure 4. The possible binding modes of 1114 (11 (c); 12 (d); 13 (a); 14 (b)) with DCA

3.2. Complexation thermodynamics for bile salts and modified CD series 3.2.1. Aminated -CDs
The microcalorimetric experiments of aminated -CDs with bile salts clearly indicate that the majority of the inclusion complexes had a 1:1 stoichiometry [17]. Thermodynamically, the binding constants of 4 upon inclusion complexation with DCA, GCA, and TCA are less than that with natural -CD 1. It is reasonable that modified -CD 4 decreased the microenvironment hydrophobicity of natural -CD cavity due to the hydrophilic carboxylic group in the sidearm, and at the same time there is electrostatic repulsion between the anionic carboxylate at the sidearm of 4 and anionic carboxylate or sulfonate of bile salts. Unexpectedly, the resulting complex stability of aminated -CD 4 with CA is higher than that of native -CD 1, which is mainly attributed to the more favorable enthalpy change. The possible reason may be the enhanced cooperative van der Waals, hydrogen-bonding, and electrostatic interactions exceeding the decreased hydrophobicity of the interior of -CD 4. Positively charged monoamino-modified -CD 2 and modified -CD 3 possessing an additional binding site in the chiral arm evidently enhance the molecular binding ability and selectivity towards CA and DCA compared to those for native -CD 1, which is mainly attributed to the more favorable enthalpy change accompanied with unfavorable entropy change [17]. The more favorable enthalpy change most likely originates from effective electrostatic interactions and the additional binding site of hydroxyl group. In addition, the

312 Thermodynamics Fundamentals and Its Application in Science

unfavorable entropy change is likely to originate from the conformation fixation of host and guest and the rigid complex formation upon complexation. -CD derivatives 2 and 3 give a lower binding ability upon complexation with GCA and TCA as compared to the complexation with CA and DCA, which is similar to that for the complexation of -CD 1 and derivative 4. For the same reason, the more polar side chains at C23 for GCA and TCA remarkably affect their binding thermodynamics. A study of 13C chemical shifts as a function of concentration at different pH values has been performed by Tato et al., which shows a different behavior of complexation for CA and DCA with 5 resulting in 1:1 and 1:2 inclusion complexes [22]. However, the complexation phenomena do not depend on the pH of the solution. 13C NMR chemical shifts of the host and guest molecules change on passing from the free to the complexed state. The side chains in 5 at position C-6 have a significant effect on the complexation process with the bile salts. The ROESY experiments confirm the overlap of the CA molecule with 5 resulting a 1:1 inclusion complex, while in the case of DCA molecule, the first molecule of 5 encapsulates the bile salt to a larger extent than the second molecule of 5, resulting a 1:2 inclusion complex. Hence the most important factors for the formation of a stable inclusion complex are the relative size of 5 and the bile salt molecules, the nonpolar cavity of 5, the hydrophobicity of the bile salts, and the presence of an electrostatic environment outside the toroidal cavity.

3.2.2. Nucleobase-modified -CDs

The nucleobase-modified -CDs 810 exhibit distinguishable binding abilities toward bile salts compared with parent -CD 1 [19]. Host 10 shows increased binding of TCA/GCA. Host 9 exhibits increased binding of GCA while hosts 810 show less binding of the other bile salts. The inclusion complexation of hosts 810 is driven by favorable enthalpy changes, accompanied with unfavorable entropy changes. The driven forces are hydrogen-bonding and van der Waals interactions, simultaneously producing marked geometric configuration change. Host 8 displays weaker binding ability for every bile salt than hosts 9 and 10 owing to expelling adenine group from -CD cavity to accommodate bile guests in hosts 8, which is unfavorable to the hostguest complexation.

3.2.3. Tryptophan- and tyrosine-modified -CDs

The microcalorimetric titrations of L/D-Trp-modified -CD (11 and 12) with a series of bile acids, i.e., CA, DCA, GCA, and TCA, showed typical titration curves, which can be nicely analyzed by assuming the 1:1 complex stoichiometry [20]. Modified -CDs 11 and 12 exhibited appreciably smaller binding abilities for GCA and TCA guests than those of native -CD 1 since GCA and TCA, possessing a strongly hydrophilic and hydrated sulfonate tail, are not expected to deeply penetrate into the CD cavity by removing the originally included L/D-Trp group out of the hydrophobic cavity. In contrast, DCA and CA, possessing a less hydrophilic/hydrated carboxylate tail, showed comparable or even stronger binding and higher selectivities for hosts chirality than TCA and GCA.

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 313

The ITC experiments of hosts 13 and 14 with bile salts (CA, DCA, GCA, and TCA) also showed the typical titration curves of the 1:1 complex formation [21]. The stoichiometric ratio N observed from the curve-fitting results was within the range 0.9 to 1.1, which clearly indicated that the majority of the inclusion complexes had a 1:1 binding mode. Thermodynamically, the binding of all CDs with the bile salts was entirely driven by the favorable enthalpy changes accompanied by the unfavorable entropy changes. 14 gave the higher bind ability toward CA and DCA than 1 and 12 due to the introduction of D-tyrosine substituent and the conformational difference between 12 and 14. In addition, the bind constant of 14 for DCA was slightly bigger than that for CA. Possessing a more hydrophobic structure due to the absence of the C-7 hydroxyl group as compared with CA, DCA was easier to bind to the -CD cavity than CA, which consequently led to the more favorable hydrophobic interactions between hosts and guests. Host 14 exhibited the obviously smaller binding abilities for GCA and TCA guests than 1 and 12. Thermodynamically, the decreased binding affinities of host 14 toward GCA and TCA arose from the entropy change rather than the enthalpy change due to the weakened hydrophobic interactions and the relatively poor size-fit between host and guest. Compared with 1 and 11, 13 showed clearly decreased binding abilities toward all four of the bile salts, especially for GCA and TCA. Thermodynamically, the inclusion complexation of 13 with four bile salts exhibited the favorable enthalpy changes and unfavorable entropy changes. The favorable enthalpy gain of 13 was slightly higher than those of 1 and 11, but the entropy loss of 13 was much more than those of 1 and 11 toward corresponding guests.

3.2.4. Methyl--CD and 2-hydroxypropyl--CD

The interactions of CA, DCA, GCA, and TCA with 15 and 16 have been studied by Ollila et al. by means of isothermal titration calorimetry [23]. The results show that both CA and DCA bound to 15 and 16 with a 1:1 stoichiometry. The binding constant was significantly higher for DCA to 15 and 16 compared to CA. This difference in binding affinity is likely explained by the more hydrophobic nature of DCA due to the absence of the C-7 hydroxyl group, which is present in CA. The binding affinity was somewhat lower for CA binding to 15 compared to 16, while DCA showed a markedly lower affinity for 15 compared to 16. GCA and TCA have lower affinities to 15 and 16 compared to CA and DCA. TCA bound with lower affinity to 15 compared to GCA. Both GCA and TCA gave the same 1:1 stoichiometry for binding to 15 and 16 as did CA and DCA. For 17, all the hydroxyls are methylated, and the loss of hydrogen bonds for the resulting complexes is inevitable [24]. Therefore, host 17 only shows weak complex stability constants to bile salts, which are much lower than those of 1 and 16. In addition, the release of higher energy water molecules in the cavity of -CD upon complexation with guests makes the inclusion complexation more favorable, which cannot be obtained in the cases of 17 because almost no water molecule resides in the cavity of 17. Besides that, 17 should need some conformational adjustment to accommodate bile guests, which is entropy-unfavorable for the inclusion complexation.

314 Thermodynamics Fundamentals and Its Application in Science

3.3. Binding modes for bile salts and chromophore-modified CD series 3.3.1. Anthryl-modified -CDs
1

H ROESY experiment has been performed by Liu et al. to confirm the binding model of host 19 with CA [25]. The results indicate that CA molecule is included into the hydrophobic cavity from the secondary side of -CD, with the side chain folded towards the steroid skeleton, and the anthracene group is excluded outside the cavity of -CD. CA molecule and the tether of -CD can be co-included into the cavity through the induced-fit interaction between host and guest.

3.3.2. Quinolinyl- and naphthyl-modified -CDs

2D ROESY NMR experiments accompanied with molecular modeling studies have been performed by Liu et al. to investigate the binding modes of DCA with 21 and 22 [26]. The results show that the side chain and D-ring of bile salts were encapsulated in the -CD cavity from the wide opening (Figure 5). 2D ROESY NMR experiment of complex of 23 with CA has also been performed to investigate the binding geometry between permethylated -CDs and bile salts [24]. The results show that CA is deeply included into the cavity of host 23 with its ring A in the region of the narrow side and ring D in the region of the broad side. However, upon complexation with CA guest, the appended naphthalene group in 23 is not entirely expelled out of the cavity of permethylated -CD but is removed from the central cavity to the region of the narrow torus rim. The cooperative inclusion manner of both guest molecule and substituent sidearm into the cavity is mainly benefited from the extended framework of permethylated -CD.

3.4. Complexation thermodynamics for bile salts and chromophore-modified CD series 3.4.1. Anthryl-modified -CDs
The stoichiometric ratios gotten from curve-fitting results of the binding isotherm fell within the range of 0.91.1, indicating that the resulting complexes of bile salts and CDs (1820) are 1:1 [25]. As compared with parent -CD 1, modified -CDs 1820 with different chain length not only enhanced molecular binding ability but also significant molecular selectivity upon inclusion complexation with homologous steroids, except for resulting complex of 20 with TCA. The stability constants for the inclusion complexation of hosts and the each steroid molecule decreased in the following order: DCA > CA > GCA > TCA. The hydroxyl group at the C7 carbon atom of CA, GCA and TCA guests prevented deeper inclusion of the steroids in the -CD cavity than that of DCA guest. On the other hand, the tether length of the host and induced-fit interactions also played crucial roles in the selective molecular binding process of modified -CD 1820 with guests. Host 19 possessing suitable tether length could

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 315

encapsulate more tightly the steroid guests than the other, through the size/shape-matching and the induced-fit interactions between the host and guest. Thermodynamically, the inclusion complexation of 1820 with steroid guests is entirely driven by favorable enthalpy contribution with negative or minor positive entropy change [25]. The strong interaction between host and guest leads to the more favorable negative enthalpy change, which is counteracted by the relative more unfavorable negative entropy change. The introduction of anthracene group with different chain length, and additional binding site to CD rim can significantly enhance the binding ability of parent CD toward steroid guests.

Figure 5. The possible binding mode of 22 with DCA

3.4.2. Quinolinyl- and naphthyl-modified -CDs

The binding behaviors of two -CD derivatives bearing 8-hydroxyquinolino and triazolylquinolino groups (21 and 22) with bile salts have been studied in aqueous buffer solution by means of microcalorimetrical titration [26]. The results showed that the hostguest binding behaviors were mainly driven by the favorable enthalpy changes, accompanied by the unfavorable entropy changes, and the hydrogen-bonding interactions and van der Waals interactions were the main driven forces governing the hostguest binding. The binding stoichiometry of the permethylated -CD derivatives 23 and 24 with bile salts has been determined by the Jobs plot method, which showed that hosts and guests formed 1:1 complexes [24]. Thermodynamically, hosts 23 and 24 show much higher binding ability to bile salts than permethylated -CD 17 when the naphthalene (or quinoline) sidearm is appended on it. The pronounced enhancement of complex stabilities for hosts 23 and 24 can be attributed to the cooperative complex interactions of both the cavity of permethylated -CD and the chromophore sidearms. Furthermore, it should be mentioned that host 24 always forms more stable complexes with bile guests than host 23, which indicates that the N atom on the quinoline ring plays a crucial role during the course of recognition of bile guests.

316 Thermodynamics Fundamentals and Its Application in Science

Hosts 1

Guests CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA

pH 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS)

Ks 4068 4844 2394 2293 11160 7705 2075 2309 16920 9382 3904 2796 4832 4034 2221 1322 11060 11350 3050 3061 25315 30300 3098 4659 25850 24785 4722 3022 1726 2839 1032 1003 2567 3137 2898 2284 2605 3813 3140 2402

H 22.98 25.79 22.99 23.77 25.53 32.16 25.90 26.89 28.11 35.78 24.74 20.37 24.90 38.91 19.75 32.75 36.44 41.15 25.48 18.43 34.26 38.13 25.82 14.86 23.53 27.59 21.22 24.29 31.0 34.8 25.7 26.6 29.3 34.0 31.2 30.0 28.6 33.7 29.6 28.8

TS 2.38 4.76 3.7 4.59 2.43 9.98 6.97 7.69 3.98 13.11 4.24 0.7 3.87 18.33 0.65 14.93 13.36 18.01 5.59 1.47 9.13 12.55 5.89 6.08 1.65 2.51 0.25 4.43 13.3 14.9 8.5 9.5 9.9 14.0 11.4 10.8 9.1 13.3 9.7 9.5

Methods ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC

Refs. 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18 18 18 18 18 19 19 19 19 19 19 19 19 19 19 19 19

10

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 317

Hosts 11

Guests CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA

pH 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS)

Ks 2020 2310 1110 1060 6680 6770 1760 1470 871 1087 428 391 8689 9962 1105 809 2510 4429 1764 1399 2693 6276 1958 2148 61 774 228 162 11760 15030 3870 2647

H 23.2 32.1 23.4 23.1 37.9 46.0 24.9 24.3 26.7 33.1 28.3 25.7 41.7 50.5 30.5 26.7 7.9 10.65 8.2 8.75 5.7 6.8 7.9 7.2

TS 4.3 12.9 6.0 5.8 14.5 24.1 6.4 6.2 9.9 15.8 13.3 10.9 19.2 27.9 13.1 10.1 38.6 34.0 34.5 31.0 46.6 49.9 36.6 39.6

Methods ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC

Refs. 20 20 20 20 20 20 20 20 21 21 21 21 21 21 21 21 23 23 23 23 23 23 23 23 24 24 24 24 25 25 25 25

12

13

14

15

16

CA DCA GCA TCA

17

18

CA DCA GCA TCA CA DCA GCA TCA

42.70 42.72 25.23 20.99

19.47 18.87 4.75 1.47

318 Thermodynamics Fundamentals and Its Application in Science

Hosts 19

Guests CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA

pH 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl)

Ks 18965 22485 4888 3755 11850 13365 4254 1833 2216 2007 2434 3478 2443 3177 2811 2809 910 4320 4340 3820 3290 7460 10690 8710 7400 6700 1280 2570

H 32.37 36.48 21.61 19.15 33.23 39.57 20.07 26.58 25.04 51.92 31.07 23.98 35.60 33.89 34.94 30.37

TS 7.95 11.46 0.56 0.7 9.98 16.20 0.65 7.96 5.94 33.07 11.74 3.76 16.25 13.90 15.24 10.68

Methods ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence

Refs. 25 25 25 25 25 25 25 25 26 26 26 26 26 26 26 26 24 24 24 24 24 24 24 24 27 27 27 27

20

21

22

23

24

CA DCA GCA TCA

25

CA DCA

22.3 32.1 28.3 33.3

0.2 10.2 10.5 13.8

ITC ITC ITC ITC

26

CA DCA

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 319

Hosts 27 28 29 30

Guests CA DCA CA DCA CA DCA CA DCA GCA CA DCA GCA CA DCA GCA

pH 7.0 (PBS) 7.0 (PBS) 7.0 (PBS) 7.0 (PBS) 7.0 (PBS) 7.0 (PBS) aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution

Ks 1650 2660 588 1520 60.4 1030

TS

Methods Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence

Refs. 38 38 38 38 38 38 36 36 36 36 36 36 36 36 36

31

32

PBS: Phosphate Buffer Solution; ITC: Isothermal Titration Calorimetry; Tris: Tris(hydroxymethyl)aminomethane; : The guest-induced variations in the excimer emission are too small for these values to be determined.

Table 1. Complex stability constants (Ks/M1), enthalpy (H/(kJmol1)), and entropy changes (TS/(kJmol1)) for intermolecular complexation of bile salts with natural -CD and its mono-modified derivatives in aqueous solution

All the permethylated -CD derivatives (17, 23 and 24) present the weakest binding ability to CA guest because the cavity of permethylated -CD possesses a broader hydrophobic region in comparison with 1, and then permethylated -CD is more suitable to include bile guests with longer tails (GCA and TCA) than 1 [24]. Moreover, there are similar structures between CA and DCA except for the difference of one hydroxyl in ring B. It is attractive that DCA can be included more tightly by 17, 23 and 24 than CA. One reasonable explanation is that the absence of one hydroxyl in ring B makes the whole framework of DCA more hydrophobic than CA, and thereby DCA is more suitable to be immersed into the cavity of permethylated -CDs.

4. Bridged CD series
4.1. Binding modes for bile salts and bridged CD series

4.1.1. Diseleno- and bipyridine-bridged -CDs

ROESY experiments for the complexes of CDs (25, 26, 33, and 35) and DCA have been performed to illustrate the binding modes between the CDs and bile salts [27]. The results show that the bridge linker does not interact with DCA and the bile salt molecule is not

320 Thermodynamics Fundamentals and Its Application in Science

cooperatively bound by the two cavities of one dimer molecule. DCA is not included in the cavity of the dimer from the primary side (narrow open), but penetrates slightly into the cavity from the secondary side (wide open) using the side chain and D-ring moiety. For 33 (Figure 6), the A-ring moiety of DCA is simultaneously shallowly included in one of the cavities of another CD to form a liner structure. For monomer 25, the D-ring moiety of DCA penetrates deep into the cavity of 25 from the secondary side. However, for monomer 26, DCA is included in the cavity of 26 from the secondary side by its A-ring moiety, differing from other CDs (by D-ring moiety). To further obtain the information about the binding modes of bile salts with diseleno- and bipyridine-bridged -CDs, 2D ROESY spectra for typical hostguest pairs have also been determined by Liu et al. [28]. For dimer 35 and CA, the results indicate that the carboxylate side chain and D-ring of CA may penetrate into the CD cavity from the secondary side shallowly and two CA molecules are bound separately into two cavities of 35 from the secondary side, which is consistent with the 1:2 binding stoichiometry (Figure 7a). For dimer 39 and DCA, the results are quite different and show a 1:1 cooperative binding mode. The A-ring of DCA penetrates deeply into one CD cavity of 39, attributing to the less steric hindrance and higher hydrophobicity of the substituent group on the C-7 position of DCA (Figure 7b). Under the same experiment using DCA as guest, host 38 adopts a different binding mode from 39. The carboxylate side chain of two DCA molecules deeply penetrates into the CD cavity of 38 from the secondary side separately.

4.1.2. Oligoethylenediamino-bridged -CDs

To obtain the information about the binding modes between bile salts and oligoethylenediamino-bridged -CD dimers (4244), 2D ROESY spectra for typical host guest pairs have been determined by Liu et al. [29]. The results of ROESY experiments indicated that the D ring and side-chain of bile salt guest enter one -CD cavity from the wide opening, and the linker group is partially self-included in the other -CD cavity (Figure 8).

4.1.3. Aromatic diamino- and sulfonyldianiline-bridged -CDs

From ROESY experiments, Zhao et al. found that the D-ring of CA is wholly included in the CD cavity of 45 from the wide opening, while the side-chain is located near the narrow opening of CD cavity and folded toward the steroid body and the phenyl moiety is not driven out of the CD cavity even after the guest inclusion [30]. Similar binding mode is also observed in other cases of 45/bile salts complexes. The binding modes between the aromatic diamino-bridged -CDs 4648 and bile salts have also been investigated by Zhao et al. via 2D ROESY experiments and the results show that the D-ring of CA is wholly included in the CD cavity with the wide opening, while the side chain is located near the narrow opening of the CD cavity and is folded toward the steroid body [31]. The phenyl moiety is not driven out of the CD cavity even after the guest inclusion.

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 321

Figure 6. Structures of bridged -CDs

322 Thermodynamics Fundamentals and Its Application in Science

To obtain the information about the binding modes between bile salts and sulfonyldianilinebridged -CD 49, 2D ROESY spectra for typical hostguest pairs have further been determined by Zhao et al. [32]. The correlation signals, along with the 1:1 binding stoichiometry, jointly indicate a host-linker-guest binding mode between 49 and CA. That is, upon complexation with 49, the carboxylate tail and the D ring of CA penetrate into one CD cavity of 49 from the wide opening deeply, while the phenyl moiety of the CD linker is partially self-included in the other -CD cavity. Similar binding modes are also observed in other cases of 49/bile salt complexes.

4.1.4. Binaphthyl-, biquinoline- and dithio-bridged -CDs

The binding modes of binaphthyl-, biquinoline- and dithio-bridged -CDs (5055) and bile salts have been investigated by 2D ROESY experiments in aqueous solution [33]. The results show that CA enters the CD cavity of 53 from the second side of CD with the side chain and D-ring. The side chain with the negative carboxylate group of CA moves toward the positive protonated amino group of 53. The other binaphthyl-, biquinoline- and dithio-bridged CDs/bile salts complexes show a similar binding mode as the complex 53/CA, with only a slight degree of difference in the depth of guest insertion.

Figure 7. The possible binding modes of 35 with CA (a) and 39 with DCA (b)

Figure 8. The possible binding mode of 4244 with CA

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 323

4.2. Complexation thermodynamics for bile salts and bridged CD series 4.2.1. Diseleno- and bipyridine-bridged -CDs
To elucidate the difference in binding behavior between the CD dimer and monomer, two CD dimers (33 and 35) and their monomer analogs (25 and 26) have been used for titration microcalorimetry with CA and DCA [27]. It is interesting that the results of the thermodynamic measurements show a 1:1 binding stoichiometry for hosts 25, 26 and 33, but 1:2 stoichiometry for host 35. In addition, although the stability constants for the complexation between dimer 33 and the bile salts are much larger than those for monomer 26, the long-linked dimer 35 unusually displays a lower cavity binding ability than its corresponding monomer 25 upon complexation with both guests CA and DCA. The enhancement of the binding ability of dimer 33 compared to monomer 26 could be ascribed not only to the cooperative binding but also partly to the peculiar self-inclusion conformation of 26 that leads to more unfavorable entropy changes, especially for the 26 CA pair. For 35, the two guest molecules are separately and independently included in the two cavities of 35 because the longer linker, especially the ethylenediamino moiety of dimer 35, makes it possess a relatively large conformational freedom. As the considerable entropy loss cancels the advantage of enthalpy gain, dimer 35 displays relatively weak binding abilities. Both hosts 35 and 25 show similar binding ability for DCA and CA. The reason is that either binding with host 35 or host 25, the two guest bile salts are included into the cavity of CDs by its D-ring and side-chain moiety, which reduces the influence of the substituent in C7. However, while binding with hosts 33 and 26, the A-ring moiety participates in the binding process, so the more hydrophobic C7 substituent of DCA makes it bind more strongly with the host CDs, giving the higher binding constants than with CA, especially for host 26. Either for diseleno-bridged -CDs (3437) or for bipyridine-bridged -CDs (3841), the host guest stoichiometry changes in the same order, that is, from 1:2 to 1:1 with the increase of spacer length [28]. For diseleno-bridged -CDs, only 36 and 37 adopt the 1:1 binding mode. However, for bipyridine-bridged -CDs, only host 38 adopts the 1:2 binding mode; the others all show the 1:1 cooperative binding mode. The thermodynamic results reveal that, with the longest spacer, 37 gives the largest stability constants in all diseleno-bridged -CDs, while the largest stability constants of bipyridine-bridged -CDs toward each guest molecule is obtained by the dimers 39 and 40 with the moderate spacer lengths, which suggests that only the CD dimers possessing the proper spacer length can give the perfect cooperative binding toward guests. For the dimers adopting 1:1 cooperative binding mode, the enthalpy changes are not only the main contribution to the binding process but also the determining factor for the binding abilities [28]. Comparing the diseleno-bridged -CDs with bipyridine-bridged -CDs, all of the bipyridine-bridged -CDs display much stronger binding abilities toward bile salts than corresponding diseleno-bridged -CDs, which indicate that the presence of rigid spacer favors formation of a relatively fixed binding mode and results in the close contact between

324 Thermodynamics Fundamentals and Its Application in Science

two CD cavities and guest molecule, leading to the stronger binding abilities. On the other hand, due to the presence of the bipyridine fragment, the hydrogen bond between the hydroxyl group of the bile salt and the nitrogen atom of bipyridine might also be taken as a plausible explanation for the strong binding abilities of bipyridine-bridged -CDs as compared with diseleno-bridged -CDs. Upon complexation with CA and DCA, all dimer hosts adopting a 1:1 binding mode show higher binding abilities than native -CD 1 due to more favorable enthalpy changes, which perfectly confirms the advantage of cooperative binding of guests by two CD cavities.

4.2.2. Oligoethylenediamino-Bridged -CDs

1:1 binding stoichiometry is observed for all the complexes between bile salts and oligoethylenediamino-bridged -CDs (4244) [29]. The inclusion complexation of bile salts with 4244 is driven by favorable enthalpy changes, accompanied by slight to moderate entropy loss. Interestingly, the enthalpy changes for the inclusion complexation of 4244 increased, while the entropic changes decreased, with the elongation of the linker group, giving a binding constant 42 > 43 > 44. The stronger binding of bile salts by the short-linked -CD dimer is not thermodynamically accomplished by an increase of the originally favorable enthalpy gain, but by a reduction of the unfavorable entropy loss. The shortlinked -CD dimer, with a better size and hydrophobicity match to bile salts, may experience more extensive desolvation upon complexation, and thus exhibits the less unfavorable entropy loss. With the elongation of linker group, the protonated amino group in the linker is located distant from the anionic carboxylate (or sulfonate) tail of bile salt, which consequently weakens the electrostatic interactions between the linker group and bile salt. Moreover, the increase of the number of -NH- fragments in the linker group decrease the hydrophobicity of -CD dimer to some extent, which is also unfavorable to the hydrophobic interactions between host and guest. The stability constants of the complexes formed by -CD dimers 4244 with bile salts are larger than those of the complexes formed by native -CD 1 [29]. These enhanced binding abilities of -CD dimers may be mainly attributed to the cooperative host-linker-guest binding mode between host and guest. The electrostatic interactions between the protonated amino groups in the linker and the anionic carboxylate (or sulfonate) tail of bile salt may strengthen the inclusion complexations of these -CD dimers with bile salts. Moreover, the hydrogen bond interactions of the hydroxyl groups of -CD and the -NH- fragments of the oligo(ethylenediamino) linker with the carboxylate (or sulfonate) tail of bile salt also contribute to the enhanced binding abilities of -CD dimers 4244. Compared with CA, GCA and TCA, DCA possesses a more hydrophobic structure due to the absence of C-7 hydroxyl group, which consequently leads to stronger hydrophobic interactions between host and guest. Therefore, DCA gives the highest binding abilities among the bile salts examined upon complexation with most CDs [29]. Possess more polar side-chains, GCA and TCA show weak binding abilities upon inclusion complexation

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 325

complexation with -CD dimers due to the relatively poor hydrophobic interactions between host and guest.

4.2.3. Aromatic diamino- and sulfonyldianiline-bridged -CDs

The stoichiometry for the inclusion complexation of 45 with bile salts were determined by the continuous variation method and the results showed a 1:1 inclusion complexation between 45 and bile salts [30]. The stability constants for the inclusion complexation of 45 with bile salts are much higher than those values for the native -CD 1. These enhanced binding abilities of 45 may be mainly attributed to the cooperative host-linker-guest binding mode between host and guest because the linker group provides some additional binding interactions towards the accommodate guest. Host 45 displays higher binding ability for CA than for DCA due to the hydrogen bond interactions between the 7-hydroxy group of CA and the 2- and 3-hydroxy group of CD. Host 45 shows the weaker binding abilities upon inclusion complexation with GCA and TCA than that of CA and DCA because GCA and TCA are unfavorable to insert into the cavity from the second side of CD cavity with their D ring attributing to the more hydrophilic tail attached to the end of the D ring. The stoichiometries for inclusion complexation of aromatic diamino-bridged -CDs 4648 with bile salts were further determined by the continuous variation method and the results show that all the hosts and guests form 1:1 complexes [31]. -CD dimers 4648 also show enhanced binding ability toward bile salts as compared with -CD 1. The enhanced binding abilities of aromatic diamino-bridged -CDs may be mainly attributed to the cooperative host-linker-guest binding mode between host and guest. In addition to the association of the CD cavity with a guest molecule, the linker group provides some additional binding interactions towards the accommodated guest. Unlike the -CD 1, the bridged -CDs 4648 show larger binding constants for CA than for DCA [31]. Among them, the host 47 gave the highest stability constant for inclusion complexation with CA. One possible reason for the stronger affinity for CA may involve hydrogen-bond interactions between the 7-hydroxy group of CA and the 2- and 3-hydroxy groups of CD, which subsequently strengthen the hostguest association. Moreover, all the hosts show lower binding ability for complexation with GCA and TCA as compared with complexation with CA and DCA. The highest binding constants towards GCA and TCA are with host 47. The universally decreased binding ability toward GCA and TCA must be related to structure differences between CA and DCA. Attributing to the more hydrophilic tail, which is attached to the end of the D ring, GCA and TCA are unfavorable for insertion into the cavity from the second side of the -CD cavity with their D ring. The binding constants for the complexation of each bile salt by hosts 4648 increases in the following order: 47 > 48 > 46 [31]. That is, host 47 with a tether of moderate length and rigidity among the -CD dimers studied is the most suitable for inclusion complexation with bile salts. This may be attributable to the strict size fit between these bile salts and the moderate length-tethered -CD dimer 47, which consequently exhibits strong van der Waals and hydrophobic interactions between host and guest.

326 Thermodynamics Fundamentals and Its Application in Science

The stoichiometry for the inclusion complexation of sulfonyldianiline-bridged -CD 49 with bile salts has also been determined by the continuous variation method and the results indicate that all the bile salts can form 1:1 complexes with 49 [32]. Thermodynamically, the binding constants of 49 with bile salts are larger than those of native -CD 1. The enhanced binding abilities of 49 may be also mainly attributed to the cooperative host-linker-guest binding mode between host and guest. In addition to the association of the CD cavity with a guest molecule, the linker group provides some additional binding interactions towards the accommodate guest. Distinctly, the binding constant is significantly higher for DCA compared to CA by native -CD 1. However, different from native -CD 1, sulfonyldianiline-bridged -CD 49 reverses this binding selectivity, showing larger binding constants for CA than DCA. One possible reason for the stronger affinity for CA may involve H-bond interactions between CA and CD, which subsequently strengthen the hostguest association. Moreover, all the hosts show a weaker binding ability upon complexation with GCA and TCA than with CA and DCA. The universal decreased binding ability toward GCA and TCA must relate to the structure differences from CA and DCA. Attributing to the more hydrophilic tail, which is attached to the end of the D ring, GCA and TCA are unfavorable to insert into the cavity from the second side of -CD cavity with their D ring. It is worthy to note that the binding ability of 49 is significantly larger for TCA than for GCA, which leads to a relatively strong molecular selectivity.

4.2.4. Binaphthyl-, biquinoline- and dithio-bridged -CDs

The stoichiometric ratios from the binding patterns for the titrations of steroids with binaphthyl-, biquinoline- and dithio-bridged -CDs 5055 fell within the range of 1.8-2.1, which clearly indicates that the majority of the inclusion complexes have a 1:2 stoichiometry of steroids and bridged -CDs [33]. Thermodynamically, bridged -CD 52, possessing a relatively short and rigid tether without amino groups, still gives an enhanced binding ability upon complexation with steroids, except TCA, when compared its one single unit of cavity with that of native -CD 1. The enthalpy changes for the inclusion complexation of bridged -CD 52 with DCA and CA are more negative than that of native -CD 1, resulting in the relatively stronger binding. On the other hand, the enthalpy change for the complexation of 52 with DCA is higher than that with CA, which directly contributes to the increased complex stability. It is reasonable that, possessing the more hydrophobic structure due to the absence of C-7 hydroxyl group as compared with CA, DCA is easier to bind into the -CD cavity than CA, which should lead to the more favorable van der Waals interactions. All the complexation of aminated bridged -CDs (50, 51, and 5355) toward DCA and CA give more negative enthalpy changes as compared with that of neutral bridged -CD 52, validating the contribution of the attractive electrostatic interactions between positively charged protonated amino group of -CD tethers and negatively charged carboxylate group of DCA and CA [33]. Accompanied with the more exothermic reaction enthalpies, the inclusion complexation of DCA and CA by aminated bridged -CDs (50, 51, and 5355) exhibits more unfavorable entropy changes compared to that for neutral bridged bis(-CD)

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 327

52, which possibly originates from the conformation fixation of host and guest and the rigid complex formation upon complexation. Mostly, bridged -CDs 50, 51, and 5355 give the lower binding ability upon complexation with GCA and TCA as compared with the complexation with CA and DCA, which is similar as the complexation of -CD 1 and bridged -CD 52 [33]. The universal decreased binding ability toward GCA and TCA must relate to the structure differences from CA and DCA. The more polar side chains at C23 for GCA and TCA remarkably affect their binding thermodynamics.

4.3. Binding modes for bile salts and metallobridged CD series 4.3.1. Metallobridged -CDs with naphthalenecarboxyl linkers
2D ROESY NMR and circular dichroism spectroscopy experiments for the complexes of bile salts with bridged and metallobridged CDs with naphthalenecarboxyl linkers have been performed by Liu et al. to investigate the binding modes between host and guests [34]. The result of 57/DCA complex showed that the guest DCA was included in the -CD cavity with the D-ring and the carboxylic tail located near the narrow opening but the B-ring located near the wide opening and the naphthyl group was excluded from the -CD cavity upon inclusion complexation. Moreover, the result of 2D ROESY NMR showed that the ethylenediamino moiety of the linker group was also partially self-included in the -CD cavity from the narrow opening. Similar results were also found in other ROESY experiments of hosts 57 and 59 with bile salts.

4.3.2. Metallobridged -CDs with biquinoline linkers

2D NMR experiments in D2O and molecular modeling studies for the complexes of bridged and metallobridged -CDs with biquinoline linkers and bile salts have been performed by Liu et al. to deduce the binding modes between the bile salts and -CD dimers [35,36]. The results show that a cooperative host-tether-guest binding mode is operative in the association of -CD dimers with a guest molecule; upon complexation with -CD dimers, the guest steroid is embedded into one hydrophobic -CD cavity from the primary side, while the tether group is partly self-included in the other cavity. In the metallobridged CDs, the tether group is entirely excluded from the -CD cavities as a result of metal coordination. This arrangement allows two side groups of the guest molecule to be embedded into the hydrophobic -CD cavities from the primary side of the -CD to form a sandwich hostguest inclusion complex.

4.3.3. Metallobridged -CDs with oxamidobisbenzoyl linkers

1

H ROESY experiments have been performed in D2O to investigate the binding modes between bridged and metallobridged -CDs with oxamidobisbenzoyl linkers and bile salts [37]. The results show a host-linker-guest binding mode between 66 and CA. That is, upon inclusion complexation with -CD dimer, the carboxylate tail and the D-ring of CA enter

328 Thermodynamics Fundamentals and Its Application in Science

into one CD cavity of 66 from the wide opening, while the linker group of 66 is partially selfincluded in the other CD cavity (Figure 9a). A similar binding mode is also observed for the inclusion complexation of 66 with DCA.

Figure 9. The possible binding modes of 66 (a) and 67 (b) with CA, and the possible binding modes of 6972 with bile salts

With a shallowly self-included conformation, -CD dimers 65, 67, and 68 show a binding mode different from that of 66. For example, for 67/CA complex, the carboxylate tail and Dring of CA enter the CD cavity from the wide opening, and the carboxylate tail is located close to the linker group. On the other hand, the linker group is mostly moved out from the CD cavity after complexation with CA (Figure 9b). 65/CA, 65/DCA, 67/DCA, 68/CA, and 68/DCA complexes show a similar binding mode to the 67/CA complex. In the cases of the metallobridged -CDs 6972, the strong electrostatic attraction from the coordinated CuII ions in the linker group may also favor the penetration of the carboxylate tail of bile salt into the CD cavity through the wide opening. Moreover, the 1:2 or 2:4 binding stoichiometry indicates that each CD cavity of a metallobridged -CD is occupied by a bile salt (Figure 9c).

4.4. Complexation thermodynamics for bile salts and metallobridged CD series 4.4.1. Metallobridged -CDs with naphthalenecarboxyl linkers
The interactions between hosts (2729, 5759) and bile salts have been studied by Liu and Ueno et al. by the method of fluorescence [34,38]. The results show that all the hosts (2729,

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 329

5759) can form 1:1 complexes with bile salts CA and DCA. Thermodynamically, bridged CDs possess much stronger binding abilities compared with mono-modified -CDs. These enhanced binding abilities should be attributed to cooperative binding of the -CD cavity and the linker group towards the guest molecule, leading to greatly strengthened van der Waals and hydrophobic interactions between host and guest when compared with monomodified -CDs. Furthermore, after metal coordination, the metallobridged bis(-CD)s 58 and 59 significantly enhance the original binding ability of native -CD 1, mono-naphthylmodified -CDs 2729 and even parent bridged -CD 57. This enhancement may be subjected to a multiple recognition mechanism of metallobridged -CDs towards model substrates. On one hand, the coordination of a metal ion to the linker group shortens the effective distance of two -CD cavities to some extent and thus improves the size-fit degree between host and guest. On the other hand, the electrostatic attraction between the anionic carboxyl group of guest bile salt and the coordinated metal ion of metallobridged -CD may also favour the hostguest binding to some extent.

4.4.2. Metallobridged -CDs with biquinoline linkers

The interactions between host 51 and bile salts have been investigated by Liu et al. by the method of fluorescence [35]. The results show that all the bile salts can form 1:1 complexes with 51. Thermodynamically, the binding constants obtained for CA and DCA are much larger than those reported for mono-modified -CDs by Ueno et al. under practically the same experimental conditions [38]. This enhancement is probably due to the cooperative binding of the steroids by 51. The complex stability decreases in the order: DCA > CA > GCA > TCA. The highest affinity for DCA is likely to arise from its more hydrophobic steroid skeleton. Host 51 shows comparable affinities toward CA and GCA, whereas TCA, possessing a highly polar anionic tail gives the lowest binding constant. The stoichiometry for the inclusion complexation of hosts 6064 with bile salts has also been determined by Jobs method [36]. The results show that the stoichiometry of the inclusion complex formed by the 63/CA system is likely to be 2:2, with intramolecular complexation. Stoichiometries of 1:1 (for bridged -CD) or 2:2 (for metallobridged -CD) were obtained in other similar cases of hostguest inclusion complexation. Thermodynamically, the stability constants of the complexes of bridged -CDs 51, 60 and 61 with bile salts are larger than those of the complexes formed by mono-modified -CDs 2729 by a factor of about 1.1 to around 200 benefitting from cooperative binding. In addition to inclusion complexation of the guest molecule within one hydrophobic CD cavity, the tether group located near the accommodated guest provides some additional interactions with the guest. In control experiments, the changes in the fluorescence spectra of 3032 upon addition of guest steroids were too small to allow calculation of the stability constants, which may be attributed to strong self-inclusion of the substituted group preventing penetration of the guest into the CD cavity. Except 60, the mono- and bridged--CDs display higher binding affinities for DCA than for CA. This stronger affinity for DCA is likely to arise from the

330 Thermodynamics Fundamentals and Its Application in Science

more hydrophobic steroid skeleton of this compound compared with that of CA. The abilities of both the short-tethered compound 60 and the long-tethered host 61 to bind CA and DCA are unexpectedly limited compared to the binding abilities of mono-modified CDs 2729 due to the self-inclusion of the tether group for the short-tethered -CD dimer 60 and the steric hinderance from the relatively large 5-amino-3-azapentyl-2-quinoline-4carboxyamide fragment on the exterior of the CD cavity for the long-tethered -CD dimer 61, respectively. The metal-ligated oligomeric -CDs 6264 have significantly enhanced (around 504100 higher) binding affinities for the tested guest molecules compared with those of the monomodified -CDs [36]. These results can be explained by considering a mechanism involving an uncommon multiple recognition behavior of metallobridged -CDs. A metallobridged CD affords four hydrophobic binding sites (four CD cavities) and one (or three) metal coordination center(s), which jointly contribute to the cooperative binding of the oligomeric host with the guest molecule upon inclusion complexation. In addition, ligation of a CuII ion shortens the effective length of the tether to some extent and thus improves the size fit of the host with the guest. The cumulative result of these factors is that the metal-ligated -CD oligomers have binding abilities around 6200 times higher than those of their parent bridged -CDs.

4.4.3. Metallobridged -CDs with oxamidobisbenzoyl linkers

The stoichiometry for the inclusion complexation of hosts 6572 with bile salts has been determined by Jobs method [37]. The results indicate that each of the Jobs plots for the inclusion complexation of 6568 with bile salts shows a maximum at a -CD dimer molar fraction of 0.5, confirming the 1:1 binding stoichiometry between host and guest. For the inclusion complexation of metallobridged -CDs 6972 with bile salts, however, each of the Jobs plots shows a maximum at a bridged -CD unit molar fraction of 0.33, which indicates 1:2 stoichiometry between each bridged -CD unit and guest. The metallobridged -CDs 69 and 70 may only bind two bile salts to form a stoichiometric 1:2 inclusion complex. However, the metallobridged -CDs 71 and 72 may adopt intramolecular 2:4 stoichiometry upon inclusion complexation with bile salts. Thermodynamically, the binding constants for the inclusion complexation of CA and DCA with bridged -CDs 6568 are higher than the KS values reported for the inclusion complexation of these bile salts with native or mono-modified -CDs [33,38]. These enhanced binding abilities highlight the inherent advantage of the cooperative hostlinker-guest binding mode of bridged -CDs 6568. In addition to the association of the CD cavity with a guest molecule, the linker group provides some additional binding interactions towards the accommodated guest. The bile salts CA and DCA are better bound by bridged -CD 65, which possesses the shortest linker group, than by the long-linked bridged -CDs [37]. This may be attributable to the strict size-fit between these bile salts and the short-linked bridged -CD 65, which

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 331

consequently gives strong van der Waals and hydrophobic interactions between host and guest. Significantly, metallobridged -CDs 6972 show greatly enhanced binding abilities with regard to the bridged -CDs 6568 [37]. These significant enhancements in the binding abilities may be attributable to a more complicated multiple recognition mechanism involving the cooperative binding of several CD cavities, conformation adjustment by the metal coordination, and additional binding interactions between the metal-coordinated linker group and the accommodated guest molecules. Except for 66, all of the hosts examined display higher binding abilities for CA than for DCA [37]. One possible reason for the stronger affinities for CA may involve hydrogen bond interactions between the 7-hydroxy group of CA and the 2- and 3-hydroxy groups of CD.

4.4.4. Metallobridged -CDs with aminated linkers

The microcalorimetric experiments of -CD 1 and modified -CDs 2, 5, 6, 7 with bile acids showed typical titration curves of 1:1 complex formation [18]. However, metallobridged CD 56 displays a 1:2 hostguest binding stoichiometry. Thermodynamically, as compared with native -CD 1, most oligo(ethylenediamino)--CDs 2, 5 6, and their CuII complexes 7 and 56 show enhanced molecular binding abilities and guest selectivities towards bile acids. The inclusion complexation of bile acids with native -CD 1 and their derivatives (2, 5, 6, 7, and 56) is absolutely driven by favorable enthalpy changes accompanying with moderate unfavorable or slightly favorable entropy changes. The favorable enthalpy change is attributed to the dominant contribution of the hydrophobic interactions. Meanwhile, the unfavorable entropy given by most of the complexes is due to the decrease of rotational and structural freedom upon complex construction. As compared with native -CD 1, 5 shows increased binding abilities toward negatively charged bile acids guest molecules, which should be mainly due to the additional electrostatic interactions between the amino tether moiety of hosts and anionic carboxylate or sulfonate tail of guests [18]. Moreover, -CD dimer 56 shows a larger binding constant upon inclusion complexation with CA and DCA than 5. This may be attributed to that the coordination of copper ion onto the amino tether of CD affords a more positive charged environment as compared with its precursor 5. Compared with 5, host 6 also shows stronger binding abilities toward guest molecules. However, the introduction of copper actually decreases the original binding ability of 6 towards DCA and gives comparable stability constant upon complexation with CA. All the hosts, including native -CD 1 and modified -CDs 2, 5, 6, 7, and 56, show the weaker binding abilities upon inclusion complexation with GCA and TCA than those of CA and DCA. It is also found that complexes stabilities enhance with the extended length of spacer for the same guest except for 2/CA to 5/CA. It is reasonable to believe that the increased stability is due to the enlarged hydrogen binding interactions.

332 Thermodynamics Fundamentals and Its Application in Science

Hosts 33

Guests CA DCA

35

CA DCA

36

CA DCA

37

CA DCA

39

CA DCA

40

CA DCA

41

CA DCA

42

43

44

45

CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA

pH 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.4 (TrisNaCl) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS)

Ks 6860 9700 2700 3300 4100 5400 5030 6100 12700 12400 12400 13100 6800 7500 21065 22780 9707 6848 5868 7017 4031 2947 5606 5511 2847 1877 27050 22930

H 30.5 37.0 27.1 35.7 24.9 35.0 29.1 40.2 32.4 45.4 25.5 31.9 25.4 35.2 32.8 42.7 23.0 22.4 39.3 47.4 25.8 26.9 41.0 52.1 26.5 29.0

TS 8.6 14.3 7.5 15.7 4.3 13.7 8.0 18.6 9.0 22.0 2.2 8.3 3.5 13.1 8.1 17.9 0.3 0.5 17.7 25.5 5.2 7.1 19.6 30.7 6.9 10.3

Methods ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC Fluorescence Fluorescence

Refs. 27 27 27 27 28 28 28 28 28 28 28 28 28 28 29 29 29 29 29 29 29 29 29 29 29 29 30 30

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 333

Hosts

46

47

48

49

50

51

52

53

54

Guests GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA CA CA DCA DCA GCA GCA TCA TCA CA DCA GCA TCA CA DCA GCA TCA CA DCA GCA TCA

pH 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS)

Ks 7200 17610 15310 8790 3040 4100 39900 31880 10400 5360 25930 14330 7950 4590 26200 10140 3150 7730 7351 5504 5936 3058 5559 11300 8372 21730 2979 11040 4441 6040 5039 7900 4262 1975 10700 8912 5689 2762 9899 11150 4061 2502

TS

33.0 42.7 15.1 24.5 49.3 48.1 18.1 19.7 28.2 31.6 21.5 22.0 30.6 38.1 22.7 37.3 37.5 39.9 23.5 20.2

10.9 21.4 6.4 4.6 27.9 25.7 4.2 1.1 7.1 9.4 0.8 3.2 7.6 15.6 1.3 17.6 14.7 16.8 2.9 0.8

Methods Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence ITC ITC ITC ITC ITC Fluorescence ITC Fluorescence ITC Fluorescence ITC Fluorescence ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC ITC

Refs. 30 30 31 31 31 31 31 31 31 31 31 31 31 31 32 32 32 32 33 33 33 33 33 35 33 35 33 35 33 35 33 33 33 33 33 33 33 33 33 33 33 33

334 Thermodynamics Fundamentals and Its Application in Science

Hosts 55

56

Guests CA DCA GCA TCA CA DCA GCA TCA CA DCA

57

58

CA DCA

59

CA DCA

60

61

62

63

64

CA DCA GCA CA DCA GCA CA DCA GCA CA DCA GCA CA DCA GCA CA DCA

65

66

CA DCA

pH 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.2 (PBS) 7.4 (TrisHCl) 7.4 (TrisHCl) 7.4 (TrisHCl) 7.4 (TrisHCl) 7.4 (TrisHCl) 7.4 (TrisHCl) aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution aqueous solution 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2

Ks 6196 10325 2891 2189 13330 12065 2925 2478 10540 12400 15500 15700 31400 95900 5380 2790 3380 3710 30500 529000 1745000 196000 283700 13000 246000 54000 891000 18500 12200 8130

H 39.3 39.4 23.3 20.0 29.77 34.02 23.36 21.46

TS 17.6 16.5 3.5 0.9 6.23 10.72 3.58 2.09

Methods ITC ITC ITC ITC ITC ITC ITC ITC Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence

Refs. 33 33 33 33 18 18 18 18 34 34 34 34 34 34 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 37 37 37 37

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 335

Hosts 67

Guests CA DCA

68

CA DCA

69

CAa DCAa

70

CAa DCAa

71

CAa DCAa

72

CAa DCAa

pH (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl) 7.2 (TrisHCl)

Ks 11900 11500 8820 1870 5.73 107 2.03 107 9.93 107 3.47 107 3.96 107 3.78 107 2.95 107 6.2 106

TS

Methods Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence Fluorescence

Refs. 37 37 37 37 37 37 37 37 37 37 37 37

PBS: Phosphate Buffer Solution; ITC: Isothermal Titration Calorimetry; Tris: Tris(hydroxymethyl)aminomethane; : The guest-induced variations in the fluorescence intensities are too small for these values to be determined.
a

: Unit of Ks is in M2.

Table 2. Complex stability constants (Ks/M1), enthalpy (H/(kJmol1)), and entropy changes (TS/(kJmol1)) for intermolecular complexation of bile salts with bridged -CDs in aqueous solution

5. Conclusion
In conclusion, the binding modes, binding abilities, and molecular selectivities of four typical bile salts (CA, DCA, GCA, and TCA) upon complexation with CDs and their derivatives are summarized in this chapter from thermodynamic viewpoints. Generally, native and mono-modified CDs display relatively limited binding ability towards guest molecules, probably because of weak interactions between hosts and guests, which would result in a relative small negative enthalpy change, and then, a relative weak binding. However, bridged and metallobridged CDs have greatly enhanced the binding abilities in

336 Thermodynamics Fundamentals and Its Application in Science

relation to the parent CDs, owing to a multiple recognition mechanism, which would lead to a relative large negative enthalpy change, and then a strong binding. This summary of the binding modes and thermodynamic data for the complexation of bile salts with CDs and their derivatives is quite important to improve the understanding of molecular recognition mechanism in supramolecular systems and further guide the design and synthesis of new supramolecular systems based on different kinds of CDs in the future.

Author details
Yu Liu* and Kui Wang Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, P. R. China

Acknowledgement
This work was supported by the 973 Program (2011CB932502) and NSFC (20932004), which are gratefully acknowledged.

6. References
[1] Szejtli J (1998) Introduction and General Overview of Cyclodextrin Chemistry. Chem. Rev. 98: 17431753. [2] Connors K.A (1997) The Stability of Cyclodextrin Complexes in Solution. Chem. Rev. 97: 13251357. [3] Wallimann P, Marti T, Frer A, Diederich F (1997) Steroids in Molecular Recognition. Chem. Rev. 97: 15671608. [4] Khan A.R, Forgo P, Stine K.J, DSouza V.T (1998) Methods for Selective Modifications of Cyclodextrins. Chem. Rev. 98: 19771996. [5] Rekharsky M.V, Inoue Y (1998) Complexation Thermodynamics of Cyclodextrins. Chem. Rev. 98: 18751917. [6] Danielsson H, Sjvall J (1985) Sterols and Bile Acids. Amsterdam: Elsevier. [7] Holm R, Hartvig R.A, Nicolajsen H.V, Westh P, stergaard J (2008) Characterization of the Complexation of Tauro- and Glyco-Conjugated Bile Salts with -Cyclodextrin and 2-Hydroxypropyl--Cyclodextrin Using Affinity Capillary Electrophoresis. J. Incl. Phenom. Macrocycl. Chem. 61: 161169. [8] Holm R, Shi W, Hartvig R.A, Askjr S, Madsen J.C, Westh P (2009) Thermodynamics and Structure of Inclusion Compounds of Tauro- and Glyco-Conjugated Bile Salts and -Cyclodextrin. Phys. Chem. Chem. Phys. 11: 50705078. [9] Schnbeck C, Westh P, Madsen J.C, Larsen K.L, Stde L.W, Holm R (2010) Hydroxypropyl-Substituted -Cyclodextrins: Influence of Degree of Substitution on the Thermodynamics of Complexation with Tauroconjugated and Glycoconjugated Bile Salts. Langmuir 26: 1794917957.
Corresponding Author

Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 337

[10] Holm R, Madsen J.C, Shi W, Larsen K.L, Stde L.W, Westh P (2011) Thermodynamics of Complexation of Tauro- and Glyco-Conjugated Bile Salts with Two Modified Cyclodextrins. J. Incl. Phenom. Macrocycl. Chem. 69: 201211. [11] Schnbeck C, Westh P, Madsen J.C, Larsen K.L, Stde L.W, Holm R (2011) Methylated -Cyclodextrins: Influence of Degree and Pattern of Substitution on the Thermodynamics of Complexation with Tauro- and Glyco-Conjugated Bile Salts. Langmuir 27: 58325841. [12] Jong M.R.de, Engbersen J.F.J, Huskens J, Reinhoudt D.N (2000) Cyclodextrin Dimers as Receptor Molecules for Steroid Sensors. Chem. Eur. J. 6: 40344040. [13] Casas-Solvas J.M, Ortiz-Salmern E, Fernndez I, Garca-Fuentes L, Santoyo-Gonzlez F, Vargas-Berenguel A (2009) Ferrocene-Cyclodextrin Conjugates: Synthesis, Supramolecular Behavior, and Use as Electrochemical Sensors. Chem. Eur. J. 15: 81468162. [14] Casas-Solvas J.M, Quesada-Soriano I, Carreo-Gzquez D, Gimnez-Martnez J.J, Garca-Fuentes L, Vargas-Berenguel A (2011) -Cyclodextrin Dimers Linked through Their Secondary Faces with Rigid Spacer Arms as Hosts for Bile Salts. Langmuir 27: 97299737. [15] Cabrer P.R, Alvarez-Parrilla E, Meijide F, Seijas J.A, Rodrguez Nez E, Vzquez Tato J (1999) Complexation of Sodium Cholate and Sodium Deoxycholate by -Cyclodextrin and Derivatives. Langmuir 15: 54895495. [16] Cabrer P.R, lvarez-Parrilla E, AlSoufi W, Meijide F, Rodrguez Nez E, Vzquez Tato J (2003) Complexation of Bile Salts by Natural Cyclodextrins. Supramol. Chem. 15: 3343. [17] Liu Y, Yang Y.-W, Cao R, Song S.-H, Zhang H.-Y, Wang L.-H (2003) Thermodynamic Origin of Molecular Selective Binding of Bile Salts by Aminated -Cyclodextrins. J. Phys. Chem. B 107: 1413014139. [18] Liu Y, Cao R, Yang Y.-W (2006) Selective Binding Thermodynamics of Bile Acids by Oligo(ethylenediamino)--Cyclodextrins and Their Copper (II) Complexes. J. Incl. Phenom. Macrocycl. Chem. 56: 183191. [19] Liu Y, Zhang Q, Guo D.-S, Zhuang R.-J, Wang L.-H (2008) Thermodynamics of Complexes between Nucleobase-Modified -Cyclodextrins and Bile Salts. Thermochim. Acta 470: 108112. [20] Wang H, Cao R, Ke C.-F, Liu Y, Wada T, Inoue Y (2005) Diastereomeric Molecular Recognition and Binding Behavior of Bile Acids by L/D-Tryptophan-Modified Cyclodextrins. J. Org. Chem. 70: 87038711. [21] Chen Y, Li F, Liu B.-W, Jiang, B.-P, Zhang H.-Y, Wang L.-H, Liu Y (2010) Thermodynamic Origin of Selective Binding of -Cyclodextrin Derivatives with Chiral Chromophoric Substituents toward Steroids. J. Phys. Chem. B 114: 1614716155. [22] Singh A.P, Cabrer P.R, Alvarez-Parrilla E, Meijide F, Tato J.V (1999) Complexation of 6Deoxy-6-(aminoethyl)Amino--Cyclodextrin with Sodium Cholate and Sodium Deoxycholate. J. Incl. Phenom. Macrocycl. Chem. 35: 335348. [23] Ollila F, Pentikinen O.T, Forss S, Johnson M.S, Slotte J.P (2001) Characterization of Bile Salt/Cyclodextrin Interactions Using Isothermal Titration Calorimetry. Langmuir 17: 71077111. [24] Liu Y, Shi J, Guo D.-S (2007) Novel Permethylated -Cyclodextrin Derivatives Appended with Chromophores as Efficient Fluorescent Sensors for the Molecular Recognition of Bile Salts. J. Org. Chem. 72: 82278234.

338 Thermodynamics Fundamentals and Its Application in Science

[25] Liu Y, Zhao Y.-L, Yang E.-C, Zhang H.-Y (2004) Molecular Recognition Thermodynamics of Steroids by Novel Oligo(aminoethylamino)--Cyclodextrins Bearing Anthryl: Enhanced Molecular Binding Ability by Co-inclusion Complexation. J. Incl. Phenom. Macrocycl. Chem. 50: 311. [26] Li N, Chen Y, Zhang Y.-M, Li Z.-Q, Liu Y (2010) Binding Thermodynamics of Quinolinyl-Modified -Cyclodextrins with Bile Salts. SCIENTIA SINICA Chimica 40: 13551362. [27] Liu Y, Li L, Zhang H.-Y, Yang Y.-W, Ding F (2004) Correlation between Thermodynamic Behavior and Structure in the Complexation of Modified Cyclodextrins and Bile Salts. Supramol. Chem. 16: 371379. [28] Liu Y, Li L, Chen Y, Yu L, Fan Z, Ding F (2005) Molecular Recognition Thermodynamics of Bile Salts by -Cyclodextrin Dimers: Factors Governing the Cooperative Binding of Cyclodextrin Dimers. J. Phys. Chem. B 109: 41294134. [29] Liu Y, Kang S, Chen Y, Cao R, Shi J (2007) Thermodynamics of Molecular Recognition of Bile Salts by 3,6-(Oligoethylenediamino-Bridged) -Cyclodextrin Dimers. Comb. Chem. High T. Scr. 10: 350357. [30] Zhao Y, Gu J, Chi S.-M, Yang Y.-C, Zhu H.-Y, Wang Y.-F, Liu J.-H, Huang R (2008) Aromatic Diamino-bridged Bis(-Cyclodextrin) as Fluorescent Sensor for the Molecular Recognition of Bile Salts. Bull. Korean Chem. Soc. 29: 21192124. [31] Zhao Y, Gu J, Chi S.-M, Yang Y.-C, Zhu H.-Y, Huang R, Wang Y.-F (2009) Bis(Cyclodextrin)s Linked with an Aromatic Diamine as Fluorescent Sensor for the Molecular Recognition of Bile Salts. J. Solution Chem. 38: 417428. [32] Zhao Y, Yang Y.-C, Chi S.-M, Shi H, Zhao Y, Zhu H.-Y, Li Q.-L, Wang Y.-F (2010) Fluorescence Sensing and Selective Binding of a Novel 4,4-Sulfonyldianiline-Bridged Bis(-Cyclodextrin) for Bile Salts. Helv. Chim. Acta 93: 9991011. [33] Liu Y, Yang Y.-W, Yang E.-C, Guan X.-D (2004) Molecular Recognition Thermodynamics and Structural Elucidation of Interactions between Steroids and Bridged Bis(-Cyclodextrin)s. J. Org. Chem. 69: 65906602. [34] Liu Y, Wu H.-X, Chen Y, Chen G.-S (2009) Molecular Binding Behaviours of Bile Salts by Bridged and Metallobridged Bis(-Cyclodextrin)s with Naphthalenecarboxyl Linkers. Supramol. Chem. 21: 409415. [35] Liu Y, Song Y, Wang H, Zhang H.-Y, Wada T, Inoue Y (2003) Selective Binding of Steroids by 2,2-Biquinoline-4,4-dicarboxamide-Bridged Bis(-cyclodextrin): Fluorescence Enhancement by Guest Inclusion. J. Org. Chem. 68: 36873690. [36] Liu Y, Song Y, Chen Y, Li X.-Q, Ding F, Zhong R.-Q (2004) Biquinolino-Modified Cyclodextrin Dimers and Their Metal Complexes as Efficient Fluorescent Sensors for the Molecular Recognition of Steroids. Chem. Eur. J. 10: 36853696. [37] Liu Y, Yu H.-M, Chen Y, Zhao Y.-L (2006) Synthesis of Bridged and Metallobridged Bis(-cyclodextrin)s Containing Fluorescent Oxamidobisbenzoyl Linkers and Their Selective Binding towards Bile Salts. Chem. Eur. J. 12: 38583868. [38] Ikeda H, Nakamura M, Ise N, Oguma N, Nakamura A, Ikeda T, Toda F, Ueno A (1996) Fluorescent Cyclodextrins for Molecule Sensing: Fluorescent Properties, NMR Characterization, and Inclusion Phenomena of N-Dansylleucine-Modified Cyclodextrins. J. Am. Chem. Soc. 118: 1098010988.

Chapter 13

Thermodynamics of Hydration in Minerals: How to Predict These Entities

Philippe Vieillard
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51567

1. Introduction
Many papers have suggested that several specific types of H2O exist. These have been labelled variously as zeolitic, loosely held, structural, crystal, tightly bound and external [1-3]. These labels suggest both the differing apparent energies of H2O as well as their differing apparent structural roles. Three useful distinctions can be made about H2O in compounds: 1. 2. 3. H2O that varies in content as a continuous function of temperature and pressure H2O that changes discontinuously at a unique temperature for a given pressure H2O that is sorbed to external surfaces

The first type (continuously varying H2O) is characteristic of the zeolites and clay minerals and considers that most of the zeolites and clay minerals lose or gain H2O in response to small changes in temperature and pressure over an extended temperature, relative humidity or the nature of cations in exchanged sites. The second type of H2O is similar in nature to that found in hydrates of salts and considers that dehydration occurs over narrow temperature intervals in some compounds. Some zeolites, like analcime and laumontite, do not exchange water at room temperature. This type can be called hydrate H2O and has a specific position in the crystal structure. Hydroxides are excluded from this chapter because the H2O molecule is not identified but is only virtually present as a hydroxyl OH. The third type of H2O is externally sorbed to the crystal and may be referred to as external. This type is present in quantities much smaller than the H2O present within the structure of any zeolite grain size. In the clay minerals, whose specific surfaces are greater than those of zeolites, the water located in inter-particle spaces, in inter-aggregate spaces and at the

2012 Vieillard, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

340 Thermodynamics Fundamentals and Its Application in Science

surface of uncharged clays minerals indicates that a special status of H2O may be different in the regimes of adsorption or of capillary condensation, and this is not considered in this chapter.

2. Definition of thermodynamic entities of hydration

In evaluating the thermodynamic quantities, it is important to define the standard state chosen for a given constituent. In the present study, the standard state for water is chosen as pure water at a temperature of 25C with a vapour pressure of Po, and for the minerals, the dry compound is at a temperature of 25C with a vapour pressure of P=0. The reaction of hydration may be expressed by the following reaction:
X( c ) + n * H 2O( l ) X nH 2O( c )

(1)

If we consider any standard thermodynamic entity of hydration hyd,298 (enthalpy H hyd ,298 free energy Ghyd ,298 , entropy Shyd ,298 , heat capacity Cphyd. and molar volume VHyd.) for a given mineral having n bounded molecules, the entity of hydration is related to the total formation entity f ,298 (enthalpy of ,298.15 free energy G o ,298.15 , entropy S298 , heat f capacity Cp298.15 and molar volume V298) of the mineral by the following:

o ,298 = of ,298 ( X nH 2O ) 0 ,298 ( X ) n * of ,298 ( H 2Oliq ) hyd f

(2)

where of ,298 ( X nH 2O ) and 0 ,298 ( X ) are the thermodynamic entity of formation of the f mineral in the hydrated and dehydrated states, respectively, and 0 ,298 H 2Oliq stands for f the thermodynamic entity of formation of bulk water. The unit of the entity o hyd,298 is based per n moles of bound water or per mole of an anhydrous compound X.

The standard thermodynamic parameters of the hydration water can be calculated if the thermodynamic entities of formation (enthalpy of ,298.15 free energy G o, 298.15 , entropy f S298 , heat capacity Cp298.15 . and molar volume V298.) of the anhydrous and hydrous end members are available in thermochemical tables or calculated from calorimetric measurements. However, the thermodynamic properties of the hydration water can be estimated by considering the hypothetical intra-crystalline reaction:
X( c ) + n * H 2O( hydr ) X nH 2O( c )

(3)

where H2O(hyd) represents the hydration water. The thermodynamics of the intra-crystalline reaction can be written as follows:
o r ,298 = of ,298 ( X nH 2O ) 0 ,298 ( X ) n * of ,298 ( H 2Ohyd. ) f

(4)

By assuming that the standard thermodynamic entities of the intra-crystalline reaction are o equal to zero, i.e., r,298 = 0 , the standard values of the molar thermodynamic entity of the 0 hydration water, f ,298 H 2OHyd , is finally obtained from eqs (2) and (4):

Thermodynamics of Hydration in Minerals: How to Predict These Entities 341

0 ,298 H 2OHyd = n * 0 ,298 H 2Oliq + 0 ,298 f f hyd

) (

)n
( )

(5)

The aim of this chapter is to determine how the thermodynamic entity 0 ,298 H 2OHyd of f the hydration water varies in all inorganic compounds, such as minerals, salts, zeolites and clays. There are two main questions: 1) Is the thermodynamic entity of the hydration water strongly related to the physical-chemical properties of the inorganic compound or does it remain constant within a structural family of inorganic compounds? and 2) What are the adequate relationships that can predict the thermodynamic entity of the hydration water in any mineral?

3. Measurements of thermodynamics of hydration in minerals

Different methods of measurements of thermodynamic entities of hydration are presented in this section: Hydrofluoric acid solution calorimetry. The calorimetric measurements of the heat of dissolution of anhydrous and hydrated compounds provide the enthalpy of formation to form elements. The enthalpies of hydration are obtained by measuring the difference in the enthalpy of the solution in HF acid at approximately 70C, of a hydrated and a dehydrated zeolite [4-6] or at 25C in a HF - HNO3 solution for clay minerals [7]. Transposed-temperature drop calorimetry. The enthalpy of hydration data are obtained by measurements of the heat evolved from a sample dropped at room temperature into a calorimeter maintained at 700800C [8], [9-12]. One of the difficulties associated with this measurement includes the enthalpy effects because of the irreversible structural changes at 700800C. Adiabatic low temperature calorimetry. This is performed on the anhydrous and hydrated compounds to determine the third law of entropy for the zeolites [4-6] and clay minerals [7, 13]. Heat of adsorption combined with adsorption-desorption isotherms. This method provides measurements of integral enthalpies of hydration as a function of the degree of hydration. Some of the difficult parameters to control include the amount of H2O adsorbed by the sample (requires knowledge of the amount of H2O in the sample while immersed in water), the accurate measurement of the initial state of dehydration and the potential for irreversible change in the zeolite structure during dehydration such that the sample does not re-adsorb its full capacity of H2O during immersion [14]. For clays, the measurements of heat of adsorption were performed on eight homoionic SWy-1 montmorillonites [15-17] [18] [19] [20] and on vermiculites [21]. One advantage of the method is that it is a direct measurement of the enthalpy of hydration. Phase equilibriums. The enthalpy of hydration can be determined from the phase equilibrium measurements of the isoteric method, which are plotted as Ln P (or Ln K) versus 1/T at a constant hydration state. The slopes of these lines give the enthalpy of hydration for zeolites [22], [23] and for montmorillonites [24-26].

342 Thermodynamics Fundamentals and Its Application in Science

Gas-adsorption calorimetry. The enthalpies of hydration data are obtained by exposing a bed of zeolite to differing vapour pressures within a calorimeter [27]. One of the difficulties of this method is the kinetic limitations on attainment of equilibrium (slow kinetics requires a very sensitive and stable calorimeter). An advantage of the method is the capacity to measure partial molar enthalpies of hydration directly. Adsorption-desorption isotherms measured at different temperatures. With the Clausius-Clapeyron relationships, the ability to extract the integral and partial thermodynamic entities of hydration from isotherms at any two temperatures was developed by [28, 29] and applied on montmorillonite in [30] and [31] Thermochemistry and Raman spectroscopy. A combined study of thermochemistry and raman spectroscopy has been tested on zeolites [32] and clays [33] [34].

4. Inventory of different values from prediction methods of thermodynamic entities of hydration water
The thermodynamic data of liquid water and ice are displayed in Table 1. The formation properties of the hydration water may vary depending on the nature of the physicalchemical properties of the anhydrous compound [35]. In any case, when the minerals exist as hydrated phases, the presence of water molecules stabilises them. Thermodynamically, this corresponds to G0hyd < 0 kJ mol-1 or G0f,(H2OHyd) < -237.14 kJ mol-1, the value for bulk water at 250C and 1 bar [36]. Additionally, the maximum entropy is for bulk water and implies that S0(H2OHyd) < 69.95 J K-1 mol-1 [36]. The minimum entropy may be assessed by considering the entropy of Ih ice, as refined by Tardy et al. [37] (44.77 J K-1 mol-1). To give a minimum value for G0f(H2OHyd) is more complicated. Ice cannot be of use, for example, because it is not stable at room temperature, and on the contrary, G0f(Ice Ih) > G0f (bulk water), with 236.59 kJ mol-1. For the enthalpy term H0f(H2OHyd), because G0hyd < 0 kJ.mol-1 and S0(H2OHyd) < S0(bulk H2O) for hydrated minerals, then H0hyd must be negative or H0f(H2OHyd) < H0f(bulk H2O) with -285.83 kJ mol-1 [36]. For the heat capacity of hydration water, very few measurements have been actually performed so far. Families Liquid water Ice Ref. 1 2,3 Hf (kJ mol-1) -285.840.04 -292.750.1 Gf (kJ mol-1) -237.180.05 -236.590.1 S Cp V (J K mol-1) (J K-1 mol-1) cm3 mol-1 69.9230.03 75.576 18.064 44.7710.05 42.008 19.228
-1

References: 1 [36]; 2 [37]; 3 [35].

Table 1. Average thermodynamic entities (Hf, Gf, S, Cp and V) of liquid water and ice.

Among the numerous methods of prediction of thermodynamics entities of compounds (salts, and minerals), only twelve are retained and exhibit different values of the thermodynamic entities of ice-like water obtained from the statistical results from the anhydrous and hydrated compounds (Table 2).

Thermodynamics of Hydration in Minerals: How to Predict These Entities 343

Families Sulphates & sulphites Chlorates & Chlorides Zeolites Hydrates Silicates Silicates Hydrates RE chlorides Binary comp. of Na Silicates Silicates Silicates Borates U bearing minerals

Ref.

Nb. comp

Hf (kJ/mole) -301.47.7 -308.38.6

Gf (kJ/mole) -244.47.9 -251.88.5

Cp

(J/K/mole) (J/K/mole) cm3/mole 41.56.0 43.75.9 59.1 395.2 422.7 14.51.2 14.12.3

1 1 2 3 4 5 6 7 8 9 10 11 12 13

41 34 15 342 ? 3 ? 8 42 7 7 6 23 14

-298.620.5

-242.4

40.9 39.34.2 54.123

42.8

14.75 13.70.5

-297.06 -297 -2978.3 43.5 -306.9912.8 -292.374.6 -290.42 -295.58 -239.915.7 -237.28 -241.1 54.86 44.12.0 14 14.60.09 46.4

References: 1 - [35]; 2 - [38]; 3 - [39]; 4 - [40]; 5 - [41]; 6 - [42]; 7 - [43]; 8 - [44]; 9 - [45]; 10 - [46]; 11 - [47]; 12 - [48]; 13 - [49].

Table 2. Average thermodynamic entities (Hf, Gf, S, Cp and V) of hydration water obtained in different prediction models.

All of these models of predictions are built on a simple additive scheme and require knowledge of the thermodynamic entity of the anhydrous compound, the number of water molecules and the thermodynamic entity of formation of ice-like water or of hydration water obtained by statistical regressions. For each thermodynamic entity (enthalpy, free energy, entropy, heat capacity and molar volume), the values are significantly different within the nature of the compounds or minerals. For each prediction model, the nature of family, number of compounds and statistical errors are provided to check the extent and the validity of the model. There appear to be few models of prediction of free energies of hydration, which is the most useful parameter in geochemical modelling. The best way to reach this target is to combine the enthalpy and entropy of hydration. Despite the great diversity of the enthalpy of formation of the hydration water and its great error within different families of compounds, some recent and accurate models of prediction of the enthalpy of hydration are important to introduce for compounds such as salts, zeolites and clays minerals. To improve the accuracy of prediction, the next section develops several models of prediction based on different kinds of minerals displaying recent measurements of the thermodynamic entities of the hydration water closely related either to the environmental conditions and or to the nature and chemical formulas of the anhydrous compounds.

344 Thermodynamics Fundamentals and Its Application in Science

5. Recommended models of prediction of thermodynamic entities

5.1. Enthalpy of formation
Salts: A model of the prediction of hydration enthalpy has been developed and tested on 349 different hydrates salts [50-52]. By considering the following reaction defining the hydration of a salt Ax Bx :
1 2

Ax Bx + n * H 2O( c ) Ax Bx n H 2O
1 2 1 2

(6)

the enthalpy of hydration of the reaction (6) becomes

o H hyd ,298 = H o ,298 Ax Bx nH 2O H o ,298 Ax Bx n * H o ,298 ( H 2O( c ) ) f f f
1 2 1 2

(7)

where n is the number of molecules of crystalline water contained in the hydrate under consideration and H f ,298 (H2O)(c) represents the enthalpy of formation of ice. A parameter + H ( B z2 ) A z1 characterising the anhydrous salt Ax Bx , was defined as follows [50-52]:
1 2

H ( B z2 ) A z1 =

+ 1 o H f ,298 Ax Bx x1 * H o ,298 A z1 x2 * H o ,298 ( B z2 ) f f 1 2 z1 * z2

( )

(8)

This parameter is analogous to the enthalpy of dissolution of an anhydrous salt per equivalent (characterised by the product of charges of the cation and anion). The relationships of the enthalpy of hydration of a salt to the number of the molecules of water and to the nature of the salt is:
+ a H hyd ,298.15 = Az+ * ( n ) * H ( Bz2 ) A z1 + b +

(9)
+

where A z+ and are constants that depend on the nature of the cation A z1 present in the hydrate, n is the number of molecules of the water of crystallisation in the hydrate, and a and b are constants for all hydrates and respectively equal to 0.791 and -80.0 kJ mol-1 [50-52]. Eq. (9) shows that the enthalpy of hydration is closely related to the nature of the cation in the anhydrous salt, to the number of water molecules in the chemical formula and to the nature of the anhydrous salt. The enthalpy of the formation of ice used in Eq. (7) [50-52] comes from Robie & Waldbaum [53] and is equal to -279.8 kJ mol-1. As this value is very different from those given in table 1, the values of coefficients ( A z+ , , a and b) of Eq. (9) need to be determined with H f ,298 H2O(ice)=-292.75 kJ mol-1 by a minimisation technique of the square difference between the measured and calculated heat of hydration. The values of a and b are assumed constants for all hydrated salts and are a= 0.612 and b= 17.07; Eq (9) becomes:
H hyd ,298.15 = A z+ * ( n )
0.612

* B z2 A z1 + 17.07 +
+

( )

(10)

Thermodynamics of Hydration in Minerals: How to Predict These Entities 345

The values of A z+ and for the different salts of cation A z1 are given in table 3 with the respective standard deviations and % errors of the predicted enthalpy of formation of the hydrated salts. An example is given by considering the data of all of the sodium salts displayed in Figure 1A and shows the great variation of the enthalpy of hydration having the same number as the crystalline water. The different straight lines are obtained from Eq. (10) with values of A z+ and for Na+ and are plotted for the different values of the number of crystalline water + molecules and the nature of the crystalline salts ( H ( B z2 ) A z1 ). For a given anhydrous salt + z2 z1 (same value of H ( B ) A ), the enthalpy of hydration per mole of water appears to not be constant but decreases when the number of molecules of the crystalline water increases. Figure 1B displays the enthalpy of crystalline water versus the nature of the anhydrous salt showing the great disparity and shows that the enthalpy of the crystalline water in all of the sodic salts is more negative than those of the hexagonal ice. When the number of crystalline water molecules of any salt increases, the enthalpy of formation of the crystalline water decreases from large values (NaOH. H2O; H f ,298 H2O= -309.25 kJ mol-1) to values close to those of ice (Na2Se. 16 H2O; H f ,298 = -297.22 kJ mol-1) and are different from the average value for 61 Na salts ( H f ,298 = -297.74 kJ mol-1). Cations Li+ Na+ K+ Rb+ Cs+ Be+2 Mg+2 Ca+2 Sr+2 Ba+2 Zn2+ Cd2+ Cu+2 Ni2+ Co2+ Fe2+ Mn2+ Cr+2 UO2+2

A z+
-0.277 -0.294 -0.115 -0.360 -0.577 -0.485 -0.312 -0.270 -0.349 -0.327 -0.211 -0.322 -0.433 -0.176 -0.260 -0.136 -0.238 -0.478 -0.247

-0.341 1.759 -9.168 -6.769 18.954 -3.068 -10.708 -3.892 -1.894 -4.637 -16.461 2.266 -1.791 -18.056 -2.296 -17.806 -5.144 31.459 -7.945

Nb. of data 19 61 15 6 4 7 21 25 20 19 12 8 11 10 11 6 15 3 18

% error1 0.34 0.29 0.66 0.29 0.48 0.25 0.43 0.44 0.32 0.80 0.44 0.33 0.65 0.46 0.36 0.18 0.25 0.28 0.35

Std dev. (kJ/mol H2O) 3.58 3.44 10.70 3.38 6.35 3.48 5.39 4.64 5.93 5.31 6.57 4.29 4.22 2.81 3.60 1.58 6.14 1.77 4.80

1: the % error weighs the difference (in %) between the measured and predicted enthalpy of the formation of the hydrated salts.

Table 3. Values of A z + , , number of data, % error and statistical error per moles of crystalline water.

346 Thermodynamics Fundamentals and Its Application in Science

Figure 1. A Hydration enthalpy of sodium salts versus the parameter H ( B 2 ) A z z+ the formation of the crystalline water versus the parameter H ( B 2 ) A 1 .

+ z1

; B Enthalpy of

Zeolites: The anhydrous compound X (reaction 1) is a zeolite with the following formula:
i = nc Ai Aln Fen Sin ON , in which Al, Fe and Si represent the framework with different Al Fe Si i =1

channels occupied by various exchangeable cations present, which are represented by Az+. A compilation of the average hydration enthalpies per mole of water of 145 diversely originating zeolites measured using different technical methods [54] provided 76 data points from the transposed-temperature drop calorimetry (TTDC), 57 data points from the immersion calorimetry (IC), 6 data points from the phase equilibriums (PE), 5 data points from the gas-adsorption calorimetry (GAC) and 3 data points from the hydrofluoric acid calorimetry (HF). From the selected average enthalpies of hydration of the different zeolites with their chemical formulas (145 data points), a regression equation for the enthalpy of hydration per mole of water is proposed [54]:
H Hyd W = Al

Si

) * e a + b * WP
( )

(11)

where coefficients a and b are

a = 4.664 2.787 * Al ( Al + Si ) + 0.056 * FDanh. 0.003 * H O = site A b = 1.52 + 0.0047 * H O = site A * ( Al Si )

(12) (13)

Coefficients of Eqs. (11) (12) and (13), such as the ratio Al/Si, Al/(Al+Si), FDanh., H O = (site A)(aq) and WP, represent the extra-framework charge, the ratio of tetrahedral

Thermodynamics of Hydration in Minerals: How to Predict These Entities 347

substitution, the framework density of the anhydrous zeolite, the average cation electronegativity in the exchange site and the intracrystalline water porosity, respectively. All of these parameters can be calculated from the chemical formula and the unit cell volume for any zeolite. The framework density (FD) [55, 56] represents the number of tetrahedral atoms per 1000 3 and are obtained as:
FDanh. = ( nAl + nFe + nSi ) / Unit cell Vol * 1000

(14)

The electronegativity of site Az+, defined by HO= (site A), represents the weighed average of HO= Mz+(aq) of nc different cations in the exchanged site A:
i = nc z ni *xi .( HO= Maq+ )
i

HO (site.A) =

i =1

xA

(15)

The number of oxygens balancing site Mz+ (in extra-framework sites) is then:
xA =
i = nc i =1

ni *xi

(16)

The parameter HO= Mz+ (aq) characterises the electronegativity for a given cation Mz+ and is defined as the difference between the enthalpy of formation of the corresponding oxides
H f MiOx

H f Mizi +

(c)

and the enthalpy of formation of the corresponding aqueous cation :

zi + H O = Maq = 1

( aq )

H f MiOx i xi

(c)

-H f Mizi +

( aq )

(17)

where z is the charge of the cation Mz+ and x is the number of oxygen atoms combined with one atom of M in the oxide (x = z/2), such that the difference in Eq. (17) refers to one oxygen atom. A set of internally consistent values was presented by Vieillard & Mathieu [54] and is given in Table 4. The total intracrystalline pore volume, WP, was introduced by Barrer [57] for determining the volume of liquid water that can be recovered thorough the outgassing of the fully hydrated zeolite. Assuming that the unit cell volume of zeolitic water is the same as that of liquid water ( Vu.c . H O = 29.89 3), during the hydration-dehydration processes, the water porosity (WP) can 2 be calculated as the volume of liquid water in 13 of crystal and is expressed as follows:
WP = 29.89 * nH O

(V

u.c . hydr .

(18)

348 Thermodynamics Fundamentals and Its Application in Science

where Vu.c. hyd. represents the unit cell volume of a hydrated zeolite containing nH2O water molecules. Assuming that the number of water molecules nH2O varies from 0 to nH2O max, the unit cell volume of a zeolite can be directly related to the number of water molecules. Although such variations in the unit -cell volume do occur, let us assume a linear variation in the unit-cell volume as a function of the number of water molecules:
Vu.c. hyd = Vu.c . anh. + k * nH
2O

(19)

where Vu.c. anh. represents the unit-cell volume of the anhydrous zeolite. Parameter k weights the variation in the unit-cell volume between an anhydrous zeolite and a fully hydrated zeolite per one water molecule. This parameter can be calculated from the available unit-cell volumes of anhydrous and fully hydrated zeolites. Thus, knowledge of the number of water molecules and the unit-cell volume of anhydrous and hydrated zeolites is required for the calculation of the water porosity:
WP =

(V

29.89 * nH

2O 2

u.c . anh. + k * nH O

)
HO=Mz+(aq) (kJ mol-1) -92.1 -134.6 -181.58 -164.4 -197.07 -124.8 -285.83

(20)

Ions

HO=Mz+(aq) (kJ mol-1) -40.90 65.80 141.00 163.24 170.0 -15.6 -40.4

Ions

Li+(aq) Na+(aq) K+(aq) Rb+(aq) Cs+(aq) Ba+2(aq) Sr+2(aq)

Ca+2(aq) Mg+2(aq) Fe+2(aq) Mn+2(aq) Zn+2(aq) La+3(aq) H+(aq)

Table 4. Parameter HO=Mz+ (aq) of selected cations [54].

By eliminating 9 erroneous data points [54], the regression coefficient for 136 data is R2= 0.880, with a standard error of 3.46 kJ mol-1 for all data, regardless of the nature of the experimental data. Figure 2 displays the predicted enthalpy of hydration of zeolitic water calculated from Eqs. (11) (12) and (13) versus the experimental enthalpy of hydration coming from the different technical measurements. Regression coefficients and standard errors are different within the two main groups: R2= 0.88 and std. err. = 3.41 kJ mol-1 for TTDC data (67 data points), R2= 0.658 and std err. = 2.66 kJ mol-1 for the IC data (57 data points). When Al/Si and Al/(Al+Si) = 0, the hypothetical integral enthalpy of water in zeolites obtained by the extrapolation of Eq. (11) is 0, which corresponds to the enthalpy of hydration of water in cordierite (2.2 1.6 kJ mol-1 from Carey [58]). Unlike zeolites, the water in cordierite is not coordinated by cations, so the molecular environment of H2O in cordierite is similar to that of H2O in water.

Thermodynamics of Hydration in Minerals: How to Predict These Entities 349

Figure 2. Predicted enthalpy of the hydration of zeolitic water calculated from Eq. (11) versus the experimental enthalpy of hydration using different technical measurements.

A detailed computation of the enthalpy of hydration is given as an example for three natural clinoptilolites (-Ca, -Na and K) with the following chemical formula given by [22]:
-

Clinoptilolite-Na: (Ca0.12Mg0.29K0.75Na5.21)(Al6.78Fe0.06Si29.2)O72.05-21.3H2O Clinoptilolite-K: (Ca0.13Mg0.25K5.84Na0.27)(Al6.85Fe0.1Si29)O71..9-18.5H2O Clinoptilolite-Ca: (Ca2.34Mg0.57K0.9Na0.18)(Al6.7Fe0.017Si29)O71..8-21.9H2O

The values of the ratio Al/Si yield a constant value of 0.235. The electronegativity of the exchangeable site Az+ for clinoptilolite-Na is, for example, the average electronegativity of four cations (Na+, K+, Ca2+ and Mg2+ (table 4)) as follows:
HO= (site.A) =
+ + 2 2 2.607* HO= Naaq + 0.375 * HO= Kaq + 0.12* HO=Caaq+ + 0.29 * HO= Mgaq+

3.39

) (21)

i.e., H O = (site.A) =51.42 kJ mol-1. The unit-cell volume of the anhydrous clinoptiloliteK (V u.c.) is 2019.51 3 [59]. This means that there are 35.95 tetrahedral atoms (6.95+0.1+29) in 2019.51 3; which indicates that FDanh.= 17.8 tetrahedral atoms in 10003. The unit-cell volume of the hydrated clinoptiloliteK (at saturation or fully hydrated) with 18.5 moles of zeolitic waters is 2089.50 3 [54], which is slightly greater than the anhydrous form and allows the setting of the relationship of water porosity versus the number of hydration water moles:

350 Thermodynamics Fundamentals and Its Application in Science

WP =

( 2019.51 + 3.78 * n )
H2O

29.89 * nH O
2

(22)

From these previous examples, the parameters requested for the prediction of the enthalpy of hydration are displayed in table 5 for the three clinoptilolites (-Na, -K and Ca). Zeolite minerals V u.c. anh. (3) 2000.00 1 2019.51 2 2019.51 2 Vu.c. hydr. (3) 2140.00 1 2089.50 2 2089.50 2 k HO= Site A kJmol-1 51.39 109.16 -64.60 FD. Anh. 18.02 17.80 17.78 WP Al/Si

Clinoptilolite -Na Clinoptilolite -K Clinoptilolite -Ca

1 - [60]; 2 - [59]

6.35 3.78 3.20

0.31 0.26 0.31

0.23 0.24 0.23

Table 5. Unit-cell volume of hydrated and anhydrous clinoptilolite, factor k (eq. 20), mean HO=Az+ (site A), framework density and ratio Al/Si for 3 clinoptilolites (-Na, K and Ca).

From the values given in table 5, the enthalpy of hydration of the zeolitic water, H Hyd W , can be computed with Eqs. (11), (12) and (13) and are close to experimental values from [22] (Table 6). The model of the computation of the enthalpy of hydration of the hydration water represents a very useful tool and contributes to the knowledge of enthalpies of formation of hydrated zeolites from anhydrous ones [61]. A useful method for avoiding complications at the outset of a thermodynamic analysis is to emphasise the H2O rather than the zeolite structure. Using such an approach, the equilibriums can be considered as the equilibrium between the H2O in the fluid-vapour phase and the H2O in the zeolite. According to the definition of equilibrium, the chemical potential of H2O in the vapour phase must equal the chemical potential of the H2O component in the zeolite. Any series of measurements of the amount of H2O in zeolite at a known fugacity (or partial pressure of H2O under ideal gas conditions) provides the basis for the thermodynamic description of the system. The most elegant approach to develop a thermodynamic formulation is to know the partial molar enthalpy of hydration, H , and the partial molar entropy S . A constant partial molar enthalpy of hydration indicates an ideal mixing of the H2O. Zeolite minerals Clinoptilolite.-Na Clinoptilolite -K Clinoptilolite-Ca
H Hyd W H Hyd W

predicted (kJ mol-1 H2O) -22.20 -22.20 -20.24 -29.03

measured (kJmol-1 H2O) -30.17 -23.97 -32.87

References [22] [22] [22]

Table 6. Predicted and experimental enthalpy of hydration, H Hyd W of clinoptilolites Na, -K and Ca.

Thermodynamics of Hydration in Minerals: How to Predict These Entities 351

The bulk enthalpy of hydration or the integral enthalpy of hydration can be used as the product of the enthalpy of hydration of the water times the number of zeolitic water:

( a + b * WP ) * n H Hyd Z = H Hyd W * nH O = Al * e H2O 2 Si

(23)

As the integral hydration enthalpy H Hyd Z is the integral function of the partial molar enthalpy hydration from nH O = 0 (corresponding to an anhydrous zeolite) to a maximum 2 value of nH O max (corresponding to the fully hydrated zeolite), the partial molar enthalpy of 2 hydration relative to the liquid water, H , which is the derivative function of H Hyd Z , becomes:
H Hyd Z = 1 n= nH2O H * dn nH O n= 0
2

(24)

29.89 * nH O a + b* 2 V u.c.anh. + k * nH O 2 H = Al * e Si

* 1 + 29.89 * b * Vu.c. anh. * nH2O 2 Vu.c. anh. + k * nH O 2

(25)

The fractional water content can be obtained if the maximum number of zeolitic waters is known at the saturation state and is equal to:

nH nH

2O

(26)

2 O ,max.

From values of table 5, the partial molar enthalpy of clinoptilolites K, Na and Ca can be calculated versus the fractional water content and plotted in Figure 3 with the experimental partial molar enthalpies measured from immersion calorimetry [62] and from thermogravimetry [22]. The modelled values of the partial molar enthalpy for the three clinoptilolites appear to be closer to the data from the immersion calorimetry than from thermogravimetry. The second important point is the fact that the calculated and experimental partial molar enthalpy of hydration has a similar behaviour. The partial molar enthalpy of hydration per mole of H2O increases smoothly from low water content to high and indicates that the H2O in clinoptilolites occupies a continuum of energetic states. This is not the case for chabazite-Ca [23], which exhibits three energetically distinct types of H2O. This shows that, within different zeolites with the same exchangeable cation, the partial molar enthalpy as a function of the hydration degree may display different functions. This is the reason why the fundamental relationship verifying the enthalpy of hydration by means

352 Thermodynamics Fundamentals and Its Application in Science

of the chemical composition and the accurate knowledge of the unit-cell parameters of anhydrous and hydrated zeolites needs to be improved with new data of hydration enthalpy of the partially hydrated zeolites on the one hand and a better fit of the effective water porosity as a function of the hydration degree on the other hand. Then, the thermodynamic description of the hydration-dehydration process can be modelled as a function of pressure and temperature with the contribution of predicted enthalpies of hydration and entropies of hydration.

Figure 3. Partial molar enthalpy of hydration of K-, Na- and Ca- clinoptilolites derived from a model in [54], immersion calorimetry [62] and thermogravimetry results [22]

Clay minerals:

Unlike zeolites, smectites are clearly not inert phases, as the particles size increases with the relative humidity [15]. Adsorbed water is distributed throughout the interlayer space, the outer surfaces of particles and the open pores space in the sample. [15-17] provided measured values of the surface covering waters for both the hydration and dehydration reactions of a set of eight homo-ionic SWy-1 montmorillonites saturated by alkali and alkaline-earth cations from their BET specific surface area (Table 1) and their basal spacing variations with relative humidity. To quantify the effective amount of water involved in the hydration reaction, the amount of poral H2O must be quantified and subtracted from the total amount of H2O taken up by the clay sample. The number of external surface water molecules (expressed in mmol/g dry clay) can be expressed as a function of relative humidity [63]. There are numerous papers about the adsorption-desorption isotherms performed on various clays minerals, but few are devoted to the acquisition of enthalpy of

Thermodynamics of Hydration in Minerals: How to Predict These Entities 353

hydration-dehydration on SWy-1 [15-17, 64] [18, 19, 30] [20] [34] [24, 26, 65] [25] and on vermiculites [21]. All recent predictive models of the hydration of smectites are based on an approach that uses the solid solution initiated by Ransom & Helgeson [66]. The hydration of a smectite is considered through the following reaction between hydrated and dehydrated end-members:
Smectite + nm * H 2O( l ) Smectite nm * H 2O( i )

(27)

where nm represents the maximal number of moles of water that can be included in the smectite on the basis of a half-cell (i.e., O10(OH)2). One considers the interlayer water H2O(i) (where subscript i stands for interlayer) as a variable weighing the hydration ratio. The amount of interlayer water in a smectite is proportional to the mole fraction of hydrated end-member: x*H2O= nm*xhs=(1-nm)*xas; to the mole fraction of the hydrous end-member, xhs or to the anhydrous end-members xas. Ransom & Helgeson [66] considered the system hydrated smectite anhydrous smectite + bulk water as a strictly regular binary solid solution by considering the free energy only. Thus, the excess free energy of mixing can be expressed as follows:
Gxs = xas * ( 1 xas ) * WG

(28)

where WG is an excess mixing constant. The integral Gibbs free energy of hydration is:
GHyd = xhs * GHyd ,298 + xhs * ( 1 xhs ) * WG

(29)

in which GHyd ,298 is the standard free energy of hydration. The previous parameter and WG are determined only from adsorption isotherms by assuming a maximal number of moles of interlayer water fixed to 4.5 moles. As there are no experimental measurements of heat of adsorption, the standard enthalpy of hydration, H Hyd ,298 , is determined from GHyd ,298 by -1 mol-1 [67]. From calculated assuming a constant value of S298 H2O(i) equal to 55.02 J K H Hyd ,298 , the standard enthalpy of formation of the interlayer water, H f ,298 ( H 2O )i , is given in table 7.

Vidal et al. [68-69] have assumed that a smectite could be considered strictly regular solid solutions between four end-members with 0.7 H2O, 2 H2O, 4 H2O, and 7 H2O. Those compositions correspond to four different hydrated states (with 0, 1, 2, and 3 water sheets, respectively). For any strictly regular solid solution, the integral enthalpy of hydration is expressed as the following:
H Hyd = xhs * H Hyd ,298 + xhs * ( 1 xhs ) * WH

(30)

with
0 H hyd ,298 = nm * H 0 ,298 H 2O( i ) H 0 ,298 H 2Oliq f f

(31)

354 Thermodynamics Fundamentals and Its Application in Science

The hydration enthalpy is retrieved from data of [24] for montmorillonite Na and K and derived from differential heats of adsorption obtained from the measurements of the heat of immersion [18, 20] for Na-, Ca- and Mg- montmorillonite. Thus, an integral enthalpy of hydration H f ,298 ( H 2O )i is provided for each of the four solid solutions with nm equal to 0.7, 2, 4 and 7 and is given in table 7. Vieillard et al. [63] consider the hydration of a smectite to be an asymmetrical regular solid solution between anhydrous and hydrated smectite.
Units (kJ mol-1) H2O
1 2

Cs

Rb

K -290.45 -295.50 0. -293.58 -10. -291.96 -10. -291.05 -10. -288.16 15.0 -68.0

Na -291.25 -299.71 0. -295.90 -10. -293.83 -10. -292.33 -10. -290.01 8.0 -33.0

Ba -294.14

Sr -294.57

Ca -294.86 -301.43 0. -298.60 -10. -296.25 -10. -293.86 -10.

Mg -295.71 -302.86 0. -300.05 -10. -297.62 -10. -294.69 -10. -296.56 -49.0 -129.0

H f ,298 ( H 2O)i
H f ,298 ( H 2O )i
W
H2

4.5 -289.93 -290.23 0-0.7 0-2 0-4 0-7 5.5 -287.47 -288.01 16.0 -90.0 19.0 -95.0

H f ,298 ( H 2O)i 2
WH 2

H f ,298 ( H 2O)i
WH 2

H f ,298 ( H 2O )i
WH 2

H f ,298 ( H 2O)i
WH
3
1

-292.10 -60.0 -75.0

-292.65 -55.0 -90.0

-294.72 -60.0 -100.0

WH

3
2

1 [66]; 2 [68]; 3 - [63].

Table 7. Standard thermodynamic enthalpy H f ,298 ( H 2O)i (in kJ mol-1) of interlayer water and Margules interaction parameters for the system H2O smectite.

The integral hydration enthalpy is obtained by the following relationships:

H Hyd = xhs * H Hyd ,298 + xhs * ( 1 xhs ) * WH * xhs + WH * ( 1 xhs ) 2 1

(32)

in which H Hyd ,298 and Margules parameters WH and WH are determined by a 1 2 minimisation procedure applied to the difference between computed and calorimetric integral enthalpies on eight homoionic montmorillonite SWy-1 [15-17] and given in table 7. The maximum number of moles of interlayer water was set to 5.5 moles. Figure 4A displays the comparison of integral enthalpy of hydration of a smectite- Na computed from the three models developed previously with different experimental values.

The curve 1 in Figure 4A (yellow dotted line) comes from model of Ransom & Helgeson [66], is linear and is obtained from the following equation of integral enthalpy of hydration:

H Hyd ,298 = 24.39 * xhs

(33)

Thermodynamics of Hydration in Minerals: How to Predict These Entities 355

where the coefficient -24.39 is computed from H f ,298 ( H 2O )i given in Table 7. The curves 2b, 2c and 2d (green dotted lines) displayed in Figure 4A come together from the model of Vidal et al. [68] and are graphically represented by four truncated lines with their respective equations:

0 layer ( 0 < x hs < 0.7 ) : H Hyd ,298 = 9.716 * xhs 1 layer ( 0<xhs <2.0 ) : H Hyd ,298 = 20.14 * xhs + xhs * ( 1 xhs ) * 10.0
2 layers ( 0 < x hs < 4.0 ) : H Hyd ,298 = 32.0 * xhs + xhs * ( 1 xhs ) * 10.0

(34) (35) (36)

Figure 4. A Integral enthalpy of hydration versus the number of interlayer cation; B Standard enthalpy of formation of interlayer water versus the nature of the interlayer cation.

3 layers ( 0 < xhs < 7.0 ) : H Hyd ,298 = 45.5 * xhs + xhs * (1 xhs ) * 10.0

(37)

The curve 3 (black line) in Figure 4A comes from the model of Vieillard et al. [63] and is represented by the following equation:
H Hyd = 23.0 * xhs + xhs * ( 1 xhs ) * 8.0 * xhs 33.0 * ( 1 xhs )

(38)

It appears that integral enthalpy of hydration modelled by Vieillard et al. [63] (black line) based on experimental measurements of heat of adsorption from [15-17] encompasses nearly all experimental data. As the standard entropy of hydration is assumed constant in [66] and [68] models, the integral hydration enthalpies provided by these two previous models are nearly linear. Those obtained by [68] exhibit three sections of curves corresponding to the three states of hydration (1, 2 and 3 water layers). In Figure 4B, a relationship between the standard state enthalpy of interlayer water with the nature of the interlayer cation located in the SWy-1 montmorillonite with a constant layer

356 Thermodynamics Fundamentals and Its Application in Science

charge of 0.38, characterised by its electronegativity (HO=Mz+ (aq), Table 4) is proposed [63] and given as follows:
H f ,298 ( H 2O )i H f ,298 ( H 2O )( l ) = 0.02784 * H O = M z + 6.275

(39)

Lowering the electronegativity of cation in the interlayer sites stabilises the enthalpy of formation of the interlayer water. It should be kept in mind that Eq. (39) has been settled for the same support, i.e., a constant layer charge. For natural montmorillonite-Na, most enthalpies of hydration of the interlayer water are consistent within a narrow range of interlayer charge, IC (0.31<IC<0.38) [63]. Due to the lack of calorimetric measurements of enthalpy of hydration for high charge (IC>0.5) and low charge (IC<0.3) montmorillonites, the variation of the standard hydration enthalpy as a function of the layer charge remains highly questionable. An important remaining matter of discussion is the extent to which the model is able to predict hydration properties of dioctahedral and trioctahedral smectites with different layer charges and compositions.

5.2. Entropy
Salts: Average values of the entropy of hydration water were obtained [39] and [35] within chlorides, sulphates and salts (table 2). These average values of salts appear very similar to the value of entropy for crystalline water, S=40.17 J/K-1 Mol-1 [70]. To improve the accuracy of prediction, statistical relationships between entropy and the molar volume of hydration should be investigated. Zeolites: Initially, an average value of entropy of zeolitic water was proposed by Helgeson et al. [70] and was equal to SH2O (zeol) = 58.99 J/K-1 Mol-1. From very few available calorimetric measurements of anhydrous and hydrated zeolites [4, 6, 71], it has been shown that the entropy of hydration water, at saturation, remains constant at approximately 52.0 J/K-1 Mol-1 [72]. Some authors provide slight deviations of entropy of hydration depending of the nature of cations in clinoptilolite [22]. Clay minerals: Entropies of interlayer water in clay minerals have never been measured directly, but have been evaluated from indirect measurements such as a contribution of experimental enthalpies of immersion and adsorption-desorption isotherms [63] [34] or from the Clausius-Clapeyron rules with adsorption isotherms performed at different temperatures [31], [30]. A constant value 55.0 J/K-1 Mol-1 for the entropy of interlayer water has been chosen [67] and [68] regardless of the nature of the interlayer water and the numbers of interlayer waters layers. By considering the hydration of a smectite always as a symmetrical regular solid solution, the integral entropy is expressed as in [63]:
SHyd = xhs * SHyd R xhs * ln ( xhs ) + (1 xhs ) * ln ( 1 xhs )

+ xhs * ( 1 xhs ) * WS * xhs + WS * ( 1 xhs ) 2 1

(40)

Thermodynamics of Hydration in Minerals: How to Predict These Entities 357

with

0 0 0 Shyd ,298 = nm * S298 H 2O( i ) S298 H 2Oliq

(41)

where SHyd , WS , and WS represent the standard entropy of hydration and Margules 1 2 parameters of the excess entropy of mixing, respectively. The integral entropy is expressed in J K-1 mol-1 of smectite based on O10(OH)2. The determination of these parameters is retrieved from values of H Hyd , WH , and WH obtained previously in the minimisation 1 2 procedure of integral hydration enthalpy and from the experimental adsorption-desorption isotherm interlayer water versus relative humidity. This minimisation procedure uses a least square method and provides SHyd , WS and WS (Table 8).
1 2

S298 H 2O( i ) 1

WS

WS

SHyd M z +( aq ) 2

Cs+ Rb+ K+ Na+ Ba2+ Sr2+ Ca2+ Mg2+

1 [63]; 2 - [73].

J/K/mole 64.6 63.8 63.7 59.8 55.7 54.3 51.5 45.4

J/K/mole 163.5 142.0 104.0 49.1 -116.0 -117.8 -93.5 -42.8

J/K/mole -348.0 -355.0 -267.5 -94.0 -211.5 -244.5 -270.5 -380.0

J/K/mole -78. -84. -93. -130. -224. -261. -271. -350.

Table 8. Standard thermodynamic enthalpy SHyd of interlayer water, Margules interactions

parameters and hydration entropy of the ion under its hydrated aqueous state for the eight cations.

Figure 5A displays the comparison of the integral entropy of hydration of a smectite- Na computed from the three models [67] [68] and [63] developed previously with different experimental values. As indicated in the enthalpy section, integral hydration entropies modelled by [66] (yellow dotted line, N1) and [68] (green dotted line, N2a, 2b and 2c corresponding to 1st, 2nd and 3rd layer) are linear and merge together. In the model proposed by Vieillard et al. [63], three calculated integral entropies of SWy1-Na water system were plotted in Figure 5A and correspond to the adsorption (red line), the desorption (blue line) and the theoretical equilibrium water Swy1-Na (black line, N 3), whose equation is given:
SHyd = 55.8 * xhs R xhs * ln ( xhs ) + ( 1 xhs ) * ln ( 1 xhs ) + xhs * (1 xhs ) * 49.05 * xhs 94.0 * ( 1 xhs )

(42)

The comparison of hydration-dehydration curves calculated by [63] with those provided by Fu et al. [34] show an opposite interpretation. The data from [34] show that integral entropies during adsorption are less negative than those during desorption. Data from our model show the opposite. This difference is explained by the fact that from experimental

358 Thermodynamics Fundamentals and Its Application in Science

works of [34], adsorption follows desorption, while with our data, desorption follows adsorption. Thus, a maximum entropy difference between hydration and dehydration functions can be depicted and is equal to 18 J/K/mole. These observations show the importance of movement of exchangeable cations from ditrigonal cavities and the rotation of tetrahedrals in the tetrahedral sheets when dry collapsed layers are progressively exposed to water vapour.

Figure 5. A Integral entropy of hydration versus the number of interlayer cation; B Standard entropy of formation of interlayer water versus the nature of the interlayer cation.
A correlation between the entropy of interlayer cation S298 ( H 2O )i with the theoretical z+ [73] (Table 8), of the interlayer cation [63] is displayed in hydration entropy, Shyd M Figure 5B with the following equation:

S298 ( H 2O)i S298 ( H 2O)( l ) = 0.06542 * S hyd M z + 0.413

(43)

Negative values of the hydration entropy of the hydrated ion lower the hydration entropy of the interlayer water.

5.3. Heat capacity

Salts: An acceptable average heat capacity ranging from 39.05.3 J/K-1mol-1 for sulphates and sulphites to 42.02.7 J/K-1mol-1for chlorates and chlorides has been proposed [35] and seems to be close to the average value of heat capacity for crystalline water Cp=40.04 J/K-1mol-1 [70]. Only the average heat capacity function of crystalline water was proposed [70]:
Cp( H 2O )salts = 29.75 3.448 * 10 2 * T

(44)

Zeolites: Three equations of heat capacities ([41], [74] [45] ) were proposed for a set of silicate minerals, including analcime and natrolite, and are displayed in table 9.

Thermodynamics of Hydration in Minerals: How to Predict These Entities 359

Heat capacity function (298.15- 500 K) Eq. A Eq. B Eq. C Eq. D

Cp( H 2O )sil = 56.61 2.64 * 10 2 * T 0.5 Cp( H 2O )sil = 87.62 + 7.58 * 10 2 * T 0.5 + 0.53 * 107 * T 3 Cp( H 2O)sil = 39.65 + 32.5 * 10 3 * T 4.694 * 10 5 * T 2
Cp( H 2O ) zeol. = 23.999 + 66.295 * 10 3 * T 0.3948 * 10 5 * T 2

[41] [74] [45] [72]

Table 9. Heat capacity functions for zeolites minerals

Heat capacities of the hydration in zeolites have been performed by Neuhoff & Wang [75] on three zeolites (analcime, natrolite and wairakite) and exhibit marked variations in the heat capacity of hydration with temperature. Four zeolites (mordenite, wairakite and two different values from different sources for analcime and natrolite) for which the heat capacity of zeolitic water can be obtained by a difference between the heat capacities measured on both the anhydrous and the hydrated phases [72] are represented in Figure 6A. Also displayed are the heat capacity values of water in all its states (ice, liquid and vapour) for comparison [35]. The heat capacity values of zeolitic water obtained by minimisation techniques (Eq. D of table 9, turquish line) matches with the heat capacity function equations of [74] and [45].

Figure 6. Heat capacity of zeolitic water versus temperature: A Heat capacities of zeolitic water in zeolites, in different prediction models and of water in its various states (l for liquid, c for ice and g for vapour); B Experimental heat capacities of zeolitic waters in natural zeolites and predicted heat capacities from Eq. (46).

Eq. D of table 9 provides a statistical error of 4.51%, 2.35% and 4.18% for hydrated zeolites at 298.15 K, 400 K and 500 K, respectively. To improve the accuracy of the prediction of the heat capacity of hydrated zeolites, one considers the normalised hydration volume, which is the difference of unit-cell volume (Vu.c.) between the hydrated and dehydrated forms for any zeolite per zeolitic water molecule [72]:

VHy Deh =

(V

u.c . hydr .

Vu.c.dehyd.

nH O
2

(45)

360 Thermodynamics Fundamentals and Its Application in Science

Cp( H 2O)zeol. = 55.85 13.073 * + 0.008 + 0.0048 *

( V ( V

Hy Deh

Hy Deh

) + 0.0062 + 0.0305 * ( V ) * T
2

Hy Deh

) * T

(46)

The heat capacities of hydration water given in Figure 6B have been calculated for the four hydrated zeolites (mordenite, analcime, wairakite and natrolite) from the unit-cell volumes of their dehydrated and hydrated forms [72]. It can be observed that the heat capacities of hydration water calculated in this way are much better than those obtained by Eq. D of table 9 (indicated in Fig. 6B as a turquish full line). With this improvement, the errors made on hydrated zeolites decrease to 3.5%, 2.35% and 3.89% at 298.15 K, 400 K and 500 K, respectively.
Clay minerals: The heat capacity function comes initially from [67] and is assumed to be independent of the nature of the interlayer cations:
Cp( H 2O )clays = 37.84 + 51.631 * 10 3 * T 4.0959 * 10 5 * T 2

(47)

This heat capacity equation has also been used by [68] and by [63] in the behaviour of thermodynamic entities versus temperature.

5.4. Molar volume

Salts: Only [35] provided an average value for different salts: 14.51.2 cm3/mole for sulphates and sulphites and 14.12.3 cm3/mole for chlorides and chlorates. These average values appear to be similar to the molar volume of crystalline water (V(H2O)(salts)= 13.7 cm3/mole [76]). Zeolites: No study on the variation of the molar volumes of the zeolitic water has been performed. Numerous values of molar volumes of hydrated and anhydrous zeolites have been provided and gathered in such calculations for enthalpy and entropy of hydration [77], [61], [72]. In the study of the relationship between entropy and molar volume within zeolites [72], an average value of the molar volume of hydration water has been calculated and is V(H2O)(zeol)=2.06 cm3/mole, which is not significantly different from those proposed by Helgeson (V(H2O)(zeol)= 8 cm3/mole) estimated from standard molal volumes of zeolites. The weak value of the molar volume of the hydration water is explained by the fact that the anhydrous zeolites exhibit a rigid (Si, Al) framework with different channels or cavities occupied by exchangeable cations. During the hydration process, the water molecules are bound to cations inside the cavities, do not affect the framework and have a weak impact on lattice parameters. Clay minerals: The molar volume of the interlayer water was initially determined by Ransom [67] and also used by [68] and by [63] in thermochemical calculation. Its value is V (H2O)I = 17.22 cm3/mole. This value, greater than those of salts, is explained by the fact that, during hydration, the molar volume of clay minerals increases in one dimension characterised by basal spacing (Miller index 001).

Thermodynamics of Hydration in Minerals: How to Predict These Entities 361

6. Discussion of the Gibbs free energy of the formation behaviour of the hydration water in environmental conditions
The relationships among the free energy change, enthalpy of reaction and entropy for an isothermal process is:

G = H T * S

(48)

where G stands for free energy change, H for enthalpy of reaction, S for the change in entropy and T for the absolute temperature. This relationship holds true for both the integral entities that are represented by G , H and S and for the partial quantities that are represented by G , H and S .
Salts: The free energy of formation of the hydration water of hydrated salts can be calculated from the enthalpy and entropy of hydration given previously. A relationship has been demonstrated by the statistical regressions [35] between the enthalpy and Gibbs free energy of crystalline water in the following relation:
G f ,298 ( H 2Osalts ) = 1.008*H f ,298 ( H 2Osalts ) + 59.406

(49)

The predicted values contribute to the variations of solubility products and the cation selectivity constants among the series of salts. An example is given in [78] for two series of hydrated salts of MgCl2 and SrCl2. For zeolites and clays, the adsorbent (a single smectite or zeolite phase) is supposed to be inert so that the derived enthalpy and entropy functions formally represent the energy variations between the adsorbed and the bulk water.

The integral free energy of hydration Ghyd may be determined from the gravimetric isotherms of adsorption of the water vapour by the following expression [79]:
Ghyd = R*T*
n = nw n=0

P Ln *dn P 0

(50)

where R = 8.314 J.mol-1K-1 is the ideal gas constant, n is the amount of adsorbed water, P is the partial water vapour pressure, and P0 is the saturated water vapour pressure at temperature T (P/P0 = Relative Humidity/100). This value can be determined by plotting R*T*Ln(P/Po) versus the water content n (adsorbed or desorbed) and determining the area under the curve from 0 to nw. When nw approaches 0, R*T*Ln(P/Po) approaches infinity, making integration somewhat difficult.
Zeolites: Eq. (50) has been used on three clinoptilolites (-Na, -K and -Ca) [22] and show a good correlation between the Gibbs free energies calculated from the adsorption-desorption isotherms and from the contribution of the enthalpy of hydration and the entropy of hydration extracted from the equilibrium at high temperature. The model described by Carey & Bish [62] used a solution solid model between anhydrous and hydrated zeolite, and the variation of the

362 Thermodynamics Fundamentals and Its Application in Science

integral Gibbs free energies of hydration is expressed as a function of a parameter characterising the ratio of H2O/(maximum H2O). The main difficulty in these calculations is the determination of the maximal amount of hydration water at the saturation state (p/p=1).
Clay minerals: Among the numerous measurements of adsorption-desorption isotherms on various clays, very few works provided a consistent Gibbs free energy of adsorptiondesorption due to the difficulty of measurements in the low relative humidity domains. By choosing the system of water SWy-1-Na, Figure 7 displays the adsorption-desorption isotherms (Figure 7A), the variation of the integral free energy of hydration versus the number of moles of the interlayer water (Figure 7B) and versus the relative humidity (Figure 7C) and the variation of the free energy of formation of the interlayer water versus the relative humidity (Figure 7D).

Figure 7. A - Adsorption-desorption isotherms; B - Integral free energy of hydration versus the number of moles of interlayer water; C - Integral free energy of hydration versus the relative humidity; D - Free energy of formation of the interlayer water versus the relative humidity.

Thermodynamics of Hydration in Minerals: How to Predict These Entities 363

In each figure, the data of the free energy of hydration (Eq. 50) from the experimental isotherms [15, 16] (blue square for adsorption and red square for desorption) and the free energy of hydration are computed and are reported for comparison of three different works: the Vieillard et al. model [63] (blue, red and black lines for adsorption, desorption and theoretical equilibrium, respectively), the Ransom & Helgeson model [66] (dotted yellow line), and the Vidal & Dubacq model [68] (dotted green line). For the adsorption and desorption reactions, the modelled isotherm calculated by the Vieillard et al. model [63] (blue and red lines, respectively) agrees well with the experimental data acquired by [15, 16] in high relative humidity. At low relative humidity, the uncertainty appears very important between the experimental desorption data and the desorption curve from the model in [63] (3 kJ/mol for integral free energy, Fig C) due to the analytical limits and mathematical constraints. The theoretical equilibrium (black line) suggests that the hydration of a Na-SWy-1 begins at only R.H.= 0.15 (Figure 7A), which correlates well with the experimental adsorption but not with the desorption. The integral Gibbs free energy of hydration (figure 7B and 7C) and the Gibbs free energy of the interlayer water (Figure 7D) of the theoretical equilibrium between the water and Na-Smectite (black line) are plotted and correspond to the average values of calculated adsorption-desorption isotherms. The theoretical curve of equilibrium between the water and Na-smectite provided by Ransom & Helgeson [66] displays a small number of moles of the interlayer water close to saturation, while those of Vidal & Dubacq [68] reproduce this stepwise behaviour fairly well because it assumes three solid solutions with 3 end-members (0.7 H2O, 2 H2O, 4.5 H2O). However, it does not match the behaviour of water adsorption versus relative humidity, which is not a step function. The advantage of this approach is that it allows reproducing the observed stepwise evolution of the smectite volume and water content with varying T and relative humidity. At low relative humidity, as the hydration of a Na-SWy-1 begins at only R.H.= 0.15, the computations from [68] and [66] (green and yellow dotted lines) do not match the observed isotherms because there is a strong hydration in the RH= 0.0- 0.18 range. During the interval of R.H.=0.0-0.2, the adsorption of water molecules occurs predominantly on the external surface of tactoids (basal external faces and edges of tactoids). This explains why we observe a very negative integral free energy in the low relative humidity domain for these two models (green dotted line and in a less extent, yellow dotted lines). The necessity to take into account only the hydration water, sensu-stricto, is justified. This procedure has been incompletely performed by Ransom & Helgeson [66] with the external surface of a kaolinite to estimate the amount of surface covering water, while Vidal & Dubacq [68] made no correction on the gravimetric waters. At high relative humidity, Vidal & Dubacq [68] proposed a third step of hydration, with the number of water molecules increasing up to 7 moles per O10(OH)2. All of the experimental isotherms performed by [15, 16] exhibit an increase in the water contents beyond RH = 0.9, identified as osmotic water. The osmotic swelling of the sodium montmorillonite corresponds to an

364 Thermodynamics Fundamentals and Its Application in Science

iso-enthalpic effect, with the heat of adsorption being constant. The theoretical equilibrium between water and Na-SWy-1 (black line) matches the experimental dehydration near saturation. The cationic exchange and hydration reactions are intimately related, and the cationic exchange reactions not only modify the interlayer composition but also imply changes in the interlayer water content. These changes can be quite significant and can be evaluated using the Vieillard et al. model [63], which provides a theoretical number of moles of interlayer water and integral thermodynamic properties (H, S and G) for the SWy-1 montmorillonites. Thus, the cationic exchange reactions may depend on an external parameter, such as the relative humidity.

7. Conclusions and perspectives

This chapter demonstrated some useful relationships in the prediction of thermodynamic entities. Some important areas are still lacking and deserve further study. Among the anhydrous and hydrated salts, the relationships between the entropy and molar volume may exist and will improve the prediction of the entropy of hydration. The function of the average heat capacities for the hydration water is lacking and will help in characterising the behaviour of the crystalline water versus temperature. In the zeolite field, the relationships among the molar volume, water content and relative humidity may exist within zeolites families with a reversibility in the hydration-dehydration processes. These relationships will contribute to a better understanding of the behaviour of partial molar enthalpy versus the degree of saturation or versus the relative humidity. In the clay Minerals, three following recommendations are needed: 1) to dissociate the hydration water from the gravimetric water; 2) to measure the heat of hydration among the dioctahedral and trioctahedral clays; and 3) to find a relationship between the hysteresis and the entropy of the hydration-dehydration by the molecular modellings. With these three aims, the knowledge of mechanisms of the hydration within clay minerals will advance our understanding of cationic exchange in soils under various physical and chemical constraints.

Author details
Philippe Vieillard CNRS IC2MP, UMR 7285, Hydrasa, France

Acknowledgement
Financial support from the French National Radioactive Waste Management Agency (ANDRA), from the French Geological Survey (BRGM) and from the national

Thermodynamics of Hydration in Minerals: How to Predict These Entities 365

council for scientific Research (CNRS) is gratefully acknowledged. Special thanks to Ph. Blanc, H. Gailhanou and Cl. Fialips for their effective and decisive contribution to this document.

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[46] Van Hinsberg VJ, Vriend SP, Schumacher JC (2005) A new method to calculate end-member thermodynamic properties of minerals from their constituent polyhedra I: enthalpy, entropy and molar volume. J. Metamorph. Geol. 23: 165-179. [47] Chermak JA, Rimstidt JD (1989) Estimating the thermodynamic properties (Gf and Hf) of silicate minerals at 298 K from the sum of polyhedral contributions. Amer. Mineral. 74: 1023-1031. [48] Li J, Li B, Gao S (2000) Calculation of thermodynamic properties of hydrated borates by group contribution method. Physics and Chemistry of Minerals 27: 342-346. [49] Chen FR, Ewing RC, Clark SB (1999) The Gibbs free energies and enthalpies of formation of U6+ phases: An empirical method of prediction. Amer. Mineral. 84: 650664. [50] Vieillard P, Jenkins HDB (1986) Empirical relationships for estimation of enthalpies of formation of simples hydrates. Part I Hydrates of alkali- metal cations, of hydrogen and of monovalent cations. J. Chem. Res.: 444-445. [51] Vieillard P, Jenkins HDB (1986) Empirical relationships for estimation of enthalpies of formation of simples hydrates. Part 2. Hydrates of alkaline-earth metal cations. J. Chem. Res.: 446-447. [52] Vieillard P, Jenkins HDB (1986) Empirical relationships for estimation of enthalpies of formation of simples hydrates. Part 3. Hydrates of transition metal cations (Cr2+,Fe2+,Co2+,Ni2+,Cu2+,Zn2+,Cd2+and UO22+). J. Chem. Res.: 448-449. [53] Robie RA, Waldbaum DR (1968) Thermodynamic properties of minerals and related substances at 298.15K (25C) and one atmosphere (1.O13 bars) pressure and at higher temperatures. U. S. Geol. Surv. Bull., 1259, 256 p. [54] Vieillard P, Mathieu R (2009) A predictive model for the enthalpies of hydration of zeolites. . Amer. Mineral. 94: 565-577. [55] Meier WM, Olson DH, Baerlocher C (1996) Atlas of Zeolite Structure types: 4th revised Edn. Zeolites 17: 1-230. [56] Meier WM, Olson DH (1971) Zeolites Frameworks In: Flanigen EM, Sand LB, editors. Molecular Sieve Zeolites 155-170. [57] Barrer RM (1982) Hydrothermal chemistry of Zeolites. Press A, editor. London New York: Harcurt Brace Jovanovich. 1-360 p. [58] Carey JW (1995) A thermodynamic formulation of hydrous cordierite. Contrib. Miner. Petrol. 119: 155-165. [59] Armbruster T (1993) Dehydration mechanism of clinoptilolite and heulandite: Singlecrystal X-ray-study of Na-poor and K-Mg-rich clinoptilolite at 100K. Amer. Mineral. 78: 260-264. [60] Bish DL, Carey JW (2001) Thermal behavior of natural zeolites. In: D.W. BDLM, editor. Natural zeolites:occurrence, properties Applications. Blacksburg: Mineralogical Society of America. pp. 403-452. [61] Mathieu R, Vieillard P (2010) A predictive model for the enthalpies of formation of zeolites. . Microporous Mesoporous Mat. 132: 335-351.

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[62] Carey JW, Bish DL (1997) Calorimetric measurement of the enthalpy of hydration of clinoptilolite. Clays Clay Minerals 45: 826-833. [63] Vieillard P, Blanc P, Fialips CI, Gailhanou H, Gaboreau S (2011) Hydration thermodynamics of the SWy-1 montmorillonite saturated with alkali and alkaline-earth cations: a predictive model. Geochim. Cosmochim. Acta 75: 5664-5685. [64] Fripiat J, Cases J, Francois M, Letellier M (1982) Thermodynamic and microdynamic behavior of water in clay suspensions and gels. J. Colloid Interface Sci. 89: 378-400. [65] Koster van Groos AF, Guggenheim S (1987) Dehydration of a Ca- and a Mg-exchanged montmorillonite (SWy-1) at elevated pressures. Amer. Mineral. 72: 292-298. [66] Ransom B, Helgeson HC (1994) A Chemical and Thermodynamic Model of Aluminous Dioctahedral-2/1 Layer Clay Minerals in Diagenetic Processes - Regular Solution Representation of Interlayer Dehydration in Smectite. Amer. J. Sci. 294: 449484. [67] Ransom BH, H.C. (1994) Estimation of the standard molal heat capacities, entropies, and volumes of 2:1 clay minerals. Geochim. Cosmochim. Acta 58: 4537-4547. [68] Vidal O, Dubacq B (2009) Thermodynamic modelling of clay dehydration, stability and compositional evolution with temperature, pressure and H2O activity. Geochim. Cosmochim. Acta 73: 6544-6564. [69] Dubacq B, Vidal O, De Andrade V (2010) Dehydration of dioctahedral aluminous phyllosilicates: thermodynamic modelling and implications for thermobarometric estimates. Contri. Miner. Petrol. 159: 159. [70] Helgeson HC, Delany JM, Nesbitt HW, Bird DK (1978) Summary and critique of the thermodynamic properties of the rock-forming minerals. Am. J. Sci. 278-A: 1-229. [71] Johnson GK, Tasker IR, Jurgens R, O'Hare PAG (1991) Thermodynamic studies of Zeolites-Clinoptilolite. J.Chem. Thermodyn. 23: 475-484. [72] Vieillard P (2010) A predictive model for the entropies and heat capacities of zeolites. Eur. J. Mineral. 22:823-836. [73] Marcus Y (1994) A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes, and shapes. Biophys. Chem. 51: 111127. [74] Berman RG, Brown TH (1985) Heat capacity of minerals in the system Na2O-K2O-CaOMgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2, representation, estimation and high temperature extrapolation. Contrib. Miner. Petrol. 89: 168-183. [75] Neuhoff PS, Wang J (2007) Heat capacity of hydration. Amer. Mineral. 92: 1358-1367. [76] Fyfe WS, Turner FJ, Verhoogen J. Metamorphic reactions and metamorphic facies. In: Memoirs GSoA, editor.1958. p. 253 p. [77] Cruciani G (2006) Zeolites uponheating: Factors governing their thermal stability and structural changes. J. Phys. Chem. Solids 67: 1973-1994. [78] Lassin A, Duplay J, Touret O, Tardy Y (2000) Thermodynamic treatment of hydrates. Comptes Rendus Acad. Sci. Paris SER II A 330: 533-540.

370 Thermodynamics Fundamentals and Its Application in Science

[79] Barshad I (1960) Thermodynamics of water adsorption and desorption on montmorillonite. Clays Clay Minerals: 84-101.

Chapter 14

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles

Nong-Moon Hwang, Jae-Soo Jung and Dong-Kwon Lee
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50324

1. Introduction
The preparation of monodisperse nanoparticles with uniform size, shape and composition has been intensively pursed because of their scientific and technological interests [1-4]. The major advantage of monodisperse particles may be attributed to the uniform properties of individual particles, which makes the property of whole particles strictly controllable. They have been widely used in industries such as pharmacy, catalysts, sensors, film precursors, and information storage. The property of nanoparticles is much more sensitive to their size than that of micro-particles. For example, the florescence of monodisperse CdSe/ZnS core/shell nanoparticles depends strongly on their size [5]. The superparamagnetism also depends strongly on the size of nanoparticles [6]. The properties of these particular size nanoparticles show great potentials in the field of bio-medicals and electronics. In general, to prepare the monodisperse nanoparticles in solution, the size had to be selected after somewhat polydisperse nanoparticles were produced. The separation procedures are very laborious and expensive because the size of nanoparticles is too small to be sorted. Moreover, the production yield of monodisperse nanoparticles decreases markedly due to the loss of nanoparticles during the separation procedures. Therefore, many efforts have been made to synthesize directly monodisperse nanoparticles without size selection procedures. Recently, several methods have been developed successfully to synthesize gram quantity monodisperse nanoparticles directly without size selection procedures. One of them is a slow heating method developed by Hyeon et al. [6,7], which utilizes the burst nucleation followed by sustained growth of particles. Although nanoparticles have some size distribution in the nucleation stage, they became gradually monodisperse during growth. In this case, the principle for the direct synthesis of monodisperse nanoparticles could be approached by sustained growth of nuclei formed by burst nucleation with some initial size distribution [8].
2012 Hwang et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

372 Thermodynamics Fundamentals and Its Application in Science

The digestive ripening developed by Klabunde et al. [9-12] is another fascinating method for the direct synthesis of monodisperse nanoparticles. During digestive ripening, nanoparticles initially ranging from 2 to 40 nm were spontaneously transformed into particles with nearly uniform sizes of 4~5 nm. Lee et al. [13,14] could explain the digestive ripening process by considering the charge effect in the Gibbs-Thomson equation. The purpose of this article is to provide the thermodynamic and kinetic basis to slow heating method and digestive ripening, which are two successful processes to synthesize the monodisperse nanoparticles.

2. Evolution mechanism of monodisperse particles

To understand intuitively the underlying principle for the evolution of monodispersed particles, lets compare the growth of two spherical particles of different diamters of 1 nm and 5 nm as shown in Fig. 1(a). The problem could be simple under the assumption that all the particles grow at the same rate regardless of the size, which is valid for interfacecontrolled growth. The size ratio of two particles is 5, which is far from the monodisperse state. If the two particles grow by 1 nm after some time, their diameters become 2 nm and 6 nm, respectively, as shown in Fig. 1(b). Now the size ratio of the two particles is 3. If the two initial particles grow by 99 nm after an appreciable amount of time, their diameters become 100 nm and 104 nm, respectively, as shown in Fig. 1(c). Now their size ratio is 1.04, which is in the monodisperse state with the size being within 5% difference. The time evolution of the two particles in Fig. 1(a)-(c) shows that just the growth induces the monodispersity. It should be noted that the initial size difference between the two particles, which is 4 nm, is maintained throughout the growth but the size ratio continues to decrease with growth, approaching unity. This tendency to approach the monodisperse distribution by growth is often called focusing effect [15].

Figure 1. Initially, two spherical particles have the diameters of (a) 1 nm and 5 nm with the size ratio of 5. After growth by 1 nm, the respective particle becomes (b) 2 nm and 6 nm with the size ratio of 3. After growth by 99 nm, the respective particle becomes (c) 100 nm and 104 nm with the size ratio of 1.04, which has the monodispersity with size difference less than 5%.

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 373

If a colloidal particle grows in supersaturated solution, the solute may diffuse from the bulk liquid phase containing a uniform concentration of solute Cb to the particle surface through a diffusion layer with some concentration gradient where Cr is the solubility of the particle. In this condition the growth rate is described by D r 1+ V C - C dr r m b r = dt D r 1+ 1+ kr

(1)

where D is the diffusion coefficient of the solute, r is the particle radius, is the diffusion radius around a particle and k is the rate constant of the interface reaction of a solute at the particle interface. If D is much larger than kr (D >> kr), the interface reaction process becomes a ratedetermining step and Eq. (1) is reduced to
dr = kVm Cb - Cr dt

(2)

In this case of the interface-controlled growth, the growth rate does not depend on the particle size. If D is much smaller than kr (D << kr), however, the diffusion process of a solute becomes a rate-determining step and thus Eq. (1) is reduced to
dr DVm = (Cb - Cr ) dt r

(3)

In this case of the diffusion-controlled growth, the growth rate is inversely proportional to the radius of each particle. This means that large particles grow more slowly than small ones, which is in contrast with the interface-controlled growth, where the growth rate was the same regardless of the size. Therefore, the diffusion-controlled growth has a stronger tendency to approach the monodisperse distribution than the interface-controlled growth. The narrowing of the size distribution was first theoretically studied in the diffusioncontrolled process by Reiss [16]. The variation of the radius distribution 2 during growth changes with time as follows.

d 2 dt

= 2DV

Cb - Cr 1 - r r

(4)

In Eq. (4), r and 1 r are the mean values of r and 1/r, respectively. Since the arithmetic

mean is larger than the harmonic mean,

1 r

is greater than 1/ r . Therefore, in the

supersaturated state, where Cb Cr , Eq. (4) is negative. This means that the variation of the radius distribution 2 decreases with time as the growth continues.

374 Thermodynamics Fundamentals and Its Application in Science

3. Interface-controlled growth
The tendency to approach the monodisperse distribution by growth can be examined by computer simulation. Consider the case of interface-controlled growth. As a starting condition of simulation, it could be assumed that the number of particles is 1000 with the average size of 0.5 nm and particles have a spherical shape. It can also be assumed that the size distribution follows the Gaussian function. Since the Gaussian distribution spreads infinitely, the size distribution is cut off when its probability is less than 0.01. The width of the Gaussian distribution, which is defined as the difference between the maximum and minimum size with the probability of 0.01, was 2 nm. The center of the distribution was 0.5 nm. The radius ratio of the largest to the average-size particle was used as a criterion for the monodispersity. If this ratio is less than 1.05, the size distribution is regarded as being monodisperse. In the simulation, the growth rate, which is the same for all particles, was arbitrarily chosen to be 0.025 nm/s. It can further be assumed that there is no additional nucleation during growth, no coagulation between particles and no Ostwald ripening among particles. Figs. 2 (a)-(c) show the particle size distribution, respectively, after 0 sec, 100 sec and 800 sec of growth. For visual representation of the result, the three-dimensional particles are projected on the two-dimensional plane. The location of the particles was randomly chosen within the square of the designated area but overlapping between particles was avoided. The broad size distribution in the initial state becomes narrower with particle growth, finally being monodisperse after 800 sec. The initial size ratio of 2.70 was decreased to 1.05 after the particle grew from the initial average radius of 0.5 nm to 21.49 nm. It should be noted that the broad size distribution in the initial state would be changed to the monodisperse state as far as the average size of particles grows from 0.5 nm to 21.49 nm regardless of the growth rate. Additional simulation was performed with the initial average radii of 1 nm and 2 nm. The final average particle radii reaching the monodisperse state were 41.18 nm and 81.02 nm, respectively. These results can explain the natural evolution of monodisperse distribution of particles with growth. However, the results indicate that the minimum average radius for the monodisperse distribution should be about 20 nm when starting from the average radius of 0.5 nm, which is implicitly assumed to be the critical nucleus size. In the direct synthesis of monodisperse nanoparticles such as iron oxide reported by Hyeon et al. [6], however, the average radius is often as small as 4 nm. The average particle size to reach the monodisperse state shown in Fig. 2 is much larger than that observed experimentally in the direct synthesis of monodisperse nanoparticles. Therefore, although the interface-controlled growth can explain the monodisperse evolution for particles larger than at least a few tens of nanometers, it cannot explain the evolution of monodisperse nanoparticles less than 10 nm, which requires that the monodisperse state should be reached at a much smaller particle size than that predicted by the interface-controlled growth. On the other hand, in the diffusion-controlled growth, the growth rate is inversely proportional to the particle radius as described by Eq. (3). Therefore, smaller particles would grow faster than larger ones, whose condition is more favorable in reaching the monodisperse state at smaller particle size. For this reason, the diffusion-controlled growth might be more suitable in explaining the evolution of the monodisperse nanoparticles less than 10 nm.

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 375

Figure 2. The numerical analysis of the particle growth under the condition of interface-controlled growth. (a) The initial size distribution: the average radius of the initial particles was set to 0.5 nm with 1 nm width between the maximum and average size. (b) The size distribution of particles in the intermediate stage after 100 s. (c) The monodisperse state evolved after 800 s with the average particle radius of 21.49 nm.

376 Thermodynamics Fundamentals and Its Application in Science

Figure 3. The numerical analysis of the particle growth under the condition of diffusion-controlled growth. (a) The initial size distribution: the average raidius of particles was set to 0.5 nm with 1 nm width between maximum and average size. (b) The size distribution of particles in the intermediate stage after 100 s. (c) The monodisperse state evolved after 1200 s with the average particle radius of 4.5 nm.

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 377

4. Diffusion-controlled growth
The diffusion-controlled growth could also be investigated using the computer simulation. The initial particle size distribution was identical to the previous case: the average radius of 0.5 nm and the width of 2 nm for Gauss distribution. The time step for calculation was 1 sec. The concentration gradient was given a constant value of 0.75 mol/cm3 without the Gibbs-Thompson effect being considered, which results in removing the Ostwald ripening effect. Figs. 3(a)-(c) show the two-dimensional display of particles, respectively, after 0 sec, 100 sec and 1200 sec by diffusion-controlled growth. The initial ratio of 2.70 was decreased to 1.05 after the particle grew from the initial average radius of 0.5 nm to 4.50 nm. It should be noted that the initial particle size distribution would become monodisperse with the size ratio of 1.05 as far as the average radius of the particles increases from 0.5 nm to 4.5 nm regardless of the growth rate if the growth is controlled by diffusion. Comparison between Figs. 2 and 3 indicates that the monodisperse state is reached much faster and in a much smaller particle size by the diffusion-controlled growth than by the interface-controlled growth. Therefore, the direct synthesis of monodisperse nanoparticles by Hyeon et al. [6] can be explained by the diffusion-controlled growth. The present analysis indicates that even if there is a broad size distribution in the nucleation stage, it becomes narrower with growth, eventually leading to a monodisperse state. Because of this focusing effect, the evolution of the monodisperse nanoparticles seems to be a rule rather than an exception. Then, a question arises as to why people have difficulty in producing the monodisperse nanoparticles. Which factor would be critical in the successful synthesis of highly monodisperse nanoparticles?

5. Factors unfavorable for monodisperse distribution

There are factors which are unfavorable for monodispersity. These are additional nucleation, random coagulation and Ostwald ripening. It is well established that coagulation among particles can be inhibited by a suitable choice of surfactants. Therefore, coagulation is not a critical factor. The effect of Ostwald ripening becomes significant when the supersaturation is small. More precisely, if the supersaturation made by the capillarity or the Gibbs-Thompson effect of particles is higher than the supersaturation for growth in the bulk, Ostward ripening would occur extensively. Then, the size distribution would deviate from monodispersity and approach the well-established distribution predicted by the Lifshitz, Slyozov and Wagner (LSW) theory. [17, 18] Therefore, to inhibit Ostwald ripening, the supersaturation for growth should be maintained much higher than that by the Gibbs-Thompson effect. This aspect was studied in detail by Kwon et al. [8]. The most critical factor unfavorable for monodisperse distribution is the additional nucleation during growth. Therefore, growth should be separated from nucleation. The thermodynamics and kinetics of nucleation are relatively well established. The rate of

378 Thermodynamics Fundamentals and Its Application in Science

nucleation is negligibly low at low supersaturation and becomes very high above certain supersaturation, varying like a step function. The supersaturation for the onset of nucleation has a special meaning and is called the critical supersaturation for nucleation, which is defined as the supersaturation to produce the nucleation rate of 1/cm3sec. Consequently, to inhibit the additional nucleation during growth, the supersaturation should be maintained below the critical supersaturation for nucleation. Normally, the critical supersaturation for homogeneous nucleation is high enough but that for heterogeneous nucleation is relatively low and can be easily achieved. Therefore, a special care must be taken to prepare the reactor for the synthesis of monodisperse nanoparticles free from the site for heterogeneous nucleation. One attempt to separate growth from nucleation is the seed-mediated growth, where the preformed nanoparticles are used as seed nuclei [7, 19]. Another attempt to separate growth from nucleation is the initial burst of nucleation, where an appreciable amount of supersaturation is consumed during the burst of nucleation and the relatively low supersaturation is maintained during growth. The hot-injection method [20-22] is an example of this attempt. Rapid injection of reagents into a hot surfactant solution raises the precursor concentration above the nucleation threshold. A burst of nucleation during a short period of time partially relieves the supersaturation. If the rate of the precursor consumption by the growing colloidal nanoparticles is not exceeded by the rate of precursor addition to solution, no new nuclei would form. This process typically produces the nanoparticles with the size distribution of 10 < < 15% in diameter, which are then narrowed to < 5% through additional size-selective processing. The heating-up method [6, 23-25] is a new attempt to separate growth from nucleation. This process is a batch process and very simple. Metal-oleate precursors are prepared from metal chloride and sodium oleate. If the metal-oleate precursors are heated in a high-boiling point solvent, they are thermally decomposed and produce monodisperse nanocrystals. This method proved to be advantageous for large-scale production. Park et al. [6] showed that as large as 40g of monodispese magnetite nanocrystals with a yield of >95% could be produced in a batch. The size uniformity of the nanoparticles is usually better than that by the hotinjection method. Since this is a batch process, the precursors are not added during growth to supplement the supersaturation. The supersaturation that has been consumed during growth can be indirectly estimated from the final size of the nanoparticles. The highly monodisperse nanoparticles were reported to grow as large as 22 nm in the heating up process. Considering that the critical nucleus size is ~ 0.5 nm, the diameter increases by more than 20 nm, which implies that a considerable supersaturation must have been consumed. Since an appreciable amount of supersaturation is consumed in the initial nucleation process, the remaining supersaturation is usually not so high. Therefore, it is highly unlikely that the nuclei should grow as large as

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 379

10 nm by remaining supersaturation without precursors being supplied additionally. It should be reminded that in the hot-injection method the additional precursors should be supplied to produce nanoparticles larger than 10 nm. Then, a question arises as to why additional nucleation does not occur during such extensive growth. It appears that all the supersaturation, which should be consumed to produce the final size of nanoparticles, is not built up simultaneously but only a very small fraction of supersaturation, which is too small to trigger the nucleation, is maintained throughout the growth. This is an ideal situation where growth is separated from nucleation. One possibility to realize such an ideal situation is that the decomposition of the metal orleate complex into metal does not occur in the solution but occurs only at the surface of nanoparticles. In other words, the surface of nanoparticles acts as the catalytic site for decomposition of the metal orleate. This type of reaction is called self-catalytic. Therefore, if a system is self catalytic, growth can be separated ideally from nucleation and monodisperse nanoparticles can be easily synthesized.

6. Digestive ripening
As mentioned earlier, the coarsening kinetics of Ostwald ripening has been well established by LSW theory [17, 18]. During Ostwald ripening, large particles with a low chemical potential grow at the expense of small particles with a high chemical potential and, as a consequence, the average size increases and the total number of particles decreases during coarsening. Eventually, only one large particle remains, which corresponds to a final equilibrium state. However, Klabunde and co-workers reported a series of articles on the synthesis of monodisperse gold or silver nanocrystals by a digestive-ripening process of polydisperse nanocrystals. [9-12, 26, 27] Gram quantities of monodisperse gold or silver nanoparticles could be produced through digestive ripening, where colloidal particles from 2 to 40 nm are transformed to nearly monodisperse particles of 45 nm diameters. Digestive ripening is the reverse process of Ostwald ripening. It is interesting and also puzzling in that small particles grow at the expense of large ones. Clearly, digestive ripening cannot be understood with the usual GibbsThomson equation solely based on a curvature effect. According to the theory of diffusion-controlled coarsening [28], the growth rate of a particle with radius, r, is given by
dr D f Vg Co (r)* -(r) = dt rRT

(5)

where R is the gas constant, T the absolute temperature, and Df and Co are the diffusivity and solubility of atoms in the solution, respectively. Eq. (5) is valid when the diffusion field does not overlap. (r)* is the chemical potential of a particle of critical size, which neither grows nor shrinks at the given instant.

380 Thermodynamics Fundamentals and Its Application in Science

Since the phenomenon of digestive ripening runs counter to the decrease of interfacial free energy, a different type of free energy must be involved. The driving force for digestive ripening must compete against the reduction of the interface free energy. There are two such free energies. One is strain energy and the other is electrostatic energy. Since solid particles dispersed in liquid do not have any appreciable strain energy, the electrostatic energy is a possible candidate. In fact, Klabunde et al, who have developed the digestive ripening process, reported that their nanoparticles were negatively charged [9, 10]. If nanoparticles are electrically charged, they have an electrostatic energy inversely proportional to the radius of the particles. Since electrostatic energy increases with decreasing particle size, charged particles cannot shrink away completely. Therefore, the presence of charge can drastically change the Ostwald ripening behavior. The chemical potential change arising from the presence of charge can be treated by modifying the Gibbs-Thomson equation in consideration of the electrostatic energy. To analyze the effect of charge on the coarsening behavior of nanoparticles, it is assumed that each particle is singly charged, electrically-conducting, and spherical with isotropic interface free energy, dispersed in a matrix phase with a dielectric constant of 1. According to this assumption, ions are regarded as the primary embryos of charged nanoparticles. It is further assumed that the charged nanoparticles do not coagulate with each other and that the atomic transfer between particles is diffusion-controlled. The Gibbs free energy of a spherical conducting particle with radius r and charge e (corresponding to the unit charge of an electron) is expressed as

G = 4r 2 + k

e2 , 2r

(6)

where is the interface free energy of the particle and k is defined by 1/(4), where is the vacuum permittivity [29]. ke2 is 2.306810-28 Nm2. It should be noted that with decreasing r, the interface free energy term decreases but the electrostatic energy term increases. From Eq. (6), the modified Gibbs-Thomson equation is derived as
= r - o = RTln 2 Cr q2 = Vm - k , r Co 8r 4 (7)

where Co is the solute concentration in the matrix without capillary effect. If the difference between Cr and Co is small, the equation can be approximated as C C -C V 2 q2 ln r r o = m - k . C r Co RT 8r 4 o (8)

The coarsening behavior can be analyzed quantitatively by solving Eqs. (5) and (8) simultaneously under the constraint of mass conservation for a total number of particles Np, and is expressed as

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 381

Np n

4rn 2
Substituting Eq. (5) into Eq. (9) yields

drn = 0. dt

(9)

rn D f Vm C* - C0 - Cr,n - C0 = 0.
n

Np

(10)

From Eqs. (5), (9) and (10), the following equation can be derived:

drn = dt

2 D f Vm C0

RTrn

N 2 2 p rn 2 2 q q - . -k Np - k 4 r 4 rn 8rn n 8rn n rn n

(11)

If the growth rate of each particle is determined by Eq. (11), the new radius after dt is given by

dr rn (t + dt)= rn (t)+ n dt. dt

(12)

Once the initial size distribution of particles is given, the time-dependent size distribution can be obtained by solving equations (11) and (12) simultaneously by iteration. To demonstrate that this approach reproduces simple digestive ripening, one large charged nanoparticle of 15 nm radius and 600 ions of 0.2 nm radius were chosen as an initial state. A diffusivity, Df, of 10-9 m-1sec-1 and a temperature of 393 K were chosen for calculation.[11] Besides, the interface energy of = 1 mJm-2, C0 = 0.01 molm-3, and Vm =1.0210-5 m3 mol-1, which is the molar volume of gold, were chosen. Here, the interface free energy of 1mJm-2 is chosen, simply because it produces monodisperse nanoparticles of the 1.5 ~ 2 nm size after digestive ripening. Experimentally, the surfactant, dodecanethiol, which is expected to diminish the interface free energy between gold and solution, appears to play a critical role in inducing digestive ripening. [30, 31] As the interface free energy decreases and the electric charge density increases, the size of finally-evolved monodisperse nanoparticles increases. Fig. 4 shows the size evolution of charged nanoparticles with time. a1 and a2 in Fig. 4(a) represent the radius of charged embryos at 200 s and 600 s, respectively. Likewise, b1 and b2 in Fig. 4(a) represent the radius of the 15 nm particle at 200 sec and 600 sec, respectively. The size of the small charged embryos increases, whereas the size of the large charged particles decreases. Figs 4(b)-(d) show a display of the size distribution of nanoparticles at 200 s, 600 s and 900 s, respectively. Finally, the radius of every nanoparticle becomes 1.78 nm at 900 s, as shown in Fig. 4(d), which corresponds to F in Fig. 4(a), producing perfect monodisperse

382 Thermodynamics Fundamentals and Its Application in Science

nanoparticles. This calculation reproduces the experimentally observed digestive ripening behavior.

Figure 4. Coarsening behavior of one big particle of 30 nm and 300 embryos of 0.4 nm. (a) a1 and a2 indicate the size of embryos at 200 s and 500 s, respectively. Likewise b1 and b2 indicate the size of the large nanoparticle at 200 s and 500 s, respectively. Finally, the size of every nanoparticle becomes the same on F at 900s. The size distribution of nanoparticles at (b) 200 s, (c) 500 s and (d) 900 s, respectively. In (b), the size of small nanoparticles is 4 nm and that of a large nanoparticle is 19.9 nm. In (c), the size of small nanoparticles is 4.3 nm and that of a large nanoparticle is 14.9 nm. In (d), the size of every nanoparticle becomes 4.5 nm. Reprinted with permission from [13]. Copyright 2007 Elsevier.

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 383

7. Digestive ripening in a binary system

Smetana et al. [26] reported digestive ripening in a binary system, where separately prepared monodisperse Au and Ag nanoparticles with a radius of ~3.3 nm, mixed in a colloid solution, were transformed into monodisperse Au/Ag alloy nanoparticles with a radius of ~2.8 nm. The final monodisperse nanoparticles did not have a coreshell structure but had uniform composition distribution. The size of the final monodisperse nanoparticles was reduced in comparison to that of the initial unalloyed monodisperse nanoparticles, which implied that additional nucleation had occurred during digestive ripening. To analyze the coarsening behavior of a binary system of Au and Ag nanoparticles, the chemical potential of a binary system needs to be derived. According to the phase diagram of an Au/Ag binary system [31], Au and Ag, which have the same face-centered cubic (FCC) structure and a small difference in atomic size, have a complete solid solution. Therefore, it is assumed that Au and Ag nanoparticles behave like an ideal binary solid solution, and then, the Gibbs-free energy is expressed in the whole composition range as follows [32]:
G = X Au G Au + X Ag G Ag + RT(X Au lnX Au + X Ag lnX Ag )

(13)

From Eq. (13), the chemical potentials of Au and Ag for the alloy are given, respectively, by
Au = G Au + RTlnX Au

Ag = G Ag + RTlnX Ag

(14)

where GAu and GAg are the molar free energies of pure Au and Ag, respectively; and XAu and XAg are the mole fractions of Au and Ag, respectively. From Eqs. (7) and (14), the chemical potentials of spherically charged nanoparticles of Au and Ag with radius r can be derived as
2 kz 2 q 2 Au (r)= G Au + RTlnX Au +VSS SS 8r 4 r 2 kz 2 q 2 Ag (r)= G Ag + RTlnX Ag +VSS SS 8r 4 r

(15)

where SS and VSS are the interface free energy and the molar volume of the Au/Ag solid solution, respectively. To investigate the time evolution of the coarsening behavior of the mixed Au and Ag nanoparticles, the growth rate of particles should be calculated. Substituting Eq. (5) for dr/dt in Eq. (9) and rearranging the result yield
Np (r)* = rn (rn ) / n=1

n=1

rn

Np

(16)

Expressing (r)* in terms of dri/dt and using Eq. (15) for (r) in Eq. (16), the growth rate of the ith particle by diffusion of Au and Ag atoms is obtained as

384 Thermodynamics Fundamentals and Its Application in Science

-1 2 N N dri D f VSS Co RT 2 SS kz 2 q 2 p p RT 2 kz 2 q 2 = lnX Au + + rn rn lnX Au + SS , dt ri RT VSS ri rn 8ri4 n=1 n=1 VSS 8rn4 i = 1,2,... for Au -1 2 N N 2 dri D f VSS Co RT 2 SS kz 2 q 2 p p RT kz 2 q 2 lnX Ag + SS = lnX Ag + + rn rn , rn dt ri RT VSS ri 8rn4 8ri4 n=1 n=1 VSS i = 1,2,... for Ag

(17)

With Eq. (17), the radius of the ith particle can be calculated at a time, t +t, by

ri (t + t)= ri (t)+

dri t, i = 1,2,... dt

(18)

The analytic expression for the composition change of nanoparticles cannot be derived. Therefore, the composition change of nanoparticles should be computed from the mass change of each element, which is determined from the size change by Eq. (18) for each iteration. To check whether these schemes reproduce the experimental result of alloy digestive ripening, a simple system of 500 Au charged nanoparticles of RAu = 3.3 nm, 500 Ag charged nanoparticles of RAg = 3.3 nm and 500 charged nuclei of Rnuclei = 0.5 nm was considered. This system is chosen to represent the experimental condition of as-prepared Au and Ag nanoparticles mixed for digestive ripening [14]. The 500 nuclei were added because the experimental fact that the number of final nanoparticles increases after digestive ripening indicates that additional nucleation occurs. The capital letter Ri indicates an initial radius with the suffix i implying the ith group of particles with identical radius. The initial mole fraction of Au nanoparticles, XAu, is set at 0.99 instead of 1 to avoid the infinity in calculation. In the same manner, XAu of Ag nanoparticles and the size of nuclei are set at 0.01 and 0.5, respectively. The parameters used are Df = 0.5 1014 m2/s, VSS = 1.02 105 m3/mol, Co = 0.01 mol/m3, kq2 = 2.3068 1028 Jm, T = 393 K, SS = 0.3 J/m2, and z = 30. It should be noted that if the particles are assumed to be singly charged with z = 1, the interface energy SS should have a much smaller value than 0.3 J/m2 to reproduce the experimentallyobserved digestive ripening. For the simplification, the diffusivities of Au or Ag atoms in the nanoparticles are assumed to be high enough to be homogenized immediately because the final structure of Au/Ag alloy nanoparticles was reported not to have a core-shell structure but to have a homogeneous solid solution. In Fig. 5, the coarsening behavior of nanoparticles with time is schematically displayed. The time evolution of the microstructure is shown in Figs. 5(a), (b), (c) and (d) at t1 = 0, t2 = 1, t3 = 2 and t4 = 16 h, respectively. Fig. 5(a) shows the initial size distribution and the composition

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 385

of nanoparticles, which is represented by the gray scale from black for Au to white for Ag as shown by the gray scale bar in Fig. 5. Therefore, black, white and gray nanoparticles represent Au-rich, Ag-rich and Au/Ag alloy nanoparticles, respectively. After 1 h, the radii of both Au and Ag nanoparticles decrease to 3.07 nm and the mole fractions, XAu, of Au and

Figure 5. Display of the nanoparticles evolved through coarsening at four different times in the system of 500 Au nanoparticles, 500 Ag nanoparticles and 500 nuclei. Composition is represented by the gray scale from Au as black to Ag as white. (a) At t1 = 0 h, RAu = 3.3 nm with XAu = 0.99, RAg = 3.3 nm with XAu = 0.01 and Rnuclei = 0.5 nm with XAu = 0.5. (b) At t2 = 1 h, rAu = 3.07 nm with XAu = 0.64, rAg = 3.07 nm with XAu = 0.36 and rnuclei = 2.4 nm with XAu = 0.5. (c) At t3 = 2 h, rAu = 3 nm with XAu = 0.54, rAg = 3 nm with XAu = 0.46 and rnuclei = 2.6 nm with XAu = 0.5. (d) At t4 = 16 h, all the particles become monodisperse at 2.88 nm with the same composition of XAu = 0.5. Reprinted with permission from [14]. Copyright 2009 Elsevier.

386 Thermodynamics Fundamentals and Its Application in Science

Ag nanoparticles become 0.64 and 0.36, respectively, as shown in Fig. 5(b). The radii of the nuclei increase to 2.4 nm with their mole fraction, XAu, maintained as 0.5. After 2 h, the size distribution becomes much narrower approaching a monodisperse state and the composition becomes more homogenized as shown in Fig. 5(c). The radii of initial Au and Ag nanoparticles decrease to 3 nm, and the radii of the nuclei increase to 2.6 nm. The mole fractions of Au and Ag nanoparticles become 0.54 and 0.46, respectively. After 16 h, all the nanoparticles eventually have the same radius of 2.88 nm and the same composition of XAu = 0.5, as shown in Fig. 5(d). By considering both the electrostatic energy and ideal solid solution, the coarsening behavior of the digestive ripening process, where the separated Au and Ag nanoparticles were transformed into monodisperse Au/Ag alloy nanoparticles, was successfully reproduced.

8. Conclusions
The evolution mechanism of monodisperse nanoparticles is approached thermodynamically and kinetically. Both interface-controlled and diffusion-controlled growth of particles can induce monodisperse distribution of particles if coagulation, additional nucleation and Ostwald ripening are inhibited. The diffusion-controlled growth reaches the monodisperse state at much smaller size than the interface-controlled growth. The evolution mechanism of monodisperse nanoparticles by digestive ripening is approached using the modified GibbsThompson equation considering electrostatic energy. The digestive ripening behavior of both pure metal and alloy which is contrary to conventional Ostwald ripening, is well explained assuming that nanoparticles are electrically charged.

Author details
Nong-Moon Hwang and Jae-Soo Jung Department of Materials Science and Engineering, Seoul National University, Seoul, Korea Dong-Kwon Lee LG Chem. Ltd, Research Park, Yoseong-gu, Daejon, Korea

Acknowledgement
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. M10600000159-06J0000-15910).

9. References
[1] K. J. Klabunde, Nanoscale Materials in Chemistry, (Wiley-Interscience, New York, 2001). [2] T. Sugimoto, Monodispersed Particles, (Elsevier, Amsterdam, 2001). [3] G. Schmid, Nanoparticles: From Theory to Application, (WILEY-VCH, Weinheim, 2004).

Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 387

[4] J. N. Park, S. G. Kwon, J. Joo, Y. G. Jang, and T. H. Hyeon, Angew. Chem. Int., 46, 4630 (2007). [5] I. L. Medintz, H. T. Uyeda, E. R. Goldman, and H. Mattoussi, Nature Mater., 4, 435 (2005). [6] J. N. Park, K. J. An, Y. S. Hwang, J. G. Park, H. J. Noh, J. Y. Kim, J. H. Park, N. M. Hwang, and T. H. Hyeon, Nature Mater., 3, 891 (2004). [7] J. N. Park, E. W. Lee, N. M. Hwang, M. S. Kang, S. C. Kim, Y. S. Hwang, J. G. Park, H. J. Noh, J. Y. Kim, J. H. Park, and T. H. Hyeon, Angew. Chem. Int., 44, 2872 (2005). [8] S. G. Kwon, Y. Piao, J. N. Park, S. Angappane, Y. G. Jo, N. M. Hwang, J. G. Park, and T. H. Hyeon, J. Am. Chem. Soc., 129, 12571 (2007). [9] G. Trivino, K. J. Klabunde, and E. Dale, Langmuir, 3, 986 (1987). [10] B. L. V. Prasad, S. I. Stoeva, C. M. Sorensen, and K. J. Klabunde, Langmuir, 18, 7515 (2002). [11] S. Stoeva, K. J. Klabunde, C. Sorensen, and I. Dragieva, J. Am. Chem. Soc., 124, 2305 (2002). [12] B. L. V. Prasad, S. I. Stoeva, C. M. Sorensen, and K. J. Klabunde, Chem. Mater., 15, 935 (2003). [13] D. K. Lee, S. I. Park, J. K. Lee, and N. M. Hwang, Acta Mater., 55, 5281 (2007). [14] D. K. Lee and N. M. Hwang, Scripta Mater., 61, 304 (2009). [15] X. Peng, J. Wickham, A.P. Alivisatos, J. Am. Chem. Soc. 120, 5343 (1998). [16] H. Reiss, J. Chem. Phys. 19, 482 (1951). [17] I. M. Lifshitz, V. V. slyozov, J. Phys. Chem. Solids 19, 35 (1961). [18] C. Wagner, Zeitschrift fuer Elektrodhemie 65, 581 (1961) [19] N. R Jana, L. Gearheart, C. J. Murphy, Chem. Mater, 12, 2313 (2001), H. Yu, P.C. Gibbons, K. F. Kelton, W. E. Buhro, J. Am Chem, Soc. 123, 9198 (2001). [20] C. B. Murray, D. J. Norris, M.G. Bawendi, J. Am. Chem. Soc., 155, 8706 (1993). [21] D. V. Talapin, A. L. Rogach, A. Kornowski, M. Haase, H. Weller, Nano Lett., 1, 207 (2001). [22] J. Hambrock, R.Becker, A. Birkner, J. Weiss, R. A. Fischer, Chem. Commun. 68 (2002), N.R. Jana, X. Peng, J. Am. Chem. Soc., 125, 14280 (2003). [23] W. S. Seo, H. H. Jo, K. Lee, J. T. Park, Adv. Mater., 15, 795 (2003). [24] W. W. Yu, J. C. Falkner, C. T. Yavuz, V.L. Colvin, Chem. Commun., 2306 (2004). [25] J. Joo, H. B. Na, T. Yu, J. H. Yu, Y. W. Kim, F. Wu, J. Z. Ahang, T. Hyeon, J. Am. Chem.Soc., 125, 11100 (2003). [26] A. B. Smetana, K. J Klabunde, C. M. Sorensen, A. A. Ponce, B. Mwale, J. Phys. Chem. B, 110, 2155 (2006). [27] D. V. Leff, P. C Ohara, J. R Heath, W .M Gelbart, J. Phys. Chem., 99, 7036 (1995). [28] P. G. Shewmon, Transformations in Metals, (McGraw-Hill, New York, 1969). [29] E. A. Boucher, Nucleation (ed. A. C Zettlemoyer), (Marcel Dekker, INC, New York, 1969). [30] I. Stalder, J. H Bilgram, J. Chem. Phys. 118, 7981 (2003).

388 Thermodynamics Fundamentals and Its Application in Science

[31] H. Okamoto, T. B. Massalski, Phase Diagrams of Binary Gold Alloys, (ASM International, Metals Park OH, 1987). [32] D. A. Porter, K. E. Easterling, Phase Transformations in Metals and Alloys, (Chapman & Hall, London, 1992).

Chapter 15

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption

Vasiliy Fefelov, Vitaly Gorbunov, Alexander Myshlyavtsev and Marta Myshlyavtseva
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51802

1. Introduction
The lattice models naturally arise in different fields of physics, chemistry and other sciences. First, it is physics of the solid state and physicochemistry of the surface. Among the many well-known lattice models the magnetic, alloys, liquid mixture, adsorption models are usually mentioned. The lattice models can be both classical and quantum. In this chapter only the classical lattice models focusing on models arising in physicochemistry of the surface will be considered. For the beginning lets give the most common formal definition of the classical lattice model. Let there be given some finite or countable set M. Its elements will be called sites or nodes of the lattice and numbered index i. Each site is associated with the vector ( ci ) having ki components. Each of the components can take a finite countable or uncountable number of values, i.e. without loss of generality, it can assume that the components of this vector take either integer or real values in some finite or infinite interval. The specific values of the ci vector components determine the i-th site state. The M set state uniquely determines the state of all its elements. The system states can be divided into allowable andunallowable ones. Each allowable state of the M ci set is match to the real number EM ci called the energy per lattice site. (Formally, unallowable state can be assigned value EM ). Accepting the Boltzmann probability distribution of the system states as an additional postulate, one can receive object called a classical lattice model. All the models considered below are particular cases of the introduced generalized lattice model.

Determination of the lattice model dimension may be connected with the number of sites where can be the particle performing a random walk on the lattice in n steps. For ddimensional regular lattice the number N is proportional to the volume of a box with an edge n, where N ~ nd , i.e. the higher the dimension, the closer neighboring sites are located.
2012 Fefelov et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

390 Thermodynamics Fundamentals and Its Application in Science

Following this approach 1,2,3,, d-dimensional lattice models (for example, d-dimensional hypercubic lattices with interaction between the nearest-sites) are naturally obtained. 1,2 and 3-dimensional lattice models are of most importance for specific applications to the natural sciences. However, besides models whose dimension is equal to some natural number models which dimension defined the same way as above is fractional or infinite are of great interest. The simplest example of a model with a fractional dimension is the Ising model on the diamond-like lattice. Concluding the general description of lattice models it is worth to introduce the concept of a homogeneous lattice model. Models properties of all their sites are identical are called homogeneous lattice models. It follows the obtained lattice model has a geometric realization possessing the property of translational invariance. As it is mentioned above, the models relating to physicochemistry of the surface are of main interest, respectively, these are primarily two-dimensional ones. It is readily to conclude that all the two-dimensional homogeneous models can be divided to three classes having in the basis the geometric realizations: the square, triangular and hexagonal lattice. Note that the lattice models having different types of sites but whose geometric realizations possess translational invariance can serve the generalization of concept of lattice model homogeneity. From the computational point of view these models are very similar to homogeneous ones. Thus, the most common definition of the classical lattice model, its dimension, homogeneity and translational invariance have been introduced. Lattice gas model and its various generalizations are one of the most important lattice models of modern statistical physics. Despite its relative simplicity these shows fantastic variety of non-trivial physical phenomena. First, this refers to the phase transitions of various types whose study is of great interest from the standpoint of the general theory. Note that the adlayers on the monocrystal faces represent the physical realization of many interesting and important models for d = 2, in particular, these admitting exact solutions. The fact causes an increased interest of theorists to such systems. Usually the lattice gas means the molecular system which differs from the continual gas following feature: molecules of such a system can occupy only such places in the space in which their centers are located at the sites of one-, two- or three-dimensional geometric lattice. The interaction energies of molecules located in different configurations respect to each other are the parameters of the model. In the general case, these parameters also depend on the relative orientation of the molecules. These interactions called lateral naturally can be divided to pairs and many-particle. Pair interactions are additive while many-particle ones are nonadditive. It is easy to see from the standpoint of common definition of classical lattice model the lattice gas model (LGM) stated above refers to the same class of models as the Ising model. Indeed, considering the dependences of the energy of lateral interaction of molecules on their relative orientation one can obtain the lattice model in which the vector ci is a scalar accepting two values (when all the molecules are the same type). From the above it immediately follows that the simplest LGM is isomorphic to the classical Ising model in the

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 391

sense of the common definition. The latter statement is a very important because the property of one model can be obtained that of another one. One of the simplest examples of the system for which LGM is quite adequate model is the monomolecular adsorption model. It is well known that chemisorption has localized character as in this case there occurs chemical bond between the adsorbed molecule and the substrate. For substrate being face of monocrystal chemisorbed molecules are located in well defined places of the periodic lattice formed by the surface atoms. Therefore, the simplest LGM introduced above is completely adequate model of monomolecular chemisorption on monocrystal face. The thermodynamic Hamiltonian of the simplest LGM with one type of particles on regular lattice (for example, hypercubic) has the form:

ninj ni ,
n ,n i

(1)

where is the lateral interaction energies of the nearest neighbors; is the chemical potential; the occupation number ni is equal to unity if the adsorption site is occupied and zero in the case of a vacant site. The Hamiltonian (1) for d = 2 in the first approximation describes the monomolecular (one-center) adsorption on a monocrystal face. In some cases this description corresponds to reality but in most cases it does not [1]. It is known that even at adsorption of the most simple gases such as Ar, Kr, Xe, nitrogen, carbon monoxide, oxygen and others the adsorbate molecule size is usually larger than the distance between neighboring active centers of adsorption [2-6]. In this connection at the adsorbate molecule adsorption on one active center it simultaneously occupies one or several neighboring active centers. The assumption of one-center adsorption becomes even more inadequate at the description of adsorption of linear and quasilinear molecules such as the simple saturated and unsaturated hydrocarbons [7,8]. In the paper complete review of the experimental results on the adsorption of simple hydrocarbons on the surface of metal monocrystals (Pt, Pd) was given and, particularly, the adsorption of such molecules was shown to occur parallel to the solid surface in connection with which multicenter nature of the adsorption becomes apparent. In addition in this review some types of ordered structures of adsorption monolayer 4 8 alkanes experimentally observed at low temperatyres on the surface of monocrystalline platinum are discussed. The necessity of describing of the n-alkane adsorption in the framework of the models with multisite adsorption is also supported by the fact that at the interpretation of experimental adsorption isotherms by using the known multisite Langmuir model and other analytical models there exists good correlation between the model parameter k (the number of active sites occupied by adsorbate molecule) and the real number of segments in the molecule of the adsorbate [7,8,10-12]. It should be noted that the above analytical models of multisite adsorption are used to determine the specific surface of porous solids and its topography (in the case of energetically heterogeneous surfaces).

392 Thermodynamics Fundamentals and Its Application in Science

Obviously that the adsorption of more complex (in regard geometry, the chemical structure the presence of double/triple bonds or several functional groups) of molecules is even more nontrivial [14-25]. First of all this is manifested in that complex organic molecules (cyclic hydrocarbons, aromatic systems etc.) depending on their geometry and chemical structure can form set of different ordered structures on the solid surface. Along with the possibility of multisite adsorption that of different orientations of molecules with respect to the interface is one of the most interesting features of these systems. Indeed, over the past ten years series of experimental works devoted to the study of organic selfassembled monolayers on metal surfaces has been published. The general conclusion of these studies is that the molecule orientation in the adlayer is a function of external parameters such as concentration, pressure, temperature, electrode potential and others[1425]. Moreover, very interesting ordered structures have been experimentally found in some of similar systems. Those are structures which simultaneously contain the molecules with different orientations in the adlayer. For example, in [18] the authors investigated behavior of the adsorption monolayer of molecules p-Sexiphenil on the Au(111) surface in ultrahigh vacuum using the method of scanning tunneling microscopy. It was shown that five various ordered structures two of which contain molecules with different orientations in the adlayer molecules oriented parallel to the surface and tilted to the surface at an angle can be formed. In [24] phase transitions in the adlayer of acid trimezin molecules on the Au(111) surface have been investigated using the method of scanning tunneling microscopy, and one of them proved to lead to formation of the ordered structure containing the acid trimezin molecules oriented both parallel and perpendicular to the surface. Another striking example of the adsorption system in which the adsorbate molecules can have different orientations with respect to the surface is the adsorption of cyclic unsaturated hydrocarbons on the reconstructed semiconductor surface especially on the reconstructed face of the Si(001) [2527]. This is connected to the fact that cycloaddition reaction [2+2] with formation of di- bond Si-C with the silicon surface atoms results from chemisorption of unsaturated organic molecules on the silicon surface. In chemisorptions of more complex hydrocarbons containing several unsaturated bonds the particle adsorbed on the surface can have several configurations depending on the number of di- bonds Si-C [28]. Moreover, the stable complex being resulted from interaction between unsaturated hydrocarbon molecule and silicon atom has been experimentally discovered recently [29,30]. In light of the above it is clear that all specified features of the behavior arising at detail studying of adsorption of simple or complex molecules can be investigated only in the framework of models taking into account the multisite character of adsorption and the possibility of different orientation of molecules both with respect to each other and with respect to the solid surface. Practically, theoretical study of organic self-assembled adsorption monolayers or thin organic films is of great interest generally in connection to the set of possible applications in which thin organic films are used anyway [31]. The potential field of application of such systems is an organic optoelectronics, in particular, electroluminescent devices [32], photovoltaics [33], organic field-effect transistors [34]. Similar systems are used as coatings on computer hard drives to provide protection against corrosion and low friction [35].

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 393

It is difficult to overestimate the applied significance of considered systems in the field of chemistry and biochemistry where they are used as active elements of chemical and biological sensors [36], in heterogeneous catalysis [37] and as coatings for biomedical implants [38]. Polymorphism of organic thin films and the ability of molecules to constitute different crystalline forms leads to is it is very difficult to control growth and properties of such systems. Moreover, it was recently shown that the structure of the organic film significantly affects epitaxial growth of crystals on the film [39]. This fact can be used to control the morphology of nanocrystalline systems. In all these cases location of the molecules on the surfaces is a decisive factor that determines process of growth of the film and its physical properties. Therefore, a detailed understanding of elementary phisical and chemical processes occurring in such systems is the primary motivator at the investigation of molecular self-organization on the solid surface. The development of realistic models of such systems can allow completely to control the process of self-assembly of organic and other molecules on the solid surface and to come nearer to dream of nanotechnology to gather material possessing the necessary properties with atomic precision. Based on the above it is clear why the interest of researchers specified both practical and theoretical considerations is now shifting towards more complex lattice models some of which will be discussed in this review. Lets consider the class of lattice models describing the so-called multisite adsorption. The simplest LGM considered above in the two-dimensional case is a model of monosite adsorption (active centers of adsorption, generally speaking, do not coincide with the surface atoms). However, as noted above at the description of many adsorption systems one is forced to abandon from idea about the monosite adsorption. In the framework of the LGM multisite adsorption is described as a system of prohibitions on certain configurations. At the same time a relatively simple lattice geometrically equivalent to the crystal lattice of the surface is persisted but the number of possible states of the site determining which part of the complex molecule is located above this site and how adsorbed molecule is oriented is increased. Further, the main results obtained in the framework of the models with multisite adsorption will be presented.

2. The models of dimer and k-mer adsorption

The simplest model of multisite adsorption is a dimer adsorption model. In the first approximation the dimer model described adsorption of molecules consisted of two the same atoms, for example H2, N2, O2 etc. when temperature is relatively low and molecules cannot dissociate. Statistical thermodynamics of the dimers lattice models has a long history. This is one of the earliest lattice models which take into account the own size of molecules in the frame of the lattice gas model. Apparently, the first model of the dimer has been studied in the context of the entropy of the adlayer in 1937 [40]. As it turned out, the dimer model has deep connections with the Ising model and many other important models in statistical physics. In the early sixties of the twentieth century an exact solution of the dimer model on a square

394 Thermodynamics Fundamentals and Its Application in Science

lattice was obtained in the case of the so-called "close-packed limit", i.e. all lattice sites belong to one and only one of the dimers [41-43]. In particular, the entropy per one lattice site was calculated. Interest in the dimer model persists to this day. Exact solutions for the dimer model were recently obtained with close-packed limit in the case of the twodimensional non-orientable surfaces, such as the Mbius strip and Klein bottle [44,45]. The problem of the packing of dimers in the presence of vacancies is much more complicated and largely solved numerically [46,47].This is mainly due to three factors: 1) there are no statistical equivalence between the particle and the vacancy, and 2) any occupied site indicates that at least one of the neighboring sites occupied too and 3) it is impossible to determine exactly whether there will be adsorption on the isolated vacancy. Exact solutions for the dimer model on lattices of dimension greater than two is currently unknown. For three- and more than three dimensional lattice models it is the overall situation characteristic not only for the dimer model, but also for the simpler one-centered model such as the classical Ising model and its many generalizations. The dimer model in the framework of the lattice gas model can be described as follows. Let consider the lattice (for simplicity, a square) of the active sites. Each lattice site can be occupied by one of the segments of a dimer, or be empty. In addition, the orientation of the dimer should be specified. The last stage of building the lattice gas model is a complete listing of prohibited configurations. In this case, the system of prohibitions describes the continuity of the dimer. Just as in the simplest of the lattice gas model, different lateral interactions can be considered in the constructed model of dimer adsorption too. The dimer model is actively studied for decades because it is the simplest model of multisite adsorption and is of theoretical and practical interest. A natural generalization of the dimer adsorption model is an adsorption model of rigid or flexible linear k-mers of having no thickness. The only difference from the dimer adsorption model is the assumption that the adsorbed molecule occupies now k lattice sites forming a certain configuration. Thus, k-mer is called the model of the adsorbate molecule, consisting of k equal-sized segments, and the bond length between the segments is equal to the lattice constant and does not change, and not broken in the process of modeling. In the case of dimers, k is equal to two. Thus, from a formal point of view the lattice gas model for the dimer adsorption does not differ from the lattice gas model for k-mers, so it makes sense to discuss the results obtained in the framework of these models together. Next, referring to the k-mers reader should keep in mind the dimers adsorption model, except where otherwise noted. Depending on whether the same or different properties are segments of the molecule, kmers differ by homonuclear and heteronuclear, respectively. Works devoted to the study of k-mers can be divided into two groups according to the shape of the molecule (flexibility), the first group is works devoted to the study of flexible k-mers [48-51], the second group is works studying the adsorption properties of rigid linear k-mers (rigid rods) [49,51,52]. Theoretical analysis of a multisite adsorption of linear molecules in the general case is rather complicated, and the exact solution for k-mers found only in the simplest one-dimensional case [52,53]. In these studies were obtained exact expressions for the free energy per active

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 395

site as a function of temperature and surface coverage. In this case, the most interesting is the dependence of the diffusion coefficient on the k-mer length and the surface coverage. Thus, with increasing size of the molecule the diffusion coefficient for noninteracting or attracting k-mers increases too, as in the case of repulsive interactions, the diffusion coefficient can either decrease or increase with the molecule length increasing, depending on the degree of coverage [52-54]. For more complex cases for the two-dimensional systems only approximate analytical expressions were obtained. The most well-known analytical approximation is: 1) the theory of Flory-Huggins [48,55-58], which is a generalization of the theory of binary solutions of polymer molecules in a monomolecular solvent for the twodimensional case. The fact that in the framework of lattice gas model the problem of k-mer adsorption on homogeneous surfaces is isomorphic to the problem of binary solutions of polymer in a monomolecular solvent, 2) Guggenheim-DiMarzio approximation [59,60], which is based on calculating the number of possible ways of packaging rigid k-mers on lattices with different coordination numbers 3) the approximation based on the extension of the exact solution for a one-dimensional case [52,53] to higher dimensions [49,61], 4) well known quasichemical approximation [62] and mean-field approximation [63], 5) fractional statistical theory (FSTA) for the adsorption of polyatomic molecules, based on Holdan statistics [64], 6) semi-empirical model [61,65], etc. Unfortunately, none of these approximations is universal, and each shows quite good results, depending on the parameters of the model a flexible or rigid k-mer, the length of k-mer, the presence or absence of lateral interactions between adsorbed molecules, etc. A brief description of the approximations and compare them with each other can be found in [49,65]. Generally, more recent analytical approximations for the k-mers adsorption include earlier ones as special cases. In this regard, lets consider the best of them FSTA and semi-empirical approximation. In ref. [51] the authors, by comparing experimental data with results obtained by means of analytical approximations and a Monte Carlo simulation, studied the adsorption of linear and flexible polyatomic molecules on honeycomb, square and triangular lattices. Data obtained by the FSTA model in the case of a square lattice are almost identical to the data obtained by the Monte-Carlo simulation. A similar analytical calculation by FSTA for the kmers adsorption on triangular lattice gives an inaccurate result, because there are a larger number of possible configurations of a single k-mer on the surface. In order to verify the accuracy of the proposed approach (FSTA) the authors have constructed and analytically calculated the two models of real processes. The first is a model of oxygen adsorption on 5A zeolite and the second one a model of adsorption of propane on the 13X zeolite. The results of analytical calculations were almost identical to the experimental data. The principal difference FSTA from earlier models of multisite adsorption is that in addition to the size of molecules, it also takes into account their shape and surface geometry. Thereby FSTA can describe the adsorption of both rigid and flexible molecules. Analyzing the results deviations for various approximations from the results of Monte Carlo, it was shown that the most accurate approximation is the semi-empirical model,

396 Thermodynamics Fundamentals and Its Application in Science

developed by Roma et al. Semi-empirical model is a combination of the exact solution for one-dimensional approximation and Guggenheim-DiMarzio approximation [65]. A new theoretical approach is significantly better than other existing approximations and allows fairly simple explaining the experimental data. When comparing the adsorption isotherms of monomers and k-mers, it was found that in the second case the symmetry of the "particle-vacancy" is broken. The isotherms are shifted toward lower coverage with increasing coordination number of the lattice. In other words, for a given value of the chemical potential the surface coverage increases with the lattice coordination number. As can be seen in most works devoted to the development of new analytical methods, the results are compared not only with the experimental data, but also with the results obtained by the Monte-Carlo, as the reference. The Monte Carlo method has proved to be a very powerful tool in the study of k-mers adsorption. Using this method with different techniques (reweighing, finite-size scaling, and others [66,67]) many important parameters of the phase behavior for different k-mers adsorption systems were identified, such as the types of ordered phase structures, the points of phase transitions and critical indexes of phase transitions, etc. [68,69]. The appearance of ordered phases for the model k-mers in the presence of lateral interactions has its own specifics, this is due to the presence of orientation in the arrangement of the adsorbed molecules relative to each other. In ref. [70] the authors, using the transfer-matrix method, investigated the ordered structures of the adsorption layer consisting of interacting dimers adsorbed on a square lattice. Analysis of the changes of the adlayer entropy and the surface diffusion coefficient showed that there is a finite number of ordered phases in case of repulsion lateral interactions between the nearest neighboring molecules. Later in ref. [71] Ramirez-Pastor et al. using the Monte Carlo method have considered both attractive and repulsive interactions between adsorbed dimers on a square lattice. It was shown that in the case of attractive interactions, the phase diagram is similar to the diagram for a monoatomic gas, but the critical temperature is shifted to higher values. The most interesting case is repulsive interactions when a variety of ordered structures take place. In the case of dimers the symmetry of the "particle-vacancy", typical of monatomic particles, disturbed, that leads to the asymmetry of the adsorption isotherm with respect to the line = 0.5, on the isotherm two steps take place. When = 0.5 c 2 4 structure formed, which is characterized by the alternation of the adsorbed dimer and two adjacent vacancies. When the chemical potential increases and close to = 2/3, adsorbed dimers form parallel zigzag rows (ZZ phase) [71.72]. A similar phase behavior of adsorbed layer of dimers is observed in the case of triangular and honeycomb lattices [73] (Fig. 1). In addition, the scientific group of Ramirez-Pastor, using Monte Carlo method and finite-size scaling techniques, calculated the critical exponents and critical temperatures, and calculated a phase diagram for dimers with repulsive lateral interactions on a square [71] and triangular

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 397

[74] lattices. It was shown that the system does not belong to the universality class of twodimensional Ising model.

Figure 1. Adsorption isotherms of dimers on square, triangular and honeycomb lattices and corresponding ordered phases [71,73].

398 Thermodynamics Fundamentals and Its Application in Science

The study of the adsorption monolayers consisting of heteronuclear dimers showed that the phase diagram of the system greatly influenced by the quantity of energy of lateral interactions between the different types of segments (it is about two different molecules). In the study of phase diagrams of these films interesting phenomena were found. In particular, the coexistence of three phases and a variety of structural transitions, and ordered linear type structure exists even at high temperatures [75]. Similar calculations were performed for the adsorption of homonuclear dimers on heterogeneous surfaces [1,10,76-79]. In the case where the surface is represented by heterogeneous clusters of active sites of one kind and another, the approximate solution is relatively simple (the solution for multisite adsorption on a homogeneous surface can be used). In describing the adsorption of dimers on heterogeneous surfaces, created at random, the task becomes more complicated. Slightly more than twenty years ago an approximate solution was suggested for this model [1,10,79]. However, the original approach of Nitta et al. could only be applied to surfaces with a discrete distribution of adsorption energy. Later on the basis of this approximation Rudzinski and Everett [1] obtained a solution for a model with continuous distribution of adsorption energy on the surface. However, the usable area of this and other approximations [78] is limited. For example, in [77], the authors investigated an analytical approximation by Monte Carlo method to describe the adsorption of homonuclear dimers on heterogeneous surfaces, created randomly (random heterogeneous surface). The calculation shows that this approximation yields accurate results when the difference between the energies of adsorption on active sites of one and other kind is small. There are papers devoted to the description of the first order phase transition such as "surface gas surface liquid" [75,76,80]. The most important conclusion from all these studies is that with increasing molecular size the critical temperature shifts to higher values. On the other hand, increasing of the molecule flexibility leads to decreasing of critical temperature. A very interesting phenomenon was observed in the study of phase transition "surface gas surfacee liquid" in the adlayer consisting of heteronuclear trimers namely, the coexistence of three phases (there is a second phase transition "liquid liquid"). In this case, the phase diagram is asymmetric there are a shift of the critical density to the unit and an increasing the critical temperature. The findings in the study of dimers adsorption on heterogeneous surfaces with a sufficient degree of accuracy can be extended to the adsorption systems of k-mers [10,78,79]. However, as was shown in ref. [81], the calculation accuracy of the approximations developed for the adsorption of dimers on heterogeneous surfaces decreases with increasing molecular size. Summarizing the results obtained in these works, one can conclude that the phase behavior of adlayer of dimers on heterogeneous surfaces defined by the following factors: 1) the distribution of the various active sites of adsorption, and 2) the relation between the k-mer length and the size of the local heterogeneity, 3) adsorption energy on different active sites. It should be noted about the theoretical studies of percolation threshold in systems with multisite adsorption. Information on transitions "percolate region" "nonpercolate area" on

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 399

the surface is of great interest both from the point of view of phase transitions science, as well as from the applied point of view, in particular the appearance of surface conductivity. In the case of the two-dimensional lattice gas model the percolation threshold is so minimum value of the coverage on an infinite surface, as infinitely large cluster of adsorbed molecules is formed. In ref. [82,83] it is shown that in addition to the dimension of the system and the lattice coordination number on the percolation threshold a size of k-mers has a significant effect. Influence of temperature on percolation in adsorption systems with flexible k-mers studied in ref. [50] by the Monte Carlo method. There was found an interesting phenomenon a nonmonotonic behavior of the percolation threshold as function of temperature, i.e. there exists a temperature at which the percolation threshold is a minimum, and the position of the minimum does not depend on the length of k-mers. Thus, all existing works on the k-mers adsorption, as in the case of dimers, are concentrated in four main areas: (1) study of the influence of the chemical structure of noninteracting adsorbed molecules on the behavior of their adsorption, (2) study of the influence of surface heterogeneity on the k-mers adsorption, (3) description of first order phase transition in the adlayer in the case of mutual attraction of the adsorbate adsorbate. Only a small number of papers devoted to the study of phase transition "order-disorder, which takes places in the case of repulsive intermolecular interactions [69,70]. In particular, in ref. [69], using Monte Carlo simulation, two important characteristics of the critical properties of repulsive k-mers were identified: (1) the minimum critical temperature have on the value of k equal to 2 (dimers) and (2) for k > 2 the critical temperature increases monotonically with increasing k. Similar results (qualitatively) have been obtained from the analytical calculation of the mean field approximation and the principle of minimum free energy. Additionally it should be noted that long before the above works, the study of the multisite adsorption was engaged by Soviet scientists in Temkin (1938 [84]), and Snagovski(1972 [8587]). In ref. [84-87] the adsorption isotherms were analytically obtained in the case of multisite adsorption of two-center (k = 2), square (k = 4) and hexagonal (k = 7) complexes. Today's papers on multicenter adsorption are essentially the development, and sometimes repeating, of the works of Temkin and Snagovski. As one can see, at present the theory of adsorption of k-mers are actively developing adsorption isotherms are calculated, phase diagrams are constructed, percolation thresholds are determined, etc. This is due primarily to a large applied importance of such research. Already, it can be concluded that the behavior of adlayers consisting of molecules that occupy more than one active site of the surface is significantly different from the behavior of systems with monosite adsorption. However, it should be noted that in all these considered works the adsorbate molecule can adsorb only one way to the surface is planar.

3. Multisite adsorption of orientable molecules

Today there is a small number of papers devoted to theoretical investigation of the behavior of adsorption monolayer consisting of molecules that can have a different orientation with respect to the surface [88-92]. Lets examine them in detail.

400 Thermodynamics Fundamentals and Its Application in Science

The earliest papers on theoretical study of molecular reorientation in the adsorption monolayer were carried out at MSU by Gorshtein and Lopatkin in 1971 [88,89]. They investigated one- and two-dimensional lattice models of diatomic molecules adsorption. It was assumed that the molecule can adsorb in two different ways with respect to the surface: vertically and horizontally. Each type of adsorption had its heat of adsorption, and adsorption energy of vertically oriented molecule was approximately two times smaller. The lateral interactions between adsorbed molecules were not taken into account. The authors derived an exact analytical expression for the adsorption isotherms in one-dimensional case and the approximate equation for two-dimensional lattice. It is shown that for the large values of adsorption heats at low pressures, most of the molecules adsorbed horizontally, and the number of vertically orientated molecules is very small. When coverage increasing the horizontally adsorbed molecules change the orientation, and the number of molecules adsorbed vertically grows fast. In addition, the authors had obtained expressions for isosteric heats of adsorption. Having analyzed calculated thermodynamic functions they concluded that the system exhibits two modes of adsorption: on two neighbor sites in the region of low pressure and on one site at high pressures. The authors of [90] studied the adsorption of heteronuclear dimers (A-B) on a homogeneous surface with a mean-field approximation. In this case the dimer can be adsorbed on the surface in three different ways: horizontal adsorption with two segments at the same time and vertical adsorption with the A segment or vertical adsorption with the B segment. It was assumed that all three types of adsorption differed in the adsorption heat, and the interaction between adsorbed molecules were absent. The authors derived analytical expressions for the adsorption isotherms and isobars. In fact, the physical results obtained in this work are in qualitatively agreement with Gorshteyn and Lopatkins ones and partially duplicate it. There is the quite interesting model of spin-1 type, which can describe the adsorption of heteronuclear dimers on different lattices [91,92]. It is assumed in the model that all adsorbed molecules are oriented vertically to the surface only, and the energy of adsorption depends on what segment, A or B, molecule adsorb with. The authors of [91,92] considered the various sets of lateral interactions between dimers, in particular, they took into account not only interactions between nearest neighbors, but also between next-nearest neighbors. Such complex lateral interactions in the system led to the set of ordered surface structures and phase transitions. It had been shown that if the lattice is completely filled the "orderdisorder" transition may occure via a continuous phase transition as well as the first-order phase transition depending on the model parameters. Moreover, the continuous phase transition is nonuniversal. It should be noted that the model does not take into account the possibility of horizontal orientation of the dimer and generally speaking this model can be attributed to the well-known Blume-Emery-Griffiths model [66]. In [93] authors proposed the general lattice gas model describing the adsorption of complex molecules. The model can be formulate by following: the molecule can be adsorbed on the surface by the k ways occupying the m1 , m2 , , mk active sites located in the corresponding configurations on homogeneous or heterogeneous lattice, respectively. The simplest model of this type is the model of homonuclear dimers adsorption. In this model it is assumed that dimer may have two different orientations in the adlayer parallel (adsorption on two active

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 401

sites) or perpendicular (adsorption on one active site) to the surface. In the language of this general model homonuclear dimers adsorption model belongs to the class of models with 2, m1 1, m2 2, and heteronuclear dimers adsorption model [90] to the class with k 3, m1 1, m2 1, m3 2. The model studied in [91,92] belongs to the class of k 2, m1 1, m2 1. It should be noted that all these simple classes of models have a single k representative and the set of numbers k , m1 , m2 , , mk uniquely identifies the type of model.

Figure 2. Phase diagrams for dimers on square and triangular lattices. Ordered structures: black circles are site occupied by dimers adsorbed on two sites; gray circles are sites occupied by dimers adsorbed on one site.

402 Thermodynamics Fundamentals and Its Application in Science

As it noted in [90], the results obtained for adsorption of complex molecules can be extended also to the gas mixtures. In other words, the general model can be considered as a special case of gas mixtures adsorption model. In this case the number of mixture components will be characterized by a number k and the molecule kind by value m . So if one consider the simplest representative of the general model dimer adsorbed on two or one active site, it would be analogous to a binary mixture of dimers and monomers. These systems will be equivalent to each other if the model of binary mixture has the fixed difference between the chemical potentials of the components. From a physical point of view this means that the adsorbed molecules of one kind, and the behavior of the system is very similar to the adsorption of the gas mixture. Indeed, when the adsorption properties of complex molecules [93-97] was studed, it was discovered the phenomenon of non-monotonic changes in surface coverage with the chemical potential increasing, and a similar phenomenon was observed in the study of adsorption of binary mixtures [98,99]. In order to evaluate the influence of surface geometry on the phase behavior of adsorbed monolayer the model of orientable dimers on the square and triangular lattice was studied [100,101]. It was shown that the influence of the coordination number (the number of nearest neighbors) plays an important role in the phase formation process. Namely, in the case of square lattice only two ordered structures consisting of dimers adsorbed only vertically or only horizontally can form, in the case of triangular lattice except for the phases of this type another phase consisting of differently oriented molecules appears. Phase diagrams are presented in Fig.2. The simplest special case of the general model of adsorption of molecules with different orientations in the adsorbed monolayer is the lattice model of dimers adsorption discussed in detail above. Extending the model of dimers adsorption on molecules with more complex form (cyclic hydrocarbons, aromatic systems, etc.) one can get the lattice model of complex organic molecules adsorption, which takes into account, firstly, the possibility of different orientations with respect to the solid surface and, secondly, the diversity and complicated structure of surface complexes (non-linear shape of the adsorbate molecules). Further, a special case of the generalized model, which allows to study the effect of varying the orientation of the complex organic molecules on the behavior of the adsorbed layer in pure form will be considered. The fact is the model of dimers adsorption along with the possibility of different orientations of the molecules with respect to the surface takes into account the ability to the different orientation of molecules relative to each other a priori. Indeed, in the case of square lattice, the dimer adsorbed parallel to the surface can have two different orientations which does not allow us, in the framework of this model, to focus on studying the effect of varying the orientation of the molecule with respect to the solid surface on the structure and thermodynamic properties of the adlayer. As model of solid surface homogeneous square lattice is considered and it is assumed that the molecule can be adsorbed in two different ways: 1) on four active sites (Fig. 3a) and 2) on one active site (Fig. 3b). In the first case the four active sites involved in adsorption process form the square. Thus, for the constructed model one have k=2, m1=1, m2=4. In addition, an

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 403

Figure 3. Possible configurations of the adsorbed molecules. The small circles represent molecules adsorbed on one active site, and the large ones molecule adsorbed on the four active sites. The numbers from 0 to 5 correspond to all possible states of the active site (cell).

infinitely strong repulsion between the nearest neighboring molecules in the model (a nearest neighborhood between two adsorbed molecules independently of the adsorption way is prohibited as well) are assumed, which in a first approximation, take into account the complex structure of the molecule. Active sites prohibited for the adsorption, in the case of two different orientations of the adsorbed molecules are indicated on Fig. 3 by the cross. It is seen that the proposed model of multisite adsorption eliminates the effect of varying the orientation of molecules relative to each other on the structure and thermodynamic properties of the adsorbed layer, since all possible orientations of the molecules in the plane parallel to the interface are taken into account simultaneously (Fig. 3). Thus, this model is the simplest model, which allows to study the effect of varying the orientation of complex organic molecules relative to the interface on the structure and properties of the adsorbed layer regardless of other factors. To reduce the dimensionality of the model the value q2 q1 is introduced as the difference between the heats of adsorption of the four-site location and the mono-site one. The effective Hamiltonian of the model under consideration can be written as

1 H ni ni ci 4 i 4 i i

(2)

where the occupation numbers ci and ni are equal to unity for occupied by molecule adsorbed on one and four sites respectively and zero for empty sites; is the chemical potential of the adsorbed particles. The thermodynamic properties of the model have been investigated with standard importance sampling Monte Carlo method [93]. The calculations of the isotherms and the surface coverage as the function of the gas phase pressure (chemical potential) are carried out with the linear size of the lattice L 96 and L 24, 36, 48, 60 used for finite-size scaling procedures. The linear lattice size was chosen for the adlayer structures to be not perturbed.

404 Thermodynamics Fundamentals and Its Application in Science

Thermodynamic equilibrium is reached by spin-flip (Glauber) dynamics [102] and diffusion relaxation (Kawasaki dynamics) [103]. To calculate thermodynamic functions successive configurations of the adlayer are generated using Metropolis transition probabilities [104] in the grand canonical ensemble. Analysis of the ground state (T = 0K) of the model allowed to conclude that in the adlayer due to the infinitely strong repulsive interactions between nearest-neighbor molecules the set of chessboard type ordered structures forms: c(44)4, c(33)4-1 and c(22).The structures are schematically shown in Fig. 4. In addition, the lattice gas phase (LG) with zero coverage exists in the ground state of the system. The corresponding phase diagram of the adsorption monolayer in the ground state of the system shown in Fig. 5.

Figure 4. Ordered structure of the adlayer. Gray circle denotes a molecule adsorbed on the four active sites, and the black circle molecule adsorbed on one active site. The structures are shown in order of their formation with the chemical potential increasing.

Figure 5. Phase diagram of the adlayer in the ground state. The solid line separates the stability region of the LG phase and stability region of phase c(44)4, while the dashed and dotted lines separate the stability region of phases c(44)4 c(33)4-1 and phases c(33)4-1 c(22), respectively.

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 405

The adsorption isotherms calculated for different values of the ratio /RT are shown in Fig. 6. It is seen that for sufficiently large values of /RT there are three distinct plateaus on the isotherms, which correspond to thermodynamically stable phases of the adsorption monolayer at =0,125, =0,22(2) =0,5, where is density of the adlayer (the amount of adsorbed molecules per site). Based on the values of corresponded to each horizontal plateau one can conclude that the first plateau determines the existence region of the ordered phase c(44)4, the second plateau the existence region of the phase c(33)4-1, and the third the existence region of the phase c(22). In addition, according to the shape of the adsorption isotherms it can be assumed that the ordered structure c(44)4 is formed from disordered lattice gas phase via second-order phase transition, which associated with the origin of a new symmetry element in the system. On the other hand, the phase transitions c(44)4 c(33)4-1 and c(33)4-1 c(22) are the first-order phase transitions which associated with sharp changing in the first derivatives of the free energy of the system, in this case it is expressed by the sharp changing in the number of adsorbed molecules in the system. It is worth to note that along with an abrupt changing in the number of adsorbed molecules in the system, phase transitions c(44)4 c(33)4-1 and c(33)4-1 c(22) are also attended by the reorientation of the adsorbed molecules with respect to the solid surface.

Figure 6. Adsorption isotherms (left) and the dependencies of surface coverage on reduced chemical potential (right) calculated for different values of /RT.

The dependencies of surface coverage on reduced chemical potential /RT demonstrate the same phase behavior of adsorbed monolayer (Fig. 6). Namely, there are three horizontal plateaus on the surface coverage curves at =0,5, =0,55(5) and =0,5 for sufficiently large values of the ratio /RT. These values of surface coverage, as in the case of the adsorption isotherms, coincide with the values of surface coverage for the above mentioned phases c(44)4, c(33)4-1 and c(22), respectively . However, there is one significant difference between the adsorption isotherms and the dependencies of surface coverage on reduced chemical potential: the isotherm is not only coincides with the curve of surface coverage, but

406 Thermodynamics Fundamentals and Its Application in Science

even out of proportion to it. Indeed, the dependencies of surface coverage on the reduced chemical potential are non-monotonic function for sufficiently large values of /RT. While the adsorption isotherms in accordance with the general conditions of stability of thermodynamic systems

G(T , p , N ) 2 1 2G N N 2! N 2 N m n 3 4 1 3G 1 4G 1 mG 1 nG N 4! 4 N ... m! m N n! n N 0, 3 3! N N N N n m
()Tp G N
Tp

(3)

G(T , p , N ) , N

0, N T

are monotonically increasing functions for all values of /RT, where grand potential, G Gibbs free energy, chemical potential, N amount of adsorbed molecules, T temperature and p pressure in gas phase. The same effect is observed in the dimer adsorption models on square and triangular lattices. Apparently, this effect takes a place in any adsorption monolayer of molecules with different orientations with respect to the interface. In order to uniquely identify the ordered structures appearing in the adsorption monolayer the authors of [93] calculated the curves of partial surface coverage by molecules adsorbed on one and four active sites as functions of the reduced chemical potential /RT (Fig. 7). It is seen the phase with coverage = 0,5 formed at low values of /RT consists only of molecules adsorbed on four active sites, so it is obvious that it has the structure of c(44)4. Then, with increasing chemical potential (gas phase pressure) or decreasing in temperature of the substrate, the system undergoes the phase transition from phase c(44)4 to the phase with coverage =0,55(5). It is clear from Fig. 7 that this phase consists of both molecules adsorbed on four active sites and on one active site. Therefore, this phase has the structure of c(33)4-1. With further increase of the chemical potential or when the temperature decreases the system undergoes the phase transition from phase c(33)4-1 to the phase c(22) with =0,5 and =0,5 which is formed only by molecules adsorbed on one active site. Recently, a similar phase behavior of adlayer of complex organic molecules was observed experimentally (Fig. 8). In [24] the authors investigated the behavior of the adsorption monolayer of trimesic acid on Au (111) with electrochemical scanning tunneling microscopy. It was shown that with increasing electrode potential the ordered structure of the adlayer consisting only of molecules oriented parallel to the surface changes into the ordered phase, which contains molecules adsorbed both parallel and perpendicular to the electrode surface. Further increasing in the electrode potential leads to the surface phase which is formed only by molecules oriented perpendicular to the surface.

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 407

Figure 7. The curves of partial surface coverage calculated at /RT = 12. 1 partial coverage of the surface by molecules adsorbed on one active site; 4 partial coverage of the surface by molecules adsorbed on four active sites; total surface coverage; density of the adlayer (adsorption isotherm).

Figure 8. Ordered structure of the trimesic acid adsorption monolayer on Au (111) [21] and the corresponding structures calculated in the framework of the proposed model.

Analogous sequence of the ordered structures was also observed in other systems, in particular, in p-sexiphenyl [18] and pyridine adsorption monolayers [23] on Au (111). Thus, the phase behavior of monolayer adsorption which is realized in the model under consideration is qualitatively the same as the phase behavior of real adsorption monolayers of complex organic molecules on homogeneous surfaces. Therefore, a detailed study of the

408 Thermodynamics Fundamentals and Its Application in Science

model and models similar to that is very useful for deeper understanding of the thermodynamics of self-assembled monolayers of complex organic molecules. In the framework of the model under consideration, the modern methods of theoretical physics such as the multiple-histogram reweighting and finite-size scaling techniques (the fourth-order cumulant of the order parameter) have been used to estimate the phase diagram (T, ) of complicated organic molecules adsorbed on the homogenous square lattice (Fig. 9) [93].

Figure 9. Phase diagram of adsorption monolayer of complex organic molecules on homogenous square lattice.

The phase diagram shown in Fig. 9 differs from the phase diagrams of dimers adsorption monolayer on square and triangular lattices that: 1) there is the phase consisting of molecules oriented in both ways (parallel and perpendicular to the solid surface) simultaneously, and 2) the critical temperature of this phase (c(33)4-1) is higher than the critical temperature of the ordered phase formed only by molecules adsorbed parallel to the surface. Indeed, the phase diagram of dimers adsorption on square lattice contains only two regions corresponding to the ordered phases due to the fact that when dimers adsorb on square lattice the ordered phase consisting of both dimers adsorbed parallel and perpendicular to the surface does not appear. In contrast, when dimers adsorb on triangular lattice that ordered phase is formed, but its critical temperature is lower than the critical temperature of the ordered structure formed only by dimers adsorbed parallel to the surface. Thus, the numerical analysis of the thermodynamic properties of the lattice models which take into account the possibility of varying the orientation of the adsorbate molecules both with respect to each other and with respect to the solid surface showed that:

Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 409

1.

2.

3. 4.

The phenomenon of non-monotonic changes of the surface coverage as function of the chemical potential is a general property of the systems under consideration and is not observed in models of single-site or multisite single-component gas adsorption which exclude different orientations in the adsorption monolayer. There are ordered structures in the adsorption monolayer of complex organic molecules consisting of the molecules with different orientations relative to the solid surface, simultaneously. The transition between the ordered structures of the adsorption monolayer occurs abruptly through the first-order phase transition. The phase behavior of adsorption monolayer of complex organic molecules strongly depends on two factors: a) the geometry and chemical structure of the adsorbed molecule, and b) the geometry of the surface.

It is worth to note that the adsorption of single-component gas consisting of molecules with complex shape can exhibit the features which typical for the adsorption of multicomponent gas mixtures [90]. In particular, the model of adsorption of a gas mixture A (adsorb on m1 active sites) and B (adsorb on m2 active sites) is equivalent to the considered models (with k = 2) when the chemical potentials of the gas mixture components are the same, A = B.

4. Conclusion
Lattice gas model and its various generalizations are one of the most important models of modern statistical thermodynamics and are currently experiencing a new stage of development. On the one hand, it is related to the solution of some fundamental issues concerning the limiting behavior of two-dimensional lattice models, and, on the other hand, it is related to successful attempts to describe with the help of this model complex systems, in particular, multisite adsorption of various molecules on the solid surface. Lattice models of multisite adsorption can take into account the number of characteristic features of complex adsorption systems, the most important of which is the possibility of the orientation varying of the adsorbate molecules, both with respect to each other and relative to the solid surface. Analysis of the thermodynamic properties of models of this type showed that despite its relative simplicity they exhibit a fantastic variety of non-trivial physical phenomena. First of all, it refers to the processes of self-assembly and phase transitions of various types, whose study is of considerable interest from the standpoint of the general thermodynamic theory. In addition, referring to the results of the experimental data, it can be argued that discussed in this chapter multisite adsorption model is firstly qualitatively, and in some cases quantitatively, reproduce the behavior of real systems and secondly have considerable predictive power. The results of study of multisite adsorption models can be summarized in following conclusions: 1. The adlayer of complex organic and inorganic molecules can form ordered structures consisting of molecules with different orientations simultaneously (both with respect to each other and relative to the solid surface).

410 Thermodynamics Fundamentals and Its Application in Science

2.

3.

4.

The phase diagram of such systems is asymmetric. Its shape depends essentially firstly on the size and shape of the adsorbate molecules and secondly on the coordination number and type of heterogeneity of the substrate surface. The critical temperature of the ordered phases of the adlayer on the one hand increases with the size of the molecule and on the other hand decreases with increasing coordination number of the lattice (entropy factor). In models that take into account the possibility of the orientation varying of molecules adsorbed on the solid surface one can see the phenomenon of non-monotonic change in the coverage with increasing chemical potential, and the transition between the ordered structures of the monolayer adsorption occurs abruptly, through first order phase transition.

From applied point of view a theoretical study of such systems in general is of great interest because of the many possible applications in which used the adsorption monolayers one way or another (self-assembled monolayers adsorbed, thin organic films). The potential application range of such systems is an organic optoelectronics, the development of active elements of chemical and biological sensors, biomedical materials, heterogeneous catalysis. In this paper it is shown that the development of lattice models of these systems and study of its thermodynamic properties allows ones to understand and generalize laws of physical and chemical processes occurring in such systems, and brings the scientists closer to being able to fully control the phase behavior of monolayers of organic and other molecules on solid surfaces.

Author details
Vasiliy Fefelov, Vitaly Gorbunov and Marta Myshlyavtseva Omsk State Technical University, Russia Alexander Myshlyavtsev Omsk State Technical University, Russia Institute of Hydrocarbons Processing SB RAS, Russia

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Section 5

Non-Equilibrium Thermodynamics

Chapter 16

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing
Adela Ionescu
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51585

1. Introduction
Although the turbulence is often associated with fluid dynamics, it is in fact a basic feature for most systems with few or infinity freedom degrees. It can be defined as chaotic behavior of the systems with few freedom degrees and which are far from the thermodynamic equilibrium. In this area two important zones are distinguished: The theory of transition from laminar smooth motions to irregular motions, characteristic to turbulence; Characteristic studies of completely developed turbulent systems.

In hydrodynamics, the transition problem lays back to the end of last century, at the pioneering works of Osborne Reynolds and Lord Rayleigh. Since the beginnings, it was pointed out the fruitful investigation method of considering the linear stability of basic laminar flow until infinitesimal turbulences. Nonlinearity can act in the sense of stabilizing the flow and therefore the primary state is replaced with another stable motion which is considered as secondary flow. This one can be further replaced with a tertiary stable flow, and so on. It is in fact about a bifurcations sequence, and Couette-Taylor flow is maybe the most widespread example in this sense. The situation becomes hard to approach if the non-linearity is acting in the sense of increasing the rate of growing the unstable linear modes. Although it was anticipated that the flows can be stable according to the linear theory, in experiments it was concluded that they are unstable. It must be noticed that Reynolds himself understood this possibility, and suggested that for the transition from laminar to turbulence for a pipe flow, the condition must be of instability at certain size perturbations and stability at smaller perturbations.
2012 Ionescu, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

420 Thermodynamics Fundamentals and Its Application in Science

The issue of transition in flows such Poiseuille flow until Reynolds numbers under the critical value, must be due to instabilities at finite amplitude perturbations. For these flows there was nothing relevant found concerning the eventual secondary stable motions, moreover it seems that turbulence issue directly from primary flow, at a fixed Reynolds number. These strong turbulence problems are quite difficult to approach and this gives evidence that still is to be added more substance to the original Reynolds suggestion, after one hundred years of stability studies. For this quite new theory, unifying with the classic turbulence is far from being solving, but the recent challenges could open new research directions. Generally, the statistical idea of a flow is represented by a map:

x , X t X t 0 X

(1)

That means X is mapped in x after a time t. In the continuum mechanics the relation (1) is named flow, and it is a diffeomorphism of class Ck. Moreover, the relation (1) must satisfy the following equation:
x J det D t X det i X j

(2)

where D denotes the derivation with respect to the reference configuration, in this case X. The equation (2) implies two particles, X1 and X2, which occupy the same position x at a moment. Non-topological behavior (like break up, for example) is not allowed. With respect to X there is defined the basic measure of deformation, the deformation gradient, F, namely the equation (3):

F X t X

x , Fij i Xj

(3)

where X denotes differentiation with respect to X. According to equation (2), F is non singular. The basic measure for the deformation with respect to x is the velocity gradient. After defining the basic deformation of a material filament and the corresponding relation for the area of an infinitesimal material surface, there can be defined the basic deformation measures: the length deformation and surface deformation , with the following relations (Ottino, 1989):

C : MM det F C 1 : NN ,

1/ 2

1/2

(4)

where C (=FTF) is the Cauchy-Green deformation tensor, and the vectors M,N - the orientation versors in length and surface respectively, are defined by:

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 421

dX dA ,N dX dA

(5)

Very often, in practice is used the scalar form of (4), namely the following relation:

2 Cij Mi N j , 2 det F Cij 1 Mi N j

(6)

where D is the deformation tensor, obtained by decomposing the velocity gradient in its symmetric and non-symmetric part. The flow x=t(X) has a good mixing if the mean values D(ln)/Dt and D(ln)/Dt are not decreasing to zero, for any initial position P and any initial orientations M and N. As the above two quantities are bounded, the deformation efficiency can be naturally quantified. Thus, there is defined (Otino, 1989) the deformation efficiency in length, e = e (X,M,t) of the material element dX, as follows: e D ln / Dt 1 (7)

D : D

1/ 2

Similarly, there is defined the deformation efficiency in surface, , e= e (X,N,t) of the area element dA: in the case of an isochoric flow (the jacobian equal 1), there exists the equation (8): e D ln / Dt 1 (8)

D : D

1/2

The deformation tensor F and the associated tensors C, C-1, form the fundamental quantities for the analysis of deformation of infinitesimal elements. In most cases the flow x t X is unknown and has to be obtained by integration from the Eulerian velocity field. If this can be done analytically, then F can be obtained by differentiation of the flow with respect to the material coordinates X. The flows of interest belong to two classes: i) flows with a special form of v and ii) flows with a special form of F. The second class is what we are interested for, as it contains the so-called Constant Stretch History Motion CSHM.

2. Issues on turbulent mixing. Results and challenges

The central problem exhibited in this chapter is the challenge of unifying the theory of turbulent mixing. This implies few levels: analytical, computational and experimental. The specific literature is rich in works both on analytical and experimental models. There were realized few comparative analysis, both for analytical and computational standpoint, for 2D and 3D models of different flow types.

422 Thermodynamics Fundamentals and Its Application in Science

2.1. Recent issues in the literature

The recent discussions and works (Dimotakis, 1983) on the empirical evidence and theoretical ansatz on turbulence support the notion that fullydeveloped turbulence requires a minimum Reynolds of order of 104 to be sustained. This value must be viewed as a necessary, but not sufficient condition for the flow to be fully developed. Presently available evidence suggests that both the fact that the phenomenon occures and the range of values of Reynolds number where it occures are universal, i.e. independent of the flow geometry. On the other hand, how sharp this transition is does appear to depend on the details of the flow. In particular, it is considerable sharp, as a function of Reynolds number, in the (Couette- Taylor) flow between concentric rotative cylinders. It is less well defined for a shear layer and, among the flows considered, the least well defined for turbulent jets. Perhaps an explanation for this variation lies in the definition of the Reynolds number itself and the manner in which the various factors that enter are specified for each flow. In the case of the Couette-Taylor flow, for example, both the the velocity UCT a and the spatial scale CT b a ., where is the differential rotation rate, with a and b - the inner and outer cylinder radii, are well-defined by the flow-boundary conditions. In the case of a zero streamwise pressure gradient shear layer, the velocity US U 1 U 2 is a constant, reasonably well specified by the flow boundary conditions U 1 at a particular station. The length scale s s x must be regarded as a stochastic variable 1 1 in a given flow with a relatively large variance. The Reynolds number for the shear layer is then the product of a well-defined variable and a less well-defined, stochastic, variable. In the case of a turbulent jet, both the local velocity Uj and the scale j must be regarded as stochastic flow variables, each with its own large variance. The Reynolds number for the jet is then the product of two stochastic variables, and, as a consequence, its local, instantaneous value is the least well-defined of the three. As regards fully-developed turbulent flow, the presently available evidence does not support the notion of Reynolds number independent mixing dynamics, at least in the case of gas phase shear layers for which the investigations span a large enough range. In the case of gas phase turbulent jets, presently available evidence admits a flame length stoichiometric coefficient tending to a Reynolds number independent behaviour. It must be noticed, however, that the range of Reynolds numbers spanned by experiments may not be large enough to provide us with a definitive statement, at least as evidenced by the range required in the case of shear layers. In comparing shear layer with turbulent - jet mixing behavior, the more important conclusion may be that they appear to respond in the opposite way to Schmidt number effects, i.e. gas- vs liquid phase behavior. Specifically, there are high Schmidt number (liquid phase) shear layers that exhibit a low Reynolds number dependence in chemical product formation, if any. In contrast, there are gas- phase turbulent jets that exhibit an

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 423

almost Reynolds number independent normalized variance of the jet-fluid concentration on the jet axis, with a strong Reynolds number dependence found in liquid phase jets, in the same Reynolds number range. To summarize, recent data on turbulent mixing suppport the notion that the fully developed turbulent flow requires a minimum Reynolds number of 104, or a Taylor Reynolds number of ReT102 to be sustained. Conversely, turbulent flow below this Reynolds number cannot be regarded as fully developed and can be expected to be qualitatively different (Dimotakis 1983). The manifestation of the transition to this state may depend on the particular flow geometry, e.g. the appearance of streamwise vortices and three dimensionality in shear layers. Neverless, the fact that such a transition occurs, as well as the approximate Reynolds number where it is expected, appears to be a universal property of turbulence. It is observed in a wide variety of flows and turbulent flow phenomena. (Dimotakis, 1983)

2.2. Recent results from experimental and computational / analytical standpoint

Recently, it was realized (Ionescu, 2002, 2010) the analysis of the length and surface deformations efficiency for a mathematical 3D model associated to a vortexation phenomena. The biological material used is the aquatic algae Spirulina Platensis. The mathematical study was done in association with the experiments realized in a special vortexation tube, closed at one end. Locally, there is produced a high intensity annular vorticity zone, which is acting like a tornado. The small scale at which the turbulence issues allows retaining the solid particles, mixing the textile fibbers or breaking up the multicellular filaments of aquatic algae. The special vortex tube used for achieving the breaking up of filaments is a modified version at low pressure of a Ranque-Hilsch tube (Savulescu, 1998). Completely closing an end of the tube, there is obtained in this region a high intensity swirl. The flow in the tube is generally like a swirl, with a rate tangential velocity / axial velocity maxim near the closed end, where is also created the annular vortex structure. The approaching aerodynamic circuit is made from: a pressure source, the box of tangential inputs, the diffusion zone, the tube where there is produced the swirl with additional pollutants inputs, and the closing end with a rotating end. It must be noticed that this torrential flow is concentrating and intensifying the vorticity, in contrast with the usual cyclone-type flow or other flows generators. If in the installation is introduced a pollutant, there issues a turbulent mixing in the annular vorticity zone. The spatial and temporal scales revealed the existence of different domains, starting with laboratory ones and until dissipative domains or others - corresponding to fine structure wave numbers. Thus, the applications area is very large, including collecting, aggregating, separating and fragmenting the various pollutants.

424 Thermodynamics Fundamentals and Its Application in Science

From physical standpoint (Savulescu, 1998), the vortex produced in the installation implies four mechanisms:
-

Convection (scalar transport), due to streamlines which are directed towards the ending lid near the tube walls, with the pressure source near the tube centre line; Turbulent diffusion due to the pressure and velocity variation; Stratification effects due to pressure and temperature gradients; Turbulent mixing due to the velocity concentration in annular structures.

The convection keeps in the transport and deposit of the powder pollutant when the graining diameter is greater than 5m. However, the graining spectra domain under 5m undergoes a turbulent diffusion and stratification effects which are generally out of control. For revealing the local concentration of the streamlines, 2D simplified models were tested. The multiphase 3D flows simulation is still in study. The turbulent mixing in multiphase flow reveals the following experiment components:
-

The topological limit of the multiphase flow when the pollutant enters in the aggregation state or remains fragmented, in the host fluid; The rheological behaviour of non-Newtonian compositions, under macroscopic effects of the air velocity.

The installation was realized in two versions: a small scale vortex tube (10-20mm diameter) and a large scale one (100-300mm). They correspond generally at two particles processing classes, although in most cases the classes can be superposed. The first category refers to collecting and separating various powders, from gaseous emissions to ceramic powders. The parameters which must be taken into account are the graining spectra, the atmosphere nature and concentration. The vorticity concentration can be used for processing the deposit of different particles in powder or cement form by an adequate closing lid. The second category contains the processing on small scale, including deformation and breaking up mechanisms for various particles in a host fluid. It is studied the vorticity concentration near the closing lid. During such an experiment (Ionescu, 2002), it was processed the aquatic algae Spirulina Platensis in the host fluid water. After the processing, the long chains of cellular filaments were fragmented, producing isolated cell units or sometimes there was recorded the breaking up of some cellular membranes (with less than 100 Angstrom thickness). The initial and final observations (after the vortexation) are exhibited in figure 1 below. It has been t Q used the non-dimensional parameter a 3 , where t represents the time (in seconds), Q D the installation debit (m3/sec) and D the diameter (m3). As it can be seen from the picture, the fragmentation degree starts to increase as a grows. There can also be observed the algae form before and after the fragmentation.

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 425

Following the opinion of the specialists in cellular biology, this new technological method of processing the flows is more efficient than the classical centrifugation method.

Figure 1. The fragmentation degree variation of Spirulina Platensis

Three specific applications were performed as fluid waste management: the agglomeration of short fibers (aerodynamic spinning); the retention of particles under 5m without any material filter; the breakout of cell membranes of the phytoplankton from polluted waters and the providing of a cell content solution with important bio-stimulating features.

The mathematical modeling and analytically testing of the above experiment confirmed the experimental study. Concerning the phenomenon scale, there were taken into account medium helicoidally streamlines with approximating 10m width. There were not gone further to molecular level. Also, it is important to notice that for this moment of the analytical testing of the model, there has not been studied the influence of strictly biological parameters (such as pH, the temperature, the humidity, etc). The complex multiphase flow necessarily implies a theoretical approach for discovering the ways of optimization, developing and control of the installation. Numeric simulation of 3D multiphase flows is currently in study. In the mathematical framework, the flow complexity implies the following three stages: modeling the global swirling streamlines; local modeling of the concentrated vorticity structure; introducing the elements of chaotic turbulence.

The mathematical model associated to the vortex phenomena is, basically, the 3D version of the widespread isochoric two-dimensional flow (Ottino, 1989):

426 Thermodynamics Fundamentals and Its Application in Science

. x1 G x2 . x K G x , 1 K 1, G 0 1 2

(9)

Namely, the following vortex flow model is in study: . x1 G x2 . x2 K G x1 . x c 3

, 1 K 1, c const.

(10)

In the first stage, the flow model (10) was studied from the analytical standpoint. Namely, the solution of the Cauchy problem associated to (10) was found. In order to analyze the length and surface deformations of algae filaments in certain vortex conditions, the CauchyGreen deformation tensor was calculated. There were obtained quite complex formulas for e , e (Ionescu 2002, 2010). The second stage has been a computational / simulation standpoint. It has been realized a computational analysis of the length and surface deformation efficiency, in some specific vortexation conditions. With the numeric soft MAPLE11, the analysis has been two parts. Firstly, the following Cauchy problems has been solved: e t 0, x 0 0 e t 0, x 0 0 (11)

using a discrete numeric calculus procedure (Abell, 2005). The output of the procedure is a listing of the form ti , x ti , i 0..25 . In the second part there have been realized discrete time plots, in 25 time units, following the listings obtained in the first part. The plots represent in fact the image of the length and surface deformations, in the established scale time.

Very few irrational value sets were chosen for the length, respectively surface versors, taking into account the versor condition:

Mi 1, N j 1

(12)

The studied cases are in fact represented by the events associated to different values of length and surface orientation versors: M1 , M2 , M3 and N1 , N 2 , N 3 for length and surface respectively. The events were very few, about 60. Their statistical interpretation is synthesized in (Ionescu 2010), including also the two-dimensional case. The graphical events are illustrating the analysis of the deformations for Spirulina Platensis, in 25 time units vortexation. According to (Ionescu 2001, Ottino 1989), the algae filaments represent Lagrange markers. The special spiral form of the algae gives the answer to the

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 427

computational context that the surface deformation e is significant, since it brings more cases of filaments break up. It was called rare event the event of very sudden breaking up of the algae filaments, this corresponding from mathematical standpoint to the break out of the program (because of impossibility of maintaining the required accuracy). Thus, a very important fact happened: the mathematical simulations matched the experimental analysis. Sumarising these basic stages in the behavior analysis of the turbulent mixing flow, is important to notice that the filaments breaking up is due to alternating loadings that the filament undergoes, in a space-time with random events, available to the break phenomena. The modeling has been the following basic stages: Associating known streamlines to the medium flow (that means helical flow in a cylinder); Determining the linear and surface deformations from continuum fluid mechanics; Associating a sequence of random values to the (vectorial) length and surface orientations.

In fact, there were found four types of processes, all of which were matched by the simulations 1. 2. 3. Processes with relative linear behavior; Linear-negative processes, which correspond to alternate tasks of stretching and folding of filaments and are the most; Mixing phenomena where there issue smaller or larger deviations or strong discontinuities; these concern the situations when some pieces are suddenly coming off from the whole filament, followed by the restarting of vortexation for the rest of algae; Rare events these correspond to the turbulent mixing and represent the sudden break up of spirulina filaments.

4.

The validity of the model is confirmed by two aspects: the statistic increment in time of the breaking cases, according to the experiments; the relative singularity of the events which could produce the breaking, fact which is confirmed by the quite long duration of the experiments which led to the filaments break up; in very rare cases, the cellular membrane could be broken, and the cellular content collected.

Crossing over from 2D to 3D case, it is easy to deduce the requirement of a special analysis of the influence of parameters on the behavior of this complex mixing flow. This would include more paramater analysis types for some perturbation models in 2D and 3D case, but also another mathematical analysis types, for example spectral analysis.

2.3. New influence of simulation parameters

The analysis recently has been continued with more computational simulations, for 2D model, both in periodic and non periodic case, and for 3D model, too. A lot of

428 Thermodynamics Fundamentals and Its Application in Science

comparisons between periodic and non- periodic case, 2D and 3D case were realized (Ionescu 2008, 2009). In the same time, the computational appliances were varied. If innitialy, the model was studied from the standpoint of mixing efficiency, in the works that come after, new appliances of the MAPLE11 soft were tested (Abell 2005, Ionescu 2011), in order to collect more statistical data for the turbulent mixing theory. In what follows, few of these appliances are described.

2.3.1. Few MAPLE11 apliances used in simulations

For the purpose of this chapter, there are presented only the recent used appliances of MAPLE11 soft. There have been used two graphical appliances of this soft, namely DePlot and Phaseportrait tools, from DETools package. Both of them are based on numeric methods in producing trajectories of differential equations systems. The most used numeric method is Fehlberg fourth-fifth order Runge-Kutta method - the so-called rkf45 method - with degree four interpolant (Abell 2005). DETools[DePlot] this tool plots solutions to a system of differential equations. The calling sequences are as follows: DEplot(deqns, vars, trange, options) DEplot(deqns, vars, trange, inits, options) DEplot(deqns, vars, trange, xrange, yrange, options) DEplot(deqns, vars, trange, inits, xrange, yrange, options) DEplot(dproc, vars, trange, number, xrange, yrange, options) Parameters: deqns - list or set of first order ordinary differential equations, or a single differential equation of any order; dproc - a Maple procedure representation for first order ordinary differential equations, or a single differential equation of any order; vars - dependent variable, or list or set of dependent variables; trange - range of the independent variable; number - equation of the form 'number'=integer indicating the number of differential equations when deqns is given as a function (dproc) instead of expressions; inits - set or list of lists; initial conditions for solution curves; xrange - range of the first dependent variable; yrange - range of the second dependent variable; options - (optional) equations of the form keyword=value;

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 429

Description: Given a set or list of initial conditions (see below), and a system of first order differential equations or a single higher order differential equation, DEplot plots solution curves, by numerical methods. This means that the initial conditions of the problem must be given in standard form, that is, the function values and all derivatives up to one less than the differential order of the differential equation at the same point. A system of two first order differential equations produces a direction field plot, provided the system is determined to be autonomous. In addition, a single first order differential equation produces a direction field (as it can always be mapped to a system of two first order autonomous differential equations). A system is determined to be autonomous when all terms and factors, other than the differential, are free of the independent variable. For systems not meeting these criteria, no direction field is produced (only solution curves are possible in such instances). There can be only one independent variable The default method of integration is method=rkf45. Other methods can be specified in the optional equations. Note that because numerical methods are used to generate plots, the output is subject to the characteristics of the numerical method in use. In particular, unusual output may occur when dealing with asymptotes. The direction field presented consists of either a grid of arrows or a set of randomly generated arrows. In either case, the arrows are tangential to solution curves. For each grid point, the arrow centered at (x,y) has slope dy/dx. This slope is computed using (dy/dt)/(dx/dt), where these two derivatives are specified in the first argument to DEplot. The curved arrow types (curves and comet) require additional data for the curvature of the direction field, which is computed by moving an epsilon in the direction of the slope dy/dx, and computing dy/dx, then moving an epsilon in the direction opposite the slope, and computing dy/dx. This data is then sufficient to draw a small portion of the direction field lines local to the point, which is then used to draw the curved arrows. By default, the two dependent variables are plotted, unless otherwise specified in the scene option. The deqns parameter can be given as a procedure, but must conform to the specification as given in dsolve/numeric, and the number option must be included before the initial conditions. In this instance, deqns must be of the form: proc( N, ivar, Y, YP ) ... YP[1] := f1(ivar,Y); YP[2] := f2(ivar,Y); ... end proc

where N represents the number of first order equations, ivar is the independent variable, Y is a vector of length N, and YP is a vector of derivatives which is updated by the procedure (for the equivalent first order system), also of length N.

430 Thermodynamics Fundamentals and Its Application in Science

The inits parameter must be specified as: [ [x(t0)=x0,y(t0)=y0], [x(t1)=x1,y(t1)=y1], ... ] [ [y(t0)=y0], [y(t1)=y1], ... ] [ y(t0)=y0, y(t1)=y1, ... ] where, in the above, sets can be used in place of lists, or [ [t0,x0,y0], [t1,x1,y1], ... ] { [t0,x0,y0], [t1,x1,y1], ... } [ [t0,x0], [t1,x1], ... ] where the above is a list or set of lists, each sublist specifying one group of initial conditions. The xrange and yrange parameters must be specified as follows. x(t) = x1..x2, y(t) = y1..y2 or x = x1..x2, y = y1..y2 More details about the parameters can be found in (Abell 2005). DETools[Phaseportrait]. This tool has the following parameters:

deqns - list or set of first order ordinary differential equations, or a single differential equation of any order; vars - dependent variable, or list or set of dependent variables; trange - range of the independent variable; inits - set or list of lists; initial conditions for solution curves; options - (optional) equations of the form keyword=value;
Description Given a list (or set) of initial conditions (see below), and a system of first order differential equations or a single higher order differential equation, phaseportrait plots solution curves, by numerical methods. This means that the initial conditions of the problem must be given in standard form, that is, the function values and all derivatives up to one less than the differential order of the differential equation at the same point. A system of two first order differential equations also produces a direction field plot, provided the system is determined to be autonomous. In addition, a single first order differential equation also produces a direction field (as it can always be mapped to a system of two first order autonomous differential equations). For systems not meeting these criteria, no direction field is produced (only solution curves are possible in such instances). There can be ONLY one independent variable. All of the properties and options available in phaseportrait are also found in Deplot .

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 431

inits should be specified as

[ [x(t0)=x0,y(t0)=y0], [x(t1)=x1,y(t1)=y1], ... ]

where the above is a list (or set) of lists, each sublist specifying one group of initial conditions.

2.3.2. Comparative computational analysis

In what follows there is presented the comparative analysis for 2D and 3D mixing flow models. There are followed two main leves of comparison: i. The 2D (non-periodic) mixing flow, namely the differential system (9):
. x1 G x2 . x2 K G x1 , 1 K 1, G 0

in comparison with a perturbed version of it, the system (13): . x1 G x2 x1 . x K G x G x x 1 2 1 2 ii. The 3D mixing flow model (10) . x1 G x2 . x2 K G x1 . x c 3

(13)

, 1 K 1, c const.

For all models it is used the same set of parameter values (G, KG) as used in (Ionescu 2008), containing three simulation cases:
-

case1: G K G 0.035 ; 0.25, case2: G 0.755, K G 0.65 ; case3: G K G 0.25 0.85,

Each simulation case is labelled on the figure. The time units number was succesively increased, in order to better analyse the solution behavior for each model and corresponding case. The stepsize option for the rkf45 numeric method, on which the Phaseportrait procedure is based, is implicitely assigned to 0.05. Also, it must be noticed that the above choice of parameters (one positive and another negative) is optimal for analyzing the direction field associated to the models solutions.

432 Thermodynamics Fundamentals and Its Application in Science

The scene parameter of the graphic procedure was set to {x(t), y(t)], the same in 2D and in 3D case.

Figure 2. Case1 of simulation for the model (9). Time units number: t= 0..40

Figure 3. Case1 of simulation for the model (9) with t=0..100. The movement is realized on the same trajectory

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 433

Figure 4. Case2 of simulation for the model (9). The time units number t=0..40

Figure 5. Case2 of simulation for the model (9) with t=0..100. The trajectory tends to aggregate towards the origin.

434 Thermodynamics Fundamentals and Its Application in Science

Figure 6. Case3 of simulation for the model (9). Time units number t=0.40

Figure 7. Case3 of simulation for the model (9) with t=0..100. The trajectory multiplies but does not draw near the origin

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 435

Figure 8. Case1 of simulation for the model (13). The trajectory changes, it seems to be no longer periodic, but tends to infinity

Figure 9. Case2 of simulation for the model (13). The time units number t=0..40. The trajectory changes again and becomes negative

436 Thermodynamics Fundamentals and Its Application in Science

Figure 10. Case2 of simulation for the model (13), with t=0..100.

Figure 11. Case2 of simulation for the model (13) with t=0..200

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 437

Figure 12. Case3 of simulation for the model (13), t=0..40. The trajectory becomes positive

Figure 13. Case3 of simulation for the model (13) with t=0..100

438 Thermodynamics Fundamentals and Its Application in Science

Figure 14. Case3 of simulation for the model (13) with t=0..200. The program does not show the field arrows anymore.

Figure 15. Case1 of simulation for the model (10). Time units number t=0..25

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 439

Figure 16. Case1 of simulation for the model (10) with t=0..50

Figure 17. Case2 of simulation for the model (10), t=0..25. A periodic behaviour of the trajectory

440 Thermodynamics Fundamentals and Its Application in Science

Figure 18. Case2 of simulation for the model (10), t=0..75

Figure 19. Case3 of simulation for the model (10), time t=0..25

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 441

Figure 20. Case3 of simulation for the model (10), time t=0..75. The circular loops are fewer than in the case2, for the same simulation time.

Figure 21. Case3 of simulation for the model (10) with t=0..100.

442 Thermodynamics Fundamentals and Its Application in Science

3. Remarks on the simulations and Maple appliances importance

Looking above to the figures, it is important to notice some special features. It must be pointed out the advance of the phaseportrait appliance of Maple soft, and generally of the plots package. The possibility of increasing step by step the simulation time units offers important features of the analysis and consequently of the model behaviour. For example in fig.3, when time increases, the trajectory moves on the same line. Comparing to this, in fig.4 the trajectory has some tracks which overcrowd towards the origin. In case 3, for the same simulation time, the trajectory only multiplies and does not came toward the origin. Also, figures 8-10 illustrate in a good manner the influence of time increasing on the trajectory behaviour: this can be seen from the values variation of x(t) and y(t) on the axes. All the simulations for 2D case model have been realized in the same initial conditions: (x(t), y(t)) = (1,1). This gives more accuracy for the graphical comparisons. Applying this procedure step by step gives the possibility to have a total parameter control at every stage of simulation. In 3D case the initial conditions were a little modified: (x(t, y(t), z(t))=(1,0,0). It was taken into account the fact that on the z axis is represented the velocity and is natural that the mixing process starts from a zero velocity Also, the scene parameter was the same: [x(t), y(t)] both in 2D and 3D case. That means in 3D case, the trajectory is studied by watching it from the z axis. The field arrows are an important appliance of this plot tool, as they are very suggestive concerning the trajectory features. In this context it is extremely important to notice the figure 13. In this model (simulation case3), when increasing the time, the field arrows disappear, the program doesnt show them anymore. This can be glossed like a lose of equilibrium for the 2D model, in certain parameter context, and this fact can be easily observed from the great values for x(t) and y(t) on the axis In figures 8-13 it must be noticed a similarity with the pictures obtained in (Ionescu, 2008), where the origin becomes an unstable focus. It is observed here that when increasing the time, e.g. in Fig. 10, the trajectory does not go periodic, it changes only the positivity. A special attention must be paid for the figure 17, 3D simulation case. For t=0..75 units, and looking to the trajectory from above, from the z axis, it is obvious that the vorticity of the flow appears. It is very important to notice that if in (Ionescu 2002, 2010), when searching for the mixing efficiency, there were necessary small time units for get the special events of losing the equilibrium of the model, in this case, searching for the phaseportrait needs some more time units, in order to get visible vorticity of the flow. The vorticity allure is also visible in the figures 18-20, with some changes in the loops number and their nearness to the origin.

4. Conclusion
Looking on the above computational analysis, some conclusions issue: regarding the above comparative analysis, on one hand, and, concerning the general context of random events that go with the mixing flow phenomena, on the other hand.

Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 443

Looking at the above pictures, we see that each simulation case brings significant differences: For the modified (perturbed) 2D model, just from the case1 of simulation we see that the trajectory has a great change. It is not periodic anymore like in the initial 2D model, but is more evident its trend to infinity, just from the beginning of the simulation. The parameters have a great influence in this sense Concerning the 3D model, it is obvious that the field arrows could not appear, since there is a 3D simulation. Instead, the scene parameter was chosen to [x(t), y(t)], like in 2D case model. This is optimal for studying the trajectory behaviour, since it is like we look at the trajectory from above. The scene parameter is important in analysis, and a further aim would be to change it in the simulations and make some other comparative graphical analysis

Concerning the general context of random events that go with the mixing flow phenomena, the above analysis just brings at that some important conclusions: It is obvious that the above analysis confirms the fact that the mixing flow model is a far from equilibrium model. This is confirmed by the number of parameter / time units analysis. Using different appliances mixing efficiency and computational / graphical appliances, the conclusion is the same: the model becomes far from equilibrium, in certain simulation conditions. It must be noticed that the units of time can be of any type, sufficiently small or large. It depends to the target of the analysis. Enlarging the set of parameter values would bring another important data for completing the panel of repetitive events. This would be a next aim. All this space-time context present in all these analysis, consolidates the basic statement that the turbulent mixing flows must be approached as chaotic systems. This is in fact regaining the idea of a system / model high sensitive to initial conditions (Ionescu 2009). Testing step by step each of the three models above was possible due to the flexible structure of the MAPLE11 graphical / computational appliances. In the same time this shows that these repetitive simulations are relatively easy to perform. Maybe useful comments would produce if sharing some of these files. Also the step by step analysis guides the reader by successive steps, to the so- called far from equilibrium model, by the possibility of sensitive modifying the model parameters and the time at each step of simulation. The issues of repetitive phenomena, both in 2D and 3D case, give rises to achieve some appliances of chaotic dynamical systems, whose numeric models would give new research directions on the behavior in excitable media. This would be a next aim

Author details
Adela Ionescu University of Craiova, Romania

444 Thermodynamics Fundamentals and Its Application in Science

Acknowledgement
The basic part of my work in turbulent mixing was done in the period of my Ph. D. thesis at the Polytechnic University of Bucarest Romania. Fruitful experiments and special discussions were done togheter with the scientific team of the Institute of Applied Ecology, Bucarest. I am grateful to them. But my entire acknowledgement points to Ph. D. Prof. Eng. Stefan Savulescu, from Politechnic University of Bucarest. Without the special vortexation installation constructed by him, the mixing flow experiments could not be possible. Due to his great experience in the turbulence field, and his fundamental observations, advices and suggestions, my work in turbulent mixing have an important sense and the great challenge of unifying the turbulence theory takes shape.

5. References
Abell, L. Martha.& Braselton, P. James. (2005). Maple by Example. 3rd edition. Elsevier Academic Press, ISBN 0-12- 088526-3, San Diego, California Dimotakis, P. E., Miake-Lye, R. C., and Papantoniou, D. A. (1983). Structure and Dynamics of Round Turbulent Jets. Phys. Fluids 26, ISSN 3185-3192 Ionescu, A. (2002). The structural stability of biological oscillators. Analytical contributions, InTech, Ph.D. thesis, Politechnic University of Bucarest, Romania Ionescu, A. (2010). Recent trends in computational modeling of excitable media dynamics. New computational challengs in fluid dynamics analysis, Lambert Academic Press , ISBN 978-38383-9316-2 Saarbrucken, Germany Ionescu, A. & Costescu, M. (2008). The influence of parameters on the phaseportrait in the mixing model. Int. J. of Computers, Communications and Control, vol III, Suppl. issue: Proceedings of IJCCCC2008, pp. 333-337, ISSN 1841-9836 Ionescu, A. (2009). Recent challenges in turbulence: computational features of turbulent mixing. Recent advances in Continuum Mechanics. Proceedings of the 4th IASME/WSEAS International Conference, (Mathematics and Computers in Science and Engineering). ISSN 1790-2769, Cambridge U.K., 24-26 feb 2009 Ionescu, A. & Coman, D. (2011). New approaches in computational dynamics of mixing flow. In http://dx.doi.org/10.1016/j.amc.2011.03.142 Ottino, J.M. (1989). The kinematics of mixing: stretching, chaos and transport, Cambridge University Press. ISBN .0-521-36878-2, UK Savulescu, St. N. (1998) Applications of multiple flows in a vortex tube closed at one end, Internal Reports, CCTE, IAE (Institute of Applied Ecology) Bucarest, Romania

Chapter 17

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators

Paiguy Armand Ngouateu Wouagfack and Rn Tchinda
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51547

1. Introduction
In this chapter, the optimization analysis based on the new thermo-ecological criterion (ECOP) first performed by Ust et al. [1] for the heat engines is extended to an irreversible three-heat-source absorption refrigerator. The thermo-ecological objective function ECOP is optimized with respect to the temperatures of the working fluid. The maximum ECOP and the corresponding optimal temperatures of the working fluid, coefficient of performance, specific cooling load, specific entropy generation rate and heat-transfer surface areas in the exchangers are then derived analytically. Comparative analysis with the COP criterion is carried out to prove the utility of the ecological coefficient of performance criterion.

2. Thermodynamics analysis
The main components of an absorption refrigeration system are a generator, an absorber, a. condenser and an evaporator as shown schematically in Fig. 1 [2]. In the shown model, . QH is the rate of absorbed heat from the heat source at temperature TH to generator, QC . and Q A are, respectively, the heat rejection rates from the condenser and absorber to the . heat sinks at temperatures TC and TA and Q L is the heat input rate from the cooling space at temperature TL to the evaporator. In absorption refrigeration systems, usually NH3/H2O and LiBr/H2O are used as the working substances, and these substances abide by ozone depletion regulations, since they do not consist of chlorouorocarbons. In Fig. 1, the liquid rich solution at state 1 is pressurized to state 1 with a pump. In the generator, the working fluid is concentrated to state 3 by evaporating the working medium by means . of QH heat rate input. The weak solution at state 2 passes through the expansion valve into the absorber with a pressure reduction (22). In the condenser, the working fluid at

2012 Ngouateu Wouagfack and Tchinda, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

446 Thermodynamics Fundamentals and Its Application in Science

state 3 is condensed to state 4 by removing QC heat rate. The condensed working fluid at state 4 is then throttled by a valve and enters the evaporator at state 4. The liquid . working fluid is evaporated due to heat transfer rate Q L from the cooling space to the working fluid (45). Finally, the vaporized working fluid is absorbed by the weak . solution in the absorber, and by means of Q A heat rate release in the absorber, state 1 is reached. Work input required by the solution pump in the system is negligible relative to the energy input to the generator and is often neglected for the purpose of analysis. Under such assumption, the equation for the first law of thermodynamics is written as:
Q H + Q L - QC - Q A = 0
. . . .

(1)

Absorption refrigeration systems operate between three temperature levels, if TA = TC , or four temperature levels when TA TC . In this chapter, by taking TA = TC , the cycle of the working fluid consists of three irreversible isothermal and three irreversible adiabatic processes. The temperatures of the working fluid in the three isothermal processes are different from those of the external heat reservoirs so that heat is transferred under a finite temperature difference, as shown in Fig. 2 where
QO = QC + Q A
. . .

(2)

T1 and T2 are, respectively, the temperatures of the working fluid in the generator and evaporator. It is assumed that the working fluid in the condenser and absorber has the same . temperature T3 [2]. Q LC is the heat leak from the heat sink to the cooled space.
The heat exchanges between the working fluid and heat reservoirs obey a linear heat transfer law, so that the heat-transfer equations in the generator, evaporator, condenser and absorber are, respectively, expressed as follows:
Q H = U H AH (TH - T1 )
Q L = U L AL (TL - T2 )
.

(3)

(4) (5)

QO = UO ( AA + AC )(T3 - TO )

where AH , AL , AC and AA are, respectively, the heat-transfer areas of the generator, evaporator, condenser and absorber, UH and U L are, respectively, the overall heat-transfer coefficients of the generator and evaporator, and it is assumed that the condenser and absorber have the same overall heat-transfer coefficient UO [2].

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 447

Figure 1. Schematic diagram of absorption refrigeration system [2]

Figure 2. Considered irreversible absorption refrigeration model and its TS diagram.

448 Thermodynamics Fundamentals and Its Application in Science

The absorption refrigeration system does not exchange heat with other external reservoirs except for the three heat reservoirs at temperatures TH , TL and TO , so the total heat-transfer area between the cycle system and the external heat reservoirs is given by the relationships:

A = AH + AL + AO
where

(6)

AO = AC + AA .
.

(7)

The rate of heat leakage Q LC from the heat sink at temperature TO to the cold reservoir at temperature TL was first provided by Bejan [3] and it is given as:

Q LC = K LC (TO - TL )
where K LC is the heat leak coefficient.

(8)

Real absorption refrigerators are complex devices and suffer from a series of irreversibilities. Besides the irreversibility of finite rate heat transfer which is considered in the endoreversible cycle models and the heat leak from the heat sink to the cooled space, there also exist other sources of irreversibility. The internal irreversibilities that result from friction, mass transfer and other working fluid dissipations are an another main source of irreversibility, which can decrease the coefficient of performance and the cooling load of absorption refrigerators. The total eect of the internal irreversibilities on the working fluid can be characterized in terms of entropy production. An irreversibility factor is introduced to describe these internal irreversibilities:
I= DS3 DS1 + DS2

(9)

On the basis of the second law of thermodynamics, DS3 > DS1 + DS2 for an internally irreversible cycle, so that I > 1 . If the internal irreversibility is neglected, the cycle is endoreversible and so I = 1 . The second law of thermodynamics for an irreversible threeheat-source cycle requires that:

d Q Q H Q L QO = + 0 T T1 T2 T3

(10)

From Eq. (9), the inequality in Eq. (10) is written as:

QH Q L QO + =0 T1 T2 IT3

(11)

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 449

The coefficient of performance of the irreversible three-heat-source absorption refrigerator is:

COP =
From Eq. (6), it is expressed as:

Q L - Q LC QH
.

. . Q L Q LC 1 . . QH QL

(12)

AL =

A AH AO + 1+ AL AL

(13)

Using Eqs. (3)-(5), Eq. (13) is rewritten as:

AL = A Q U (T - T2 ) Q + .O L L 1+ . H U (T - T1 ) U (T - TO ) QL H H QL O 3
. .

U L (TL - T2 )

(14)

Combining Eqs. (1) and (11), the following ratios are derived:

QL QH QO QL
. . .

T2 (T1 - IT3 )

T1 ( IT3 - T2 ) IT3 (T1 - T2 )

(15)

(T1 - IT3 )T2

(16)

The first is the coefficient of performance of the irreversible three-heat-source absorption refrigeration cycle without heat leak losses. Substituting Eqs. (15) and (16) into Eq. (14), the heat-transfer area of the evaporator is expressed as a function of T1 , T2 and T3 for a given total heat-transfer areas :

AL = 1+

U H (TH - T1 )(T1 - IT3 )T2

A U LT1 ( IT3 - T2 )(TL - T2 )

UO (T3 - TO )(T1 - IT3 )T2

U L IT3 (T1 - T2 )(TL - T2 )

(17)

By investigating similar reasoning, the heat-transfer areas of the generator and of condenser and absorber are given respectively by:

AH =

A U HT2 (T1 - IT3 )(TH - T1 ) U H IT3 (T1 - T2 )(TH - T1 ) 1+ + U LT1 ( IT3 - T2 )(TL - T2 ) UOT1 (IT3 - T2 )(T3 - TO )

(18)

450 Thermodynamics Fundamentals and Its Application in Science

and

AO =
1+

U H IT3 (T1 - T2 )(TH - T1 )

UOT1 ( IT3 - T2 )(T3 - TO )

UOT2 (T1 - IT3 )(T3 - TO ) U L IT3 (T1 - T2 )(TL - T2 )

(19)

Substituting Eq. (17) into Eq. (4):

QL =
.

U L (TL - T2 )

U H (TH - T1 )(T1 - IT3 )T2

A T1 ( IT3 - T2 )

UO (T3 - TO )(T1 - IT3 )T2

IT3 (T1 - T2 )

(20)

Combining Eqs. (8), (12), (15) and (20), the coefficient of performance of the irreversible three-heat-source refrigerator as a function of the temperatures T1 , T2 and T3 of the working fluid in the generator, evaporator, condenser and absorber is obtained:
T2 (T1 - IT3 ) T1 ( IT3 - T2 ) IT3 (T1 - T2 ) 1 1 - x (T - T ) + + O L T1 ( IT3 - T2 ) U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2

COP =

(21) where the parameter

x=

K LC A

(22)

represents the heat leakage coefficient and its dimension is w/(Km2) The specific cooling load of the irreversible three-heat-source refrigerator is deduced as:
. .

r=

-1 T1 ( IT3 - T2 ) IT3 (T1 - T2 ) Q L - Q LC 1 - x T -T = + + ( O L) A U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2 (23)

The specific entropy production rate of the irreversible three-heat-source absorption refrigerator is:

QO - Q LC Q H Q L - Q LC TO TH TL s s= = A A
.

(24)

Using Eq. (1) s is rewritten as:

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 451

1 1 1 1 Q 1 Q Q 1 Q s = - LC + - . H L + - L T T T L TO A O TH A O TL A QL
or
. . .

(25)

1 1 1 Q 1 Q - Q LC s = - H + - L T A T O TH O TL A

(26)

Substituting Eqs.(8), (15) and (20) into Eq. (25), the specific entropy production rate as a function of T1 , T2 and T3 is given by :
-1 1 erT1 ( IT3 - T2 ) T1 ( IT3 - T2 ) IT3 (T1 - T2 ) 1 1 + + s = - x (TO - TL ) - 1 TL TO T2 (T1 - IT3 ) U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 U O (T3 - TO )(T1 - IT3 )T2

(27) where
TO 1 - T H er = T O - 1 T L

(28)

is the coefficient of performance for reversible three-heat-source refrigerator. According to the definition of the general thermo-ecological criterion function for different heat engine models [4-9], a two-heat-source refrigerator [10, 11] and three-heat-source absorption refrigerator [2], the new thermo-ecological objective function called ecological coefficient of performance (ECOP) of an absorption refrigerator is defined as:

ECOP =
Putting Eq.(26) into Eq. (29):

Q L - Q LC Tenv s
.

Q L - Q LC ATenv s

(29)

ECOP =

1 1 1 1 1 1 Tenv + - T TO TH O TL COP

(30)

When Eq. (21) is put in Eq. (30), the ecological coefficient of performance of the irreversible three-heat-source absorption refrigerator as a function of T1 , T2 and T3 is derived as :

452 Thermodynamics Fundamentals and Its Application in Science

ECOP =

Tenv TO-1 - TL-1

)
(31)

-1 T1 ( IT3 - T2 ) IT3 (T1 - T2 ) e T ( IT - T2 ) 1 1 - x (T - T ) 1- r 1 3 + + O L T2 (T1 - IT3 ) U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2

where Tenv is the temperature in the environment conditions.

3. Performance optimization for a three-heat-source irreversible absorption refrigerator based on ECOP criterion
The ECOP function given in Eq. (31) is plotted with respect to the working fluid temperatures ( T1 , T2 and T3 ) for different internal irreversibility parameters as shown in Fig. 3(a), (b) and (c). As it can be seen from the figure, there exists a specific T1 , T2 and T3 that maximize the ECOP function for given I and x values. Therefore, Eq. (31) can be maximized (or optimized) with respect to T1 , T2 and T3 . The optimization is carried out analytically.

Figure 3. Variation of the ECOP objective function with respect to T1 (a), T2 (b) and T3 (c) for

different I values ( TG = 403K , TL = 273K , TO = 303K , Tenv = 290 K , UG = 1163 W / m 2 K , U E = 2326 W / m 2 K , UO = 4650 W / m 2 K , K L = 1082 W / K , A = 1100 m2 )

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 453

For the sake of convenience, let

x=

IT3 T1
IT3 T2

(32)

y=

(33)

z = IT3
Then Eq. (31) is rewritten as:

(34)

ECOP =

Tenv TO-1 - TL-1

-1 er ( y - 1) x ( y - 1) y y-x 1 - x (T - T ) + + 1 O E 1- x U L (TL y - z) U H (TH x - z)(1 - x) U ( z - T )(1 - x) (35)

where T = ITO and (36)

U=
Starting from Eq. (35), the extremal conditions:

UO . I

(37)

ECOP =0 x
ECOP =0 y

(38) (39)

ECOP =0 z
give respectively:

(40)

z ( y - 1) y 1 1 =0 x (TO - TE ) U L (TL y - z) U ( z - T ) U (T x - z)2 H H

(41)

454 Thermodynamics Fundamentals and Its Application in Science

z ( y - 1) y 1 1 =0 x (TO - TE ) U L (TL y - z) U ( z - T ) U (T y - z)2 L L

(42)

y (1 - x) U L (TL y - z)
2

x ( y - 1) U H (TH x - z)
2

y-x U (z - T )
2

=0

(43)

Combining Eqs (41)-(43), the following general relation is found:

U H (TH x - z) = U L (TL y - z) = U ( z - T )

(44)

From Eqs (44), it is derived as:

x=

(1 + b1 ) z
TH

b1T TH

(45)

y=

(1 + b2 ) z
TL

b2T TL

(46)

where
b1 = U UH

(47)

b2 =

U UL

(48)

When Eqs. (45) and (46) are substituted into Eq. (43):
z =T D + b2 1 + b2

(49)

where

T (1 - d ) 1 1 + d1 1 - L T D= 1 - d1

(50)

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 455

d1 = x

(1 + b2 )
U

T O - 1 T L

(51)

Therefore Eqs. (45) and (46) are rewritten as:

x= T B ( D + B) TH 1

(52)

y=

T D TL

(53)

where
B= b2 - b1 1 + b1

(54)

B1 =

1 + b1 1 + b2

(55)

Using Eqs. (49), (52) and (53) with Eqs.(32)-(34), the corresponding optimal temperatures of the working fluid in the three isothermal processes when the ecological coefficient of performance is a maximum, are, respectively, determined by: T1* = TH

(1 + b1 )(D + B)
D (1 + b2 )
D + b2 1 + b2

D + b2

(56)

T2* = TL

D + b2

(57)

T3* = TO

(58)

Substituting Eqs. (56)-(58) into Eqs. (21), (23), (27) and (31) the maximum ECOP function and the corresponding optimal coefficient of performance, optimal specific cooling load and optimal specific entropy generation rate are derived, respectively, as:
ECOPmax =

Tenv TO-1 - TL-1

456 Thermodynamics Fundamentals and Its Application in Science

1 -1 2 erTH (TD - TL ) 1 - x (T - T ) TH D - B1 ( D + B)(TL + BDT ) 1 O L U * B12 ( D - 1) TH - B1 ( D + B)T TL TH - B1 ( D + B)T TL

(59)

2 TH - B1 ( D + B)T TL 1 - x (T - T ) TH D - B1 ( D + B)(TL + BDT ) COP * = O L TH (TD - TL ) U * B12 ( D - 1) TH - B1 ( D + B)T TL

(60)

r* =

U * B12 ( D - 1) TH - B1 ( D + B)T TH - x (TO - TL ) TH D - B12 ( D + B)(TL + BDT )

(61)

* 2 1 erTH (TD - TL ) U B1 ( D - 1) TH - B1 ( D + B)T TL 1 s* = - x (TO - TL ) - 1 (62) T - B ( D + B)T T T D - B 2 ( D + B)(T + BDT ) TL TO 1 L 1 H L H

where U* = U (63)

(1 + b1 )

From Eqs. (17)-(19) and (56)-(58), it is found that , when the three-heat-source absorption refrigerator is operated in the state of maximum ecological coefficient of performance, the relations between the heat-transfer areas of the heat exchangers and the total heat-transfer area are determined by: AH * = A B12 ( D + B)(TD - TL ) b1 1 + b1 TH D - B12 ( D + B)(TL + BDT ) (64)

AL * = A

DB1 TH - B1T ( D + B) b2 1 + b1 TH D - B12 ( D + B)(TL + BDT ) B1 TH D - B1TL ( D + B) 1 1 + b1 TH D - B12 ( D + B)(TL + BDT )

(65)

AO * = A

(66)

From Equations (64)-(66), a concise optimum relation for the distribution of the heat-transfer areas is obtained as:

UH AH * + U L AL* = U AO*

(67)

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 457

Obviously, this relation is independent of the heat leak and the temperatures of the external heat reservoirs.

4. Comparison with COP criterion

In Fig.4, the variation of the normalized ECOP ( ECOP
COP ECOP ), normalized COP ( ECOPmax

COP ) and the specific cooling load (r) with respect to the specific entropy COPmax

generation rate (s) are demonstrated. One interesting observation from this figure is that maximum of the ECOP and COP coincides although their functional forms are different: the coefficient of performance gives information about the necessary heat rate input in order to produce certain amount of cooling load and the ecological coefficient of performance gives information about the entropy generation rate or loss rate of availability in order to produce certain amount of cooling load. The maximum ECOP and COP conditions give the same amount of cooling load and entropy generation rate. It is also seen analytically that the performance parameters T1* , T2* , T3 * , A1* , A2 * , A3* , r * ,
s* and COP* = COPmax at the maximum ECOP and maximum COP are same. Getting the

same performance at maximum ECOP and COP conditions is an expected and logical result. Since, for a certain cooling load the maximum COP results from minimum heat consumption so that minimum environmental pollution. The minimum environmental pollution is also achieved by maximizing the ECOP . Although the optimal performance conditions ECOP and COP criteria are same, their impact on the system design performance is different. The coefficient of performance is used to evaluate the performance and the efficiency of systems. This method only takes into account the first law of thermodynamics which is concerned only with the conversion of energy, and therefore, can not show how or where irreversibilities in a system or process occur. Also, when different sources and forms of energy are involved within a system, the COP criterion of a system doesnt describe its performance from the view point of the energy quality involved. This factor is taken into account by the second law of thermodynamics characterized by the entropy production which appears in the ecological coefficient of performance criterion ( ECOP ). This aspect is of major importance today since that with the requirement of a rigorous management of our energy resources, one should have brought to be interested more and more in the second principle of thermodynamics, because degradations of energy, in other words the entropy productions, are equivalent to consumption of energy resources. For this important reason, the ECOP criterion can enhance the system performance of the absorption refrigerators by reducing the irreversible losses in the system. A better understanding of the second law of thermodynamics reveals that the ecological coefficient of performance optimization is an important technique in achieving better operating conditions.

458 Thermodynamics Fundamentals and Its Application in Science

Figure 4. Variation of the normalized ECOP , normalized COP and the specific cooling load with respect to the specific entropy generation rate ( TG = 403K , TL = 273K , TO = 303K , Tenv = 290 K ,

UG = 1163 W / m 2 K , U E = 2326 W / m 2 K , UO = 4650 W / m 2 K , K L = 1082 W / K , A = 1100 m2 )

5. Conclusion
This chapter presented an analytical method developed to achieve the performance optimization of irreversible three-heat-source absorption refrigeration models having finiterate of heat transfer, heat leakage and internal irreversibility based on an objective function named ecological coefficient of performance (ECOP). The optimization procedure consists in defining the objective function ECOP in term of the temperatures of the working fluid in the generator, evaporator, condenser and absorber and using extremal conditions to determine analytically the maximum ECOP and the corresponding optimal design parameters. It also established comparative analyses with the COP criterion and shown that the performance parameters at the maximum ECOP and maximum COP are same. The three-heat-source absorption refrigerator cycles are the simplified models of the absorption refrigerators, but the four-heat-source absorption refrigerators cycles are closer to the real absorption refrigerators.

ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 459

Author details
Paiguy Armand Ngouateu Wouagfack L2MSP, Department of Physics, University of Dschang, Dschang , Cameroon Rn Tchinda LISIE, University Institute of Technology Fotso Victor, University of Dschang, Bandjoun, Cameroon

6. References
[1] Ust, Y.: Ecological performance analysis and optimization of powergeneration systems, Ph.D. Thesis Progress Report, Yildiz Technical University, Istanbul. (2004). [2] Ngouateu, Wouagfack, P. A., Tchinda, R.: Performance optimization of three-heatsource irreversible refrigerator based on a new thermo-ecological criterion. International Journal of Refrigeration. 34, 1008-1015 (2011). [3] Bejan, A.: Theory of heat transfer-irreversible refrigeration plant. International Journal of Heat Transfer. 32, 1631-1639 (1989). [4] Ust, Y., Sahin, B., Sogut, O. S.: Performance analysis and optimization of an irreversible Dual cycle based on ecological coecient of performance (ECOP) criterion. Applied Energy. 82 (1), 2339 (2005). [5] Ust, Y., Sahin, Kodal, A.: Ecological coecient of performance (ECOP) optimization for generalized irreversible Carnot heat engines. Journal of the Energy Institute. 78 (3), 145 151 (2005). [6] Ust, Y., Sahin,B., Kodal, A.: Performance analysis of an irreversible Brayton heat engine based on ecological coecient of performance criterion. International Journal of Thermal Science. 45 (1), 94101 (2006). [7] Ust, Y., Sogut, O. S., Sahin, B., Durmayaz, A.: Ecological coecient of performance (ECOP) optimization for an irreversible Brayton heat engine with variable-temperature thermal reservoirs. Journal of the Energy Institute. 79 (1), 4752 (2006). [8] Ust, Y., Sahin, B., Kodal, A., Akcay, I. H.: Ecological coecient of performance analysis and optimization of an irreversible regenerative Brayton heat engine. Applied Energy. 83 (6), 558572 (2006). [9] Sogut, O. S., Ust, Y., Sahin, B.: The eects of intercooling and regeneration on the thermo-ecological performance analysis of an irreversible-closed Brayton heat engine with variable-temperature thermal reservoirs. Journal of Physics D: Applied Physics. 39, 47134721 (2006). [10] Ust, Y., Sahin, B.: Performance optimization of irreversible refrigerators based on a new thermo-ecological criterion. International Journal of Refrigeration. 30, 527534 (2007).

460 Thermodynamics Fundamentals and Its Application in Science

[11] Ust, Y.: Performance analysis and optimization of irreversible air refrigeration cycles based on ecological coecient of performance criterion. Applied Thermal Engineering. 29, 4755 (2009).

Section 6

Thermodynamics in Diverse Areas

Chapter 18

Thermodynamics of Microarray Hybridization

Raul Mluan and Pedro Gmez Vilda
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51624

1. Introduction
Microarrays make the use of hybridization properties of nucleic acids to monitor Deoxyribonucleic acid (DNA) or Ribonucleic acid (RNA) abundance on a genomic scale in different types of cells. The hybridization process takes place between surface-bound DNA sequences - the probes, and the DNA or RNA sequences in solution - the targets. Hybridization is the process of combining complementary, single-stranded nucleic acids into a single molecule. Nucleotides will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. Conversely, due to the different geometries of the nucleotides, a single inconsistency between the two strands will prevent them from binding. In oligonucleotide microarrays hundreds of thousands of oligonucleotides are synthesized in situ by means of photochemical reaction and mask technology. Probe design in these microarrays is based on complementarity to the selected gene or an expressed sequence tag (EST) reference sequence. An important component in designing an oligonucleotide array is ensuring that each probe binds to its target with high specificity. The dynamics of the hybridization process underlying genomic expression is complex as thermodynamic factors influencing molecular interaction are still fields of important research [1] and their effects are not taken into account in the estimation of genetic expression by the algorithms currently in use.

2. State of the art

Many techniques have been developed to identify trends in the expression levels inferred from DNA microarray data, and recently the attention was devoted to methods to obtain accurate expression levels from raw data on the underlying principles of the thermodynamics and hybridization kinetics. The development of DNA chips for rapidly
2012 Mluan and Vilda, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

464 Thermodynamics Fundamentals and Its Application in Science

screening and sequencing unknown DNA segments mainly relies on the ability to predict the thermodynamic stability of the complexes formed by the oligonucleotide probes. The thermodynamics of nucleic acids have been studied from different points of view. Wu et al. [2] analyze the temperature-independent and temperature-dependent thermodynamic parameters of DNA/DNA and RNA/DNA oligonucleotide duplexes. The differences between DNA polymer and oligonucleotide nearest-neighbour thermodynamic trends, and the salt dependence of nucleic acid denaturation allowed to SantaLucia [3] to show that there is length dependence to salt effects but not to the nearest-neighbour propagation energies. An early study on DNA microarray hybridization [4] found that it was strongly dependent on the rate constants for DNA adsorption/desorption in the non-probe covered regions of the surface, the two-dimensional diffusion coefficient, and the size of probes and targets and also suggested that sparse probe coverage may provide results equal to or better than those obtained with a surface totally covered with DNA probes. A theoretical analysis of the kinetics of DNA hybridization demonstrated that diffusion was important in determining the time required to reach equilibrium and was proportional to the equilibrium binding constant and to the concentration of binding sites [5]. Newer studies on hybridization kinetics and thermodynamics reveal that perfect match sequences require less time to reach saturation than mismatches. The experimental results of Dai et al. [6] exhibit inverse temporal behaviour, resulting that surface-bound oligos hybridizing primarily with their perfect complement sequence tend to equilibrate more slowly than do those whose binding is dominated by mismatch duplexes. Considering the assumptions, it has been demonstrated [7] that the hybridization time can in fact increase the accuracy of expression ratios, and that this effect may be more dramatic for larger fold changes. Separation between specific and nonspecific binding events can avoid the confusion about what RNA hybridizes the probes. In this case analysis of the perfect match and mismatch intensities in terms of simple single-base related parameters indicates that the intensity of complementary MM introduces a systematic source of variation compared with the intensity of the respective PM probe [8]. The hybridization of nucleic acids was modelled [9] according with the supposition that the process of hybridization goes through an intermediate state in which an initial short contact region has a single-stranded conformation prior to binding. The hybridization theory gave the possibility of developing models that can be used to obtain improved measures of expression useful for data analysis. Naef and Magnasco [10] propose a simpler model to describe the probe effect that considers only the sequence composition of the probes. They demonstrate that the interactions between nearest neighbours add much predictive power for specific signal probe effects. The stochastic model proposed by Wu and Irizarry [11] can be used to improve the expression measure or in the normalization and summarization of the data.

Thermodynamics of Microarray Hybridization 465

3. DNA hybridization
DNA is a nucleic acid that contains the genetic instructions monitoring the biological development of all cellular forms of life, and many viruses. DNA is a long polymer of nucleotides and encodes the sequence of the amino-acid residues in proteins using the genetic code, a triplet code of nucleotides. DNA it is organized as two complementary strands, head-to-toe, with the hydrogen bonds between them. Each strand of DNA is a chain of chemical building blocks, called nucleotides, of which there are four types: adenine (A), cytosine (C), guanine (G) and thymine (T). Between the two strands, each base can only bond with one single predetermined other base: A with T, T with A, C with G, and G with C, being the only possible combination. Hybridization refers to the annealing of two nucleic acid strands following the base pairing rule. As shown in Figure 1, at high temperatures approximately 90C to 100C the complementary strands of DNA separate, denature, yielding single-stranded molecules. Two single strands under appropriate conditions of time and temperature e.g. 65C, will renaturate to form the double stranded molecule. Nucleic acid hybrids can be formed between two strands of DNA, two strands of RNA or one strand of DNA and one of RNA. Nucleic acids hybridization is useful in detecting DNA or RNA sequences that are complementary to any isolated nucleic acid.

Figure 1. DNA-RNA hybridization. Hybridization is the process of combining complementary, singlestranded nucleic acids into a single molecule. (from [12])

466 Thermodynamics Fundamentals and Its Application in Science

Finding the location of a gene or gene product by adding specific radioactive or chemically tagged probes for the gene and detecting the location of the radioactivity or chemical on the chromosome or in the cell after hybridization is called in-situ hybridization. In the same way, in microarray technology, hybridization is used in comparing mRNA abundance in two samples, or in one sample and a control. RNA from the sample and control are extracted and labeled with two different fluorescent labels, e.g. a red dye for the RNA from the sample population and green dye for that from the control population. Both extracts are washed over the microarray and gene sequences from the extracts hybridized to their complementary single-strand DNA molecule previously attached to the microarray. Then, to measure the abundance of the hybridized RNA, the array is excited by a laser. In the oligonucleotide microarrays the hybridization process occurs in the same way, the only difference here is that the sequences to be laid over the chip are sequences of 25 nucleotides length, perfect complementary to same length sequence of the gene, PM perfect match, and sequences of 25 nucleotides length, designed to correspond to PM, but having the middle base - the 13th one, changed by its complementary base, MM mismatch, as in Figure 2. The MM probes give some estimates of the random hybridization and cross hybridization signals. One principle to be followed in the design of oligonucleotide arrays is ensuring that the probes bind to their target with high accuracy. When the two strands are completely complementary they will bind by a specific hybridization, as it can be seen in Figure 3. On the contrary if there are mismatches between the nucleotides of the strands and they bind, a process called non-specific hybridization or cross-hybridization occurs.
5
x x x x x x x x x x x

mRNA reference sequence

TGTGATGGTGGAATGGTCAGAAGGACTCCTATGATACACCCACGCA Perfect Match CAGTCTTCCTGAGGATACTATGTGG Mismatch CAGTCTTCCTGACGATACTATGTGG

Perfect Match probe cells Probesets of PM and MM

Mismatch probe cells

Figure 2. Perfect Match Mismtach probeset strategy. Sequence of 25-mer length complementary to the selected part of mRNA sequence form a Perfect Match probe, while the Mismatch probe is artificially created by changing middle base with its complementary. In an oligonucleotide array a gene is represented by 11 to 20 probes. (modified from [13])

The hybridization process has been studied from point of view of interaction between base pairs, the interaction with unintended targets and also from its kinetics processes. Because in practice the DNA chips are immersed in the target solution for a relatively short time, the arrival to equilibrium is not guaranteed. Yet full analysis of the reaction kinetics requires

Thermodynamics of Microarray Hybridization 467

knowledge of the equilibrium state. An understanding of the equilibrium state is also necessary to identify the relative importance of kinetic controls of the performance of the DNA microarrays. The effect of the cross-hybridization on probe intensity is predictable in the oligonucleotide microarrays, and models for avoiding this have been developed [14], [15], [16] some aspects of it going to be described in the following section.

Figure 3. Cross-hybridization on a nucleotide probe. In specific hybridization the sequences are completely complementary, while in non-specific or cross hybridization the sequences contain mismatches. (from [17])

4. Technical factors affecting gene expression

4.1. Thermodynamics parameters
Black and Hartley [18] define enthalpy as the sum of the internal energy of a thermodynamic system plus the energy associated with work done by the system on the atmosphere, which is the product of the pressure times the volume, as in equation (1)
H U pV

(1)

Because enthalpy is a property, its value can be determined for a simple compressible substance once two independent, intensive thermodynamic properties of the substance are known, and the change in enthalpy is independent of the path followed between two equilibrium states In [18] the entropy, S, was defined using the following equation:
dS

Q
T

(2)

468 Thermodynamics Fundamentals and Its Application in Science

where Q is an amount of heat introduced to the system and T is a constant absolute temperature. Since this definition involves only differences in entropy, the entropy itself is only defined up to an arbitrary additive constant. The following models to be described use the state function parameters, enthalpy and entropy. State functions define the properties of a thermodynamic state. In a change between two thermodynamic states, the change in value of the state function is given by the symbol . The standard enthalpy change, H , is the difference in the standard enthalpies of formation between the products and the reactants. This state function is associated with changes in bonding between reactants and products. Changes in enthalpy during reactions are measured by calorimetry experiments. The standard entropy change, S , is the difference in standard entropies between reactants and products. Entropy is a measure of the degree of order in a chemical system due to bond rotations, other molecular motions, and aggregation. The more random a system (disorder), the greater the entropy is. The larger a structure, the more degrees of freedom it has, and the greater its entropy.

4.2. Interaction between pairs

The nucleic acid duplex stability can be endangered by the interaction between the nucleotide bases. Thermodynamics for double helix formation of DNA/DNA, RNA/RNA or DNA/RNA can be estimated with nearest neighbour parameters. Enthalpy change, H , entropy change, S , free energy change, G , and melting temperature, Tm, were obtained on the basis of the nearest-neighbour model. The nearest-neighbour model for nucleic acids, known as the NN model, assumes that the stability of a given base pair depends on the identity and orientation of neighbouring base pairs [3]. Previous studies in NN model parameters were brought forth in [15] and [19]. In the NN model, sequence dependent stability is considered in terms of nearest-neighbour doublets. In duplex DNA there are 10 such unique internal nearest-neighbour doublets. Listed in the 5-3 direction, these are AT/AT TA/TA AA/TT AC/GT CA/TG TC/GA CT/AG CG/CG GC/GC and GG/CC. Dimmer duplexes are represented with a slash separating strands in antiparallel orientation e.g. AC/TG means 5-AC-3 WatsonCrick base-paired with 3-TG-5. The total difference in the free energy of the folded and unfolded states of a DNA duplex can be approximated at 37o, with a nearest-neighbour model:
G o total

i ni G o i G o init w/term G C G o init w/term A T G o sym

(3)

where G i are the standard free-energy changes for 10 possible Watson-Crick nearest o o G37 G37 neighbours, e.g. G o 1 AA/TT . , G o 2 TA/AT . , ni is the number of o occurrences of each nearest neighbour, i, and G sym equals +0.43 kcal/mol if the duplex

Thermodynamics of Microarray Hybridization 469

is self complementary and zero if it is not self-complementary. The total difference in the o free energy at 37o, G37 , can be computed from H o and So parameters using the equation:
o G37 H o T S o

(4)

For a specific temperature one can compute the total free energy using the values from Table 1. As described in [19] the melting temperature Tm is defined as the temperature at which half of the strands are in double helical and half are in the random-coil state. A random-coil state is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. For self-complementary oligonucleotides, the Tm for individual melting curves was calculated from the fitted parameters using the following equation:

Tm H o / So R ln CT

(5)

where R is the general gas constant, i.e. 1.987cal/K mol, the CT is the total strand concentration, and Tm is given in K. For non-self-complementary molecules, CT in equation (5) was replaced by CT/4. Sequence AA/TT AT/TA TA/AT CA/GT GT/CA CT/GA GA/CT CG/GC GC/CG GG/CC Init. w/term GC Init. w/term AT Symmetry correction

H kcal/mol

S kcal/mol -22.2 -20.4 -21.3 -22.7 -22.4 -21.0 -22.2 -27.2 -24.4 -19.9 -2.8 4.1 -1.4

-7.9 -7.2 -7.2 -8.5 -8.4 -7.8 -8.2 -10.6 -9.8 -8.0 0.1 2.3 0

Table 1. Unified oligonucleotide H and S nearest neighbour parameters in 1M NaCl. The table shows the values of the total enthalpy and entropy for the dimmer duplexes as used in [3].

The nearest-neighbour parameters of Delcourt et al. (1991) [20], SantaLucia et al. (1996) [19], Sugimoto et al. (1996) [15] and Allawi et al. (1997) [21] were evaluated from the analysis of optical melting curves of a variety of short synthetic DNA duplexes in 1 M Na+.

470 Thermodynamics Fundamentals and Its Application in Science

The observed trend in nearest-neighbor stabilities at 37C is GC/CG = CG/GC > GG/CC > CA/GT = GT/CA = GA/CT = CT/GA > AA/TT > AT/TA > TA/AT, as in Table 2. This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. It has long been recognized that DNA stability depends of the percent G-C content. G 37 (kcal/mol) Sequence AA/TT AT/TA TA/AT CA/GT GT/CA CT/GA GA/CT CG/GC GC/CG GG/CC Average Init. w/term GC Init. w/term AT

Delcourt et al. -0.67 0.62 -0.70 -1.19 -1.28 -1.17 -1.12 -1.87 -1.85 -1.55 -1.20 NA NA

SantaLucia et al. -1.02 -0.73 -0.60 -1.38 -1.43 -1.16 -1.46 -2.09 -2.28 -1.77 -1.39 0.91 1.11

Sugimoto et al. -1.20 -0.90 -0.90 -1.70 -1.50 -1.50 -1.50 -2.80 -2.30 -2.10 -1.64 1.70 1.70

Allawi et al. -1.00 -0.88 -0.58 -1.45 -1.44 -1.28 -1.30 -2.17 -2.24 -1.84 -1.42 0.98 1.03

Table 2. Comparison of computed NN free energy parameters at 37oC

On the other hand, the nearest neighbour H parameters from Table 1, do not follow this trend. This suggests that stacking, hydrogen bonding, and other contributions to the H present a complicated sequence dependence.

4.3. Interaction with unintended targets

As seen in previous sections the major issue in microarray oligonucleotide technology is the selection of probe sequences with high sensitivity and specificity. It has been shown [22] that the use of MM probes for assessment of non-specific binding is unreliable. Since the duplex formation in solution has been studied using the nearest neighbour model [3], [15] the microarray design in terms of probe selection has been achieved by using a model based on the previously mentioned nearest neighbour model [16]. The model of Zhang et al. presents some modification to the nearest neighbour model, firstly to assign different weight factors at each nucleotide position on a probe with the scope of reflecting that the binding parts of a probe may contribute differently to the stability of bindings, and secondly to take into account two different modes of binding the probes: gene specific binding, i.e. formation of DNA-RNA duplexes with exact complementary sequences, and non-specific binding, i.e. formation of duplexes with many mismatches between the probe and the attached RNA molecule. They called their model, the positional-dependent-nearest-neighbour model.

Thermodynamics of Microarray Hybridization 471

According with their method, the observed signal Iij for probe i in the probe set for gene j is modelled as:

I ij

Nj 1 e
Eij

N* 1 e
* Eij

(6)

where B is the background intensity, Nj is the number of expressed mRNA molecules contributing to gene specific binding, N* represents the number of RNA molecule contributing to nonspecific binding, E and E* are the binding energies for gene specific and respectively nonspecific binding. These energies are calculated as the weighted sum of stacking energies: Eij k bk , bk 1
* * Eij k * bk , bk 1

(7)
(8)

* where k and k are the weight factors that depend on the position along the probe from the 5 to 3 end, and bk , bk 1 is the same as the stacking energy used in nearest neighbour model [15].

The positional-dependent-nearest-neighbour model appears to indicate that the two ends of a probe contribute less to binding stability according to their weight factors, see Figure 4. a). It also can be observed that there is a dip in the gene specific binding weight factors of MM probes around the mismatch position, probably due the mismatch which destabilizes the duplex structure. In Figure 4. b) it can be noted that stacking energies in the positionaldependent-nearest-neighbour model can give an explanation for the presence of negative probe pair signals. This model, together with the nearest neighbour model solves the problem of binding on microarrays, but still there are factors that affect the gene expression measuring. One of them affects the process of competing adsorption and desorption of target RNA to from probe-target duplexes at the chip surface.

Figure 4. a) weight factors; b) nearest-neighbour stacking energy. (from [16])

472 Thermodynamics Fundamentals and Its Application in Science

4.4. Kinetic processes in hybridization thermodynamics 4.4.1. Derivation of the Langmuir isotherm
For molecules in contact with a solid surface at a fixed temperature, the Langmuir Isotherm, developed by Irving Langmuir in 1916, describes the partitioning between the gas phase and adsorbed species as a function of applied pressure. The adsorption process between gas phase molecules, A, vacant surface sites, S, and occupied surface sites, SA, can be represented by the following chemical equation, assuming that there are a fixed number of surface sites present on the surface, as in Figure 5.
S A SA

(9)

When considering adsorption isotherms it is conventional to adopt a definition of surface coverage ( ) which defines the maximum (saturation) surface coverage of a particular adsorbate on a given surface always to be unity, i.e. max = 1.

4.4.2. Thermodynamic derivation

An equilibrium constant k can be written in terms of the concentrations of reactants and products:
SA k S A

(10)

where: [SA] is proportional to the surface coverage of adsorbed molecules, or proportional to ; [S] is proportional to the number of vacant sites, (1 ); [A] is proportional to the pressure of gas, P. Thus it is possible to define another equilibrium constant, b:
b

1 P

(11)

Figure 5. Absorption process.

Thermodynamics of Microarray Hybridization 473

Rearranging the equations (10) and (11) one can obtain the expression for surface coverage:

bP 1 bP

(12)

4.4.3. Kinetic derivation

The equilibrium that may exist between gas adsorbed on a surface and molecules in the gas phase is a dynamic state, i.e. the equilibrium represents a state in which the rate of adsorption of molecules onto the surface is exactly counterbalanced by the rate of desorption of molecules back into the gas phase. It should therefore be possible to derive an isotherm for the adsorption process simply by considering and equating the rates for these two processes. The rate of adsorption will be proportional to the pressure of the gas and the number of vacant sites for adsorption. If the total number of sites on the surface is N, then the rate of change of the surface coverage due to adsorption is:
d k a pN 1 dt

(13)

The rate of change of the coverage due to the adsorbate leaving the surface (desorption) is proportional to the number of adsorbed species:
d kd N dt

(14)

In these equations, ka and kd are the rate constants for adsorption and desorption respectively, and p is the pressure of the adsorbate gas. At equilibrium, the coverage is independent of time and thus the adsorption and desorption rates are equal. The solution to this condition gives us a relation for , equation (12), where b ka kd . Here b is only a constant if the enthalpy of adsorption is independent of coverage.

4.4.4. Dynamic absorption model

Burden et al. [14] develop a dynamic adsorption model based on Langmuir isotherm. If x is the concentration of mRNA target and t is the fraction of sites occupied by probe-target duplex, then in the forward absorption, target mRNA attaches to probe at a rate k f x 1 t proportional to the concentration of specific target mRNA and the fraction 1 t of unoccupied probes; and in the backward desorption reaction, target mRNA detaches from probes at a rate kb t proportional to the fractions of occupied probes. The fraction of probe sites occupied by probe-target duplexes is then given by the differential equation:

d t dt

k f x 1 t k b t

(15)

474 Thermodynamics Fundamentals and Its Application in Science

For the initial condition 0 0 , equation (15) has the following solution:

t
where K kb k f .

x x K k f t 1 e xK

(16)

Using equation (16) Burden et al. estimate the measured fluorescence intensity I, with I0 as the background intensity at zero concentration, to be:
bx x K k f t 1 e I x,t I0 xK

(17)

At equilibrium, the intensity I(x) at target concentration x follows Langmuir Isotherm (12):
I x I 0 bx xK

(18)

Figure 6. Hyperbolic response function for the intensity I(x) according to the Langmuir isotherm.

5. Hybridization dynamics compensation

5.1. Modelling hybridization by thermodynamics
It is well known that hybridization processes may be seen under the point of view of general thermodynamic conditions [23], meaning that the hybridization probability of a given test segment will be defined by its thermodynamic conditions, i.e. by its hybridization temperature. Regarding this, one can state that hybridization process will respond to the dynamic equation:
P T C
Kb

Kf

(19)

where P represents the number of oligonucleotides available for hybridization, T the concentration of free RNA target, C the number of bound complexes, kf and kb are the respective forward and backwards rate constants for the reaction. This equation has as a natural solution the following expression in the time domain:

Thermodynamics of Microarray Hybridization 475

C t

T 1 exp t TK

(20)

where K defined as in equation (16) is an equilibrium dissociation constant, and 1 denoting a characteristic time over which the system reaches equilibrium. k f T K Recent studies [24], [25] confirm the hypothesis that the hybridization process for the each of the probe pairs follows a time model according to the one from Figure 7. This model of evolution predicts that the probability of hybridization will be almost zero if not enough time interval is provided for the experiment to take place, and that in the limit, if enough time is allowed saturation will take place. A practical solution to the different hybridization dynamics can be solved by using multiple regressions to convey PM-MM probe pairs to equivalent thermodynamic conditions by processing diachronic hybridization experiments [26]. The last procedure will be explained in more detail in the following paragraphs.

Figure 7. Theoretical model for perfect match hybridization. Intensity of perfect match versus hybridization time. (adapted from [24])

5.2. Exponential regression model

From equation (20) one can assume that a model to solve the multiple regression problem implicit in this study will have the following form: a 1 e bx y

(21)

where a and b are parameters to be estimated adaptively using least square fitting and the gradient method. Vertical least square fitting proceeds by finding the sum of the squares of the vertical deviations R2 of parameters a and b:

476 Thermodynamics Fundamentals and Its Application in Science

R2

yi a 1 e bx
i

(22)

where:

i yi a 1 e bxi
is the estimation error incurred for each component. With this notation equation (22) will became:
R 2 i2
i

(23)

(24)

The condition of R2 to be at a minimum is that

R2 a

0 0
b

(25)

R2

(26)

From equations (24), (25) and (26) one will obtain:

R2 a

i
i

i i 1 e bxi 0 a i i i i axi e bx 0 b i

(27)

R2

i
i

(28)

A solution for equations (27) and (28) can be found using the gradient method. In this case the parameters are going to be computed adaptively:
ak 1 ak a R2 a

a
k

i ,k 1 e b x
k i

(29)

bk 1 bk b

R2 b

b
k

i , k ak e b x
i

k i

(30)

where i , k is defined as in equation (23) and is a parameter used as an adjust step.

5.3. Application for experimental data

The experimental part has been complemented with artificially simulated test probes used for algorithmic validation. A diachronic database was also being produced to estimate hybridization time constants for different gene segments.

Thermodynamics of Microarray Hybridization 477

Considering these assumptions data records have been created from experimental data fitted by the above mentioned models. The time dynamics of hybridization for both probe sets and their profiles were evaluated at certain time intervals. Firstly, the diachronic data distribution for an evolution from 0 to 30 minutes is shown in Figure 8 in both cases, for the PM probe set and the MM probe set, and in the following figures, i.e. Figure 9 and Figure 10, show this time evolution for 60 and 120 minutes is also shown following the model in equation (20).

Figure 8. Time dynamics of hybridization corresponding to perfect and mismatch probes, for a maximum of 30 minutes.

The next step on data analysis was to look at the probe profiles, at certain times. Figure 11 shows the regression parameters obtained for time constants. The profiles of the perfect and mismatch were extracted for two different time values underlining the fact that if enough time is allowed to some probes, the mismatches will also hybridize completely.

Figure 9. Time dynamics of hybridization corresponding to perfect and mismatch probes, for a maximum of 60 minutes.

478 Thermodynamics Fundamentals and Its Application in Science

Figure 10. Time dynamics of hybridization corresponding to perfect and mismatch probes, for a maximum of 120 minutes.

Considering this and applying the regression algorithm, we observed that this algorithm searches for the matching values of expression levels of probes sets and for estimated values of perfect and mismatch probes. One of the steps of this iterative algorithm can be seen in Figure 12.

Figure 11. Profiles corresponding to perfect and mismatch probes for time constants, at 30 and 100 minutes.

Once the iterative process was complete, certain probes have reached their target. In the expression level estimation most of the perfect match probes obtained the expected values, while some of the mismatch probes did not reach their target, Figure 13. Similar results were obtained in the case of matching hybridization for time constants.

Thermodynamics of Microarray Hybridization 479

Figure 12. Top template shows the iterative matching for hidden expression levels. Bottom template shows the iterative matching for perfect and mismatch hybridization.

Figure 13. Results for the iterative process of matching.

6. Conclusions
The thermodynamics of oligonucleotide hybridization processes where PM-MM results do not show the expected behaviour, thus affecting to the reliability of expression estimation, was studied in this chapter and the following conclusions were emphasized:

480 Thermodynamics Fundamentals and Its Application in Science

Modelling the hybridization process through thermodynamical principles reproduces exponential-like behaviour for each P-T segment pair. The hybridization process should be confined to the time interval where linear growth is granted, this is, at the beginning of the exponential curve shown in Figure 6. Adaptive fitting may be used to predict and regress expression levels on a specific test probe to common thermodynamic conditions. Time constants may be inferred from the regression parameters adaptively. The main features of the PM-MM probe sets may be reproduced from probabilistic modelling. It may be expected that more precise and robust estimations could be produced using this technique with diachronically expressed hybridization experiments.

Author details
Raul Mluan* Communications Department, Technical University of Cluj Napoca, Cluj Napoca, Romania Pedro Gmez Vilda DATSI, Universidad Politcnica de Madrid, Madrid, Spain

Acknowledgement
This work was supported by the project "Development and support of multidisciplinary postdoctoral programmes in major technical areas of national strategy of Research Development - Innovation" 4D-POSTDOC, contract no. POSDRU/89/1.5/S/52603, project cofunded by the European Social Fund through Sectoral Operational Programme Human Resources Development 2007-2013.

7. References
[1] Malutan R, Gmez Vilda P, Berindan Neagoe I, Borda M (2011) Hybridization Dynamics Compensation in Microarray Experiments. Advances in Intelligent and Soft Computing. 93: 255-261 [2] Wu P, Nakano S, Sugimoto N (2002) Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. European Journal of Biochemistry. 269:2821 2830 [3] SantaLucia Jr. J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS on Biochemistry. 95:1460 1465 [4] Chan V, Graves D.J., McKenzie S.E. (1995) The Biophysics of DNA Hybridization with Immobilized Oligonucleotides Probes. Biophysical Journal. 69:2243 2255

Corresponding Author

Thermodynamics of Microarray Hybridization 481

[5] Livshits M A, Mirzabekov A D (1996) Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides. Biophysical Journal. 71:2795 2801 [6] Dai H, Meyer M, Stepaniants S, Ziman M, Stoughton R (2002) Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Research. 30(16): e86.1 e86.8 [7] Dorris D R, et al. (2003) Oligodeoxyribonucleotide probe accessibility on a threedimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnology. 3:6 [8] Binder H, Preibisch S (2005) Specific and Nonspecific Hybridization of Oligonucleotide Probes on Microarrays. Biophysical Journal. 89:337 352 [9] Wang J Y, Drlica K (2003) Modelling hybridization kinetics. Mathematical Bioscience. 183:37 47 [10] Naef F, Magnasco M O (2003) Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays. Physical Review E., 68:011906-1 011906-4 [11] Wu Z, Irizarry R A (2004) Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Proc. of the 8th Annual International Conference on Research in Computational Molecular Biology. 98 106 [12] www.accessexcellence.org/RC/VL/GG/index.html [13] Lipshutz R L, Fodor S P A, Gingeras T R, Lockhart D J (1999) High density synthetic oligonucleotide arrays. Nature Genetics Supplement. 21:20 24 [14] Burden C, Pittelkow Y E, Wilson S R (2004) Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays. Statistical Applications in Genetics and Molecular Biology. 3:35 [15] Sugimoto N et al (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research. 24:4501 4505 [16] Zhang L, Miles M F, Aldape K D (2003) A model of molecular interactions on short oligonucleotide microarrays, Nature Biotechnology. 21(7):818 821 [17] Huang J C, Morris Q D, Hughes T R, Frey B J (2005) GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics. 21:i222 i231 [18] Black W Z, Hartley J G (1991) Thermodynamics. Second Edition. SI Version. Harper Collins Publisher [19] SantaLucia Jr J, Allawi H T, Seneviratne P A (1996) Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability. Biochemistry. 35(11): 3555 3562 [20] Delcourt S G, Blake R D (1991) Stacking Energies in DNA. The Journal of Biological Chemistry. 266: 15160 15169 [21] Allawi H T, SantaLucia Jr J. Thermodynamics and NMR of Internal GT Mismatches in DNA. Biochemistry. 36:10581 10594 [22] Li C, Wong W H (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. PNAS USA. 98(1):31 36 [23] El Samad H, Khammash M, Petzold L, Gillespie D (2005) Stochastic Modelling of Gene Regulatory Networks. Int. Journal of Robust and Nonlinear Control. 15(15):691 711

482 Thermodynamics Fundamentals and Its Application in Science

[24] Dai H, Meyer M, Stepaniants S, Ziman M, Stoughton R (2002) Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Research. 30(16):e86.1 e86.8 [25] Zhang Y, Hammer D A, Graves D J (2005) Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns. Biophysical Journal. 89:2950 2959 [26] Diaz F, Malutan R, Gomez P, Martinez R, Stetter B, Fe Paz M, Garcia E, Pelaez J (2006) Estimating Oligonucleotide Microarray Expression by Hybridization Process Modelling. Proc. of IEEE/NLM Life Science Systems and Applications Workshop. 1 2

Chapter 19

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods

Xuejing Hou and Harvey J.M. Hou
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/2615

1. Introduction
Thermodynamics of a chemical reaction is a fundamental and vital issue for complete understanding of the reaction at the molecular level and involves the elucidation of the energy level of reactant and products, direction of reaction, and driving force or spontaneity of the reaction (Tadashi, 2011). Most the chemical reactions are enthalpy driven and are determined by chemical bonding energy of the reactants and products. However, some of the chemical reaction or process is entropy driven and are largely due the probability or disorder of the system during the reaction. Protein denaturation and dissolution of potassium iodide in water are such examples. In chemistry and biology, especially electron transfer reaction, the entropy changes are often assumes small and negligible. The understanding of thermodynamics of electron transfer reactions is relatively limited (Mauzerall, 2006). To study the thermodynamics of reaction in chemistry and biology, photosynthetic reaction is an excellent model system. The photosynthesis involves multiple electron transfer reaction driven by sunlight under room temperature and neutral pH (Blankenship, 2002; Diner and Rappaport, 2002; Golbeck, 2006). The understanding of light-induced electron transfer reaction in photosynthesis will provide fundamental knowledge of chemical reactions and guide the design and fabrication in artificial photosynthetic system in address the global energy and environmental crisis in the 21st century (Lewis and Nocera, 2006). In particular the solar energy storage of solar energy using water splitting reaction mimicking photosynthesis might solved energy and pure water problems at the same time (Kanan and Nocera, 2008; Cook et al., 2010; Hou, 2010, 2011). The electron transfer reactions in photosynthesis involves four major chlorophyll binding protein complexes: Photosystem II, cytochrome b6f, photosystem I, and ATP synthase (Figure 1). Photosystem I and photosystem II are belong to two types of different reaction centers in nature, respectively. Type I reaction centers incorporate a phylloquinone or menaquinone as secondary electron
2012 Hou and Hou, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

484 Thermodynamics Fundamentals and Its Application in Science

acceptor, A1, and three tertiary iron-sulfur cluster electron acceptors, FA, FB, and FX. Type II centers use two quinone acceptors: QA undergoes one-electron reduction, and QB undergoes a two-electron reduction with concomitant protonation.

Figure 1. Four protein complexes, including photosystem II, cytochrome b6f, photosystem I, and ATP synthase, are responsible for the electron transfer reactions in photosynthesis. (from http://www.answersingenesis.org/articles/tj/v17/n3/photosynthesis).

Photosystem I is a pigment-protein complex consisting of more than 11 polypeptides embedded in the photosynthetic membrane and catalyzes light-induced electron transfer from reduced plastocyanin (or cytochrome c6) to oxidized ferredoxin (or flavodoxin). The electron transfer pathway and the electron transfer cofactors in photosystem I is shown as a black arrows in Figure 1. The primary electron donor is P700, a pair of chlorophyll a molecules. After absorbing light photon energy, P700 becomes excited species P700* and delivers one electron to the primary electron acceptor A0, a chlorophyll a molecule. The reduced A0 anion donates its electron to the secondary acceptor A1, a phylloquione or vitamin K1 molecule. The reduced A1 anion transfer the electron to FX, FA, FB, and finally to ferrodoxin for producing NADPH+. The three-dimensional structure of cyanobacterial PS I at 2.5 A resolution has been obtained and revealed much of the detailed orientation and binding site of electron transfer cofactors. These structural details offer a solid basis for structure and function studies at an atomic level (Figure 2). The almost complete symmetric arrangement of cofactors in PS I suggested the electron transfer might involve two electron transfer branches (A side and B side). This is different from the electron transfer mechanism in type II centers. For example, in bacterial and PS II, only one electron transfer branch (L side or D1 side) is active. The M-side (or D2 side) electron transfer is inactive and may provide protective role in the reaction center in regulating excess light energy.

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 485

Figure 2. X-ray crystallographic structure (upper panel) and the arrangment of the cofactors (lower pahnel) in photosystem I from cyanobacterium Synechococcus elongatus (Jordan et al., 2001) (Reproduced with permission from Nature publishing Group).

2. Quinones in photosystem I
A quinone molecule is a perfect electron transfer cofactor due to its reversible electrochemical redox properties and plays a key role in photosynthetic electron transfer process. For example, both type I and type II reaction centers contain a quinone that operates as an intermediate electron acceptor and as a one-electron carrier. However, the local protein environment and chemical properties of the quinone in these two types of reaction centers must be different. EPR measurements revealed that there are striking difference in the binding and function of phylloquinone (A1) in PS I and ubiquione (QA) in the bacterial center of R. sphaeroides (Kamlowski et al., 1998). As a type I center, PS I

486 Thermodynamics Fundamentals and Its Application in Science

contain a bound menaquinone, usually phylloquinone (A1, vitamin K1, 2-methyl-3-phytyl1,4-naphthoquinone). In contrast, PS II uses the plasoquinone (Ap). The chemical structures of A1 and AP are shown in Figure 3. To investigate the function of ubiquinone in bacterial photosynthesis, the native quinone can be removed by organic solvent extraction and replaced with 22 other quinones. The rate of electron transfer in these reconstituted reaction center, Gibbs free energy, enthalpy changes, and apparent entropy changes were determined by EPR, transient time-resolved absorption spectroscopy, theoretical calculation and modeling, and photoacoustic spectroscopy (Gunner and Dutton, 1989; Edens et al., 2000). The molecular volume changes of charge separation due to electrostriction correlates with the size of quinones as expected (Edens et al., 2000). However, the methodology of replacement of quinone is not successful in PS I.

Figure 3. Chemical structures of quinones in photosynthesis. A1 is native quinone in photosystem I, and AP is a plastoquinone in photosystem II.

A biological method to replace phylloquinone was devised by Chitnis and Golbeck (Johnson et al., 2000; Semenov et al., 2000). The strategy to disallow A1 function is to inactivate genes that code for enzymes involved in the biosynthetic pathway of phylloquinone. The synthesis of the phylloquione in Synechocystis sp. PCC 6803 was shown in Figure 4, which is similar to the biosynthesis of menoquinone in E. coli (Sharma et al., 1996). It is proposed that menF/entC, menD, menE, and menB are responsible for 1,4-dihydroxy-2-naphthoate synthesis. The menA catalyzes the addition of phytyl chain. The gerC2 gene codes for the 2thytyl-1,4-naphthoquinone methyl transferase enzyme, which catalyzed the methylation step to produce phylloquinone. To generate a recombinant DNA construction for inactivation of the menA gene, two DNA fragment were amplified from Synechocystis sp. PCC 6803 genomic DNA by polymerase chain reaction (PCR) (Figure 5). The PstI and ApaI restriction sites were incorporated in both fragments. The first amplification product was digested with EegI and PstI, and the second fragment was digested with PstI and ApaI restriction enzymes. The fragments was ligated with the pBluescript vector, and the kanamycin resistance gene was cloned. The 442-bp part

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 487

of the menA gene was yielded. The transformation of the wild type strain of Synechocystis 6803 and isolation of segregated mutants was performed to obtain the menA null strain. The recombinant DNA construct of inactivation of the menB gene was generated in the similar way. Two 1.0 kb fragments from upstream and downstream of the menB gene were amplified by PCR. The amplified fragments were cloned into pBluescript and a 2.0-kb EcoRI fragment containing the streptomycine/spectinomycine resistance cassettes.

Figure 4. Biosynthetic pathway of phylloquinone in cyanobacterium Synechocystis sp. PCC 6803 (Johnson et al., 2000) (Reproduced with permission from the American Society for Biochemistry and Molecular Biology).

488 Thermodynamics Fundamentals and Its Application in Science

In the left of the panel A in Figure 5 shows the restriction maps of the genomic regions surrounding menA gene in the wild type and mutant strains. A 440-bp fragment in the menA gene was deleted and replaced by a 1.3 kb kanamycine resistance cartridge. PCR amplification of the menA locus of the wild type produced the expected 1.9 kb fragment (panel A right, Figure 5). Southern blot hybridization analyses confirmed the interruption of the menA gene as expected. Insertional inactivation of the menB gene was also confirmed by both Southern blot hybridization and PCR amplification of menB locus from the mutant strain. The part of the menB gene was deleted and replaced with a 2-kb spectinomycin resistance cartridge (left, panel B in Figure 5). The PCR amplification of the menB locus of the wild type produced the expected fragment of 920 bp (right, panel B in Figure 5), confirming the inactivation of the menB gene.

Figure 5. Construct and confirmation of menA and menB null mutants by inactivation of menA and menB genes in Synechocystis sp. PCC 6803 (Johnson et al., 2000) (Reproduced with permission from the American Society for Biochemistry and Molecular Biology).

3. Physiological, structural, and kinetics of menA and menB null mutants

The menA and menB null mutants are able to grow photoheterotrophically and photoautotrophically under low light conditions. The expression level of active PS I in the menA and menB mutant are 50-60% of the wild type stain. HPLC analysis indicates that the absence of phylloquinone in PS I and that the presence of high level of plastoquinone in PS I (Johnson et al., 2000). EPR, electron nuclear double resonance, and electron spin echo modulation data suggested that the orientation and distance of the foreign quinone AP are

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 489

almost identical to those of the phylloquinone A1 in the wild type PS I. In addition, EPR measurements show that plastoquinone has been recruited into the A1 site and functions as an efficient one electron carrier (Zybailov et al., 2000). As shown in Figure 6, the rates of electron transfer from P700 to A0 and A1 in the mutants are similar to the wild type PS I. However, the kinetic parameter from A1 anion to FX is quite different in the menA and menB null mutants. The time-resolved optical studies revealed that the forward electron transfer from A1 anion to FX is slowed 1000-fold, to 15 and 300 s, compared to 20 and 200 ns in the wild type PS I (Semenov et al., 2000; Johnson et al., 2001). Based the kinetic data of electron transfer in menA and menB mutant, the redox potential of AP in menA and menB PS I is estimated to be more oxidizing than phylloquinone so that electron transfer from AP anion to FX is thermodynamically unfavorable in the mutants (right panel of Figure 6).

Figure 6. Kinetic data of electron transfer steps in native and menA/menB null mutants of Synechocystis sp. PCC 6803

4. Thermodynamics of menA and menB Null Mutants

Pulsed photoacoustic spectroscopy can provide a direct measurement of thermodynamic parameters such as volume change and enthalpy changes that accompany electron transfer reactions (Braslavsky, 1985; Carpentier et al., 1990; Arnaut et al., 1992; Small et al., 1992; Losi et al., 1995; Edens et al., 2000; Malkin, 2000; Herbert et al., 2001; Feitelson and Mauzerall, 2002; Delosme, 2003; Hou and Mauzerall, 2006; Hou and Sakmar, 2010; Hou, 2011; Hou and Mauzerall, 2011). With prior knowledge of the change in Gibbs free energy of the corresponding reactions, the apparent entropy change (TS) of the reaction can be calculated. This is an important parameter, knowledge of which is required to fully understand the mechanism of electron transfer, and it has been largely underreported in the literature. The H, V, and TS of electron transfer in the photosynthetic reaction center

490 Thermodynamics Fundamentals and Its Application in Science

from Rb. sphaeroides have been measured using pulsed photoacoustics (Edens et al., 2000; Nagy et al., 2001). In oxygenic photosynthetic systems, the same parameters of electron transfer in PS I trimers and in Mn depleted PS II reaction center cores from Synechocystis sp. PCC 6803 and higher plants have been investigated using similar techniques (Delosme et al., 1994; Hou et al., 2001). These data were confirmed by photoacoustic measurements on whole cells of Synechocystis sp. PCC 6803 (Boichenko et al., 2001). The thermodynamic parameters of bacterial reaction centers were found to be similar to those of PS I and dramatically different from those of PS II. Using the fit by convolution of photoacoustic waves on the nanosecond and microsecond time scales, the thermodynamic parameters of different kinetic steps in Synechocystis PS I were resolved (Hou and Mauzerall, 2006). A large negative enthalpy (-0.8 eV) and large volume change (-23 3) for the P700* to A1-FX step and a positive enthalpy (+0.4 eV) and a small volume change (-3 3) for the A1-FX to FA/B-step were observed. For the fast reaction the free energy change for the P700* A1-FX step is -0.63 eV, and the entropy change (TS, T=25 C) is -0.2 eV. For the slow reaction, A1-FX to FA/B-, the free energy is -0.14 eV (43), and the entropy change (TS) is positive, +0.54 eV. The positive entropy contribution is even larger than the positive enthalpy, indicating that the A1-FX to FA/B - step in Synechocystis PS I is entropy driven. The photoacoustic waves produced by forming a charge-separated radical pair upon light excitation of PS I trimers consist of at least two major components: (1) the heat output (QRC), which includes the enthalpy change of the reaction and other rapidly released heat, and (2) the volume change of the reaction (VRC). The thermal signal disappears at the temperature of maximum density of the suspending medium, Tm, near or below 4 C, thus leaving only the volume term (Hou, 2011). Wild-type PS I trimers produced large negative PA signals at 3.8 C (Figure 7, curve 2) which originate directly from the volume contraction via electrostriction. The volume change in wild-type PS I is -25 3. In contrast, menA/B PS I shows a smaller signal (Figure 7, curves 3 and 4). There is no major difference in the volume contraction between menA PS I and menB PS I. This may be expected since plastoquinone-9 is present in the A1 sites in PS I in both mutants. To confirm the values of the volume change and to estimate the quantum yield of charge separation in menA/B PS I, two different approaches are utilized: (1) volume yield measurements and (2) saturation measurements. The detailed description of these two procedures has been given previously (Hou et al., 2001; Hou, 2011). The fits of the volume yield curves for the mutants and wild-type PS I are shown in Figure 8. The apparent volume contractions of menA PS I and menB PS I are -14 and -16 3, respectively, compared to -25 3 for wild-type PS I. In the second saturation method, every PS I complex is excited to obtain the maximum PA signal. In this method, one must calculate the number of PS I centers in the illuminated volume of the cell (0.34 mL), N, to obtain the real volume change Vs. In this analytical method, the volume change does not contain the quantum yield. As shown in Figure 8, the saturation value of volume change (Vs) in menA/B PS I was -17 3, which is slightly higher than that using the volume yield method. These findings confirm the previous results and argue that the quantum yield of photochemistry in the mutants is not low.

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 491

Figure 7. Photoacoustic waves of photosystem I complexes from the photoacoustic reference sample (curve 1), menA (curve 3), menB (curve 4), and wild-type (curve 2) strains of Synechocystis sp. PCC 6803 on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

The quantum yield of photochemistry can be estimated from measurements of the effective cross section (). In Figure 8 (lower panel), the quantum yield of charge separation in menA/B PS I was estimated to be 85%, a value slightly lower than the 96% quantum yield in wild-type PS I. Taken together, they suggest that the volume contractions in menA/B PS I on the microsecond time scale are -172 3, and the quantum yields of photochemistry are ca. 8510%. The observed reaction on the microsecond time scale is attributed to the formation of P700+FA/B- from excited P700*for the wild-type PS I and of P700+AP- for menA/B PS I. The enthalpy changes in menA and menB null mutants were determined to be 0.640.1 eV and 0.740.1 eV from the difference in slopes in Figure 9, respectively, according to the method described previously (Hou et al., 2001; Hou et al., 2009). Figure 10 is the typical photoacoustic wave on the fast nanosecond time scale reaction. Curve 1 is the positive signal from a photoacoustic reference at 25 C, and curves 2, 3, and 4 show large negative signals from wild-type PS I, menA PS I, and menB PS I, respectively, at 3.8 C. They indicate that the volume contractions of the mutants are roughly two thirds of the wild type and are similar to those on the microsecond time scale. Figure 11 shows the analysis of photoacoustic data of the mutants and the wild type on the nanosecond time scale. The volume changes during charge separation in menA/B PS I were smaller, -17 3, than that of wild type PS I, -21 3. These values are identical to those of the mutants on the microsecond time scale, which indicate that there are no kinetic volume components between the 20 ns and 1 s time scales in the mutants. It also demonstrates that the photoacoustic methodology on both time scales is reliable. The data in Figure 11 indicate that the enthalpy changes in both mutants are similar, -0.7 eV, which is very close to that on the microsecond time scale.

492 Thermodynamics Fundamentals and Its Application in Science

Figure 8. Molecular volume changes determined by volume yield method (left panel) and saturation curve method (right panel) on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

Figure 9. Enthalpy changes determined by analyzing the linear fit of the photoacoustic intensity vs. temperature (water expansitivity) on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 493

Figure 10. Photoacoustic waves of the photoacoustic reference sample (curve 1), wild-type (curve 2), menA (curve 3), and menB (curve 4) mutants of Synechocystis sp. PCC 6803 on the nanosecond time scale (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

Figure 11. Enthalpy changes determined by plotting the linear fit of the photoacoustic intensity vs. temperature (water expansitivity) on the nanosecond time scale (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

494 Thermodynamics Fundamentals and Its Application in Science

To summarize the thermodynamic data, the volume changes, free energies, and enthalpy and entropy changes on menA/B PS I in comparison with those on the wild-type PS I are listed in Figure 12. Opened arrows are the early step forming P700+A1- from P700* for the wildtype PS I or P700+AP- from P700* for the mutants, and solid arrows are the number of the following reaction: P700+AP- to P700+FA/B-. As shown in panel A, the volume contraction of the early step of the photoreaction in the mutants (-17 3) is smaller than that in the wild type (21 3). Similarly, the enthalpy change (-0.7 eV) of the early step in the mutants is smaller than that (-0.8 eV) in wild-type PS I (Figure 12B). Assuming a redox potential of -0.6 V for plastoquinone-9 in the A1 site (21), the free energy (-0.7 eV) of this early reaction in the mutants is larger than the value (-0.6 eV) in the wild type as indicated in Figure 12C. Taking the difference of free energy and enthalpy change in the mutants, the apparent entropy change of the early step in mutants is zero. In contrast, the apparent entropy change in the wild type is calculated to be +0.2 eV. Since the apparent entropy change for the overall reaction of the generation of P700+FA/B- from P700* is +0.35 eV (32), it implies that the latter reaction in the mutants, i.e., the P700+AP-FA/B to P700+APFA/B- reaction, is almost completely entropy driven (TS ) +0.4 eV and G ) -0.1 eV) (Figure 12D).

Figure 12. Thermodynamics of electron transfer reactions in photosystem I from the menA/menB null mutants and wild-type strains of Synechocystis sp. PCC 6803 (Hou et al., 2009) (Reproduced with permission from the American Chemical Society).

In the case of menA/B PS I, photoacoustic measurements on the microsecond time scale reveal the volume contraction to be -17 3. Considering our time window of 0.1-10 s, this value is assigned to the formation of P700+AP- from P700*AP. The intermediate step of electron transfer from P700+AP-FA/B to P700+APFA/B- would be accompanied by a volume change of -9 3, assuming the replacement of A1 with AP causes no change in the FA/B clusters. For menA/B PS I, the size of the benzoquinone ring in plastoquinone-9 (AP) is smaller than the

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 495

naphthoquinone ring in phylloquinone. Electron spin-echo modulation experiments showed that the distance between P700+ and AP- (25.3 ) in menA/B PS I is the same as the distance between P700+ and A1- in wild-type PS I. The volume contraction of electron transfer from P700 to AP is estimated to be larger (-30 3) than the observed one (-17 3). Thus a positive volume due to a protein conformational change may be possible. We offer a molecular explanation of the difference in the volume change predicted via electrostriction and that of the observed value (-17 3). A simple explanation would be that the quantum yield of photochemistry is lower (for example, 0.7) in menA/B PS I. This, however, is unlikely because our pulse saturation data revealed a quantum yield of 85% in PS I from both mutants, which is only sufficiently lower than the quantum yield of 96% in wild type PS I to explain less than half of the effect. Further support for a high quantum yield is that the light saturation dependence of the flavodoxin reduction rate in menA/B PS I is similar to that of wild-type PS I. These two arguments are consistent in showing that the smaller volume change in the menA/B PS I is not caused by a low quantum yield. The smaller volume contraction may be caused by the following two factors: compressibility of protein and polarity of quinone pocket. The first factor is the effect of the foreign plastoquinone on the compressibility of the local environment of the protein. The orientation and distance of plastoquinone- 9 in the mutants are known to be similar to phylloquinone in the wild-type PS I. However, since the pocket of A1 is adapted to phylloquinone, the smaller plastoquinone with the longer tail may not fit well into the protein. If the effect of the larger tail is to crowd the hydrophobic site, this could decrease the compressibility of the local domain and so decrease Vel. Alternatively, the A1 binding region in menA/B PS I may be more polar; i.e., it has a larger effective , compared to the wild-type PS I. This could be due to the small size of plastoquinone-9, allowing a water molecule to be present. This possibility also could explain the change in potential of the quinone because of hydrogen bonding to the water. By use of the electron transfer theory and kinetic data, the redox potential of plastoquinone at the A1 site was estimated to be -0.61 V (Hou et al., 2009). However, the error to be at least 0.1 V. The G for producing P700+AP- from P700* is then -0.71 eV. Similarly, the free energy for producing P700+FA/B- from P700*FA/B is -0.77 eV (35). Thus we infer that the free energy of P700+AP-FA/B to P700+APFA/B- reaction is -0.060.10 eV in the mutants. Knowing the free energy of the electron transfer step in wild-type PS I and menA/B PS I, the entropic contribution (T S) can be determined by the Gibbs relation G = H - TS. The enthalpy change occurring on the formation of P700+AP- from P700* in menA/B PS I is -0.7 0.07 eV. This is close to the estimated free energy of this reaction (-0.70 eV), and thus the apparent entropy change is close to zero (Figure 12). Considering the enthalpy change (-0.4 eV) of the overall reaction for the formation of P700+FA/B- from P700* in the wild-type PS I, the electron transfer reaction from AP- to FA/B would be associated with a positive enthalpy change of +0.3 eV and thus is completely entropy driven as the free energy is zero in the mutants. The entropy of electron transfer reactions is often assumed to be zero. However, the free energy calculated from kinetic measurements of reverse electron transfer in bacterial

496 Thermodynamics Fundamentals and Its Application in Science

reaction centers shows that the free energy is time- and temperature dependent, particularly on the less than nanosecond time scale. The kinetics of these decays can only be described as distributed, and simple analysis in terms of a single component is not trustworthy. Protein dynamics may play a key role in this electron transfer step. However, the question of whether these relaxations are enthalpy and/or entropy driven remains to be answered. The slow (microsecond) component observed in wild-type PS I could be such a relaxation, but only the V was determined. The difference between observed enthalpies and estimated free energies as entropies highlights the problem. In addition to reaction centers of Rb. sphaeroides, similar positive entropic contribution in PS I preparations of Synechocystis sp. PCC 6803 were observed, but not in PS II preparations. Charge movement, but not charge separation due to proton transfer, may be the difference in PS II on the 1 s time scale. Clear-cut and large negative entropic contribution is seen in the model system of triplet porphyrin-to-ferricyanide electron transfer in aqueous solution, where relaxations are too fast to be relevant.

5. Conclusion
In this chapter, thermodynamics of electron transfers in biological system can be assessed by using a combination of molecular genetics and sophisticated biophysical techniques, in particular, pulsed photoacoustic spectroscopy. Photosynthesis involves light-induced charge separation and subsequently a series of electron transfer reactions and is an ideal system for the detailed study on electron transfer mechanisms in chemistry and biology. In contrast to the susceptible and vulnerable of photosystem II complex to environment, photosystem I complex is much more stable and a perfect choice for such a study. As quinones play a central role in electron transfer reactions in both anoxygenic and oxygenic photosynthesis, the phylloquinone (A1) of photosystem I is chosen as a probe to explore the effect and regulation of electron cofactors on kinetics and thermodynamics in vivo. The usual approach of chemical modification or replacement of phylloquinone may alter the bonding pocket of the cofactor and the interaction with its proteins. Molecular genetic technique is utilized to block the biosynthesis of the cofactor, phylloquinone, in the cynobacterium Synechocystis sp. PCC 6803 and replace the phylloquinone in the A1 site with different foreign quinones. The effect of the foreign quinones on the electron transfer is systematically studied by biophysical methodologies. Specifically, the menA and menB genes, which code for phytyl transferase and 1.4dihydroxy-2-naphthoae synthase, respectively, are inactivated to prevent the synthesis of phylloquinone. In spite of the demonstrated absence of phylloquinone, the menA and menB null mutants grow photoheterotrophically. HPLC and EPR measurement show that plastoquinone-9 (AP) has been recruited into the A1 site and functions as an efficient oneelectron transfer carrier. The orientation and distance between the plastoquinone and other cofactors are the same as that of the wild type. Time-resolved optical studies indicate that the forward electron transfer from A1 anion to the iron-sulfur cluster (FX) is slowed 1000-

Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 497

fold, to 15 to 300 s, compared to 20 and 200 ns in the wild type. Using the electron transfer theory and kinetic data, the redox potential of plastoquinone at the A1 site was estimated to be -0.61 V, more oxidizing that phylloquinone. The electron transfer from AP anion to FX is thermodynamically unfavorable in the menA and menB null mutants. Photoacoustic measurements reveal that the quantum yield of charge separation in menA and menB is slightly lower (85%) than that of the wild type. The thermodynamic parameters of the two electron transfer steps, including molecular volume changes, reaction enthalpy and apparent entropy, were obtained in menA and menB null mutants and are considerable different from the wild type. The experimental data demonstrates that the not only the kinetics but also the thermodynamics of electron transfer reaction in photosystem I are affected by the recruitment of the foreign quinone into the A1 site. One of the most intriguing conclusions is that although free energy for the electron transfer from AP anion to FX in menA and menB mutant is close to zero, the apparent entropy (TS) for this reaction is positive, +0.4 eV. This indicates that the entropy plays a key role in the electron transfer from AP anion to FX. As shown in Figure 13, the electron transfer from P700 to A1 is enthalpy driven; the electron transfer from A1 to FA/FB is entropy driven. The driving force of electron transfer in photosynthetic systems is not only dependent on the bonding energy of the cofactor and interaction energy with the protein (enthalpy) but also dependent on the available states of interaction with the protein (entropy).

Figure 13. The enthalpy and entropy driven steps in Synechocystis 6803 photosystem I

Author details
Xuejing Hou University of Massachusetts Dartmouth, USA Harvey J.M. Hou* University of Massachusetts Dartmouth, USA Alabama State University, USA
*

Corresponding Author

498 Thermodynamics Fundamentals and Its Application in Science

Acknowledgement
This work was supported by the Alabama State University and University of Massachusetts Dartmouth. The photoacoustic measurements were conducted in the laboratory of Professor David Mauzerall at Rockefeller University. The author thanks Professor John Golbeck and Dr. Gaozhong Shen for their collaboration and stimulating discussions on menA/menB project. He is also grateful to his students, Fan Zhang and Lien-Yang Chou, for data analysis and assistance.

6. References
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Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 499

Gunner MR, Dutton PL (1989) Temperature and G dependence of the electron transfer from BPh- to QA in reaction center protein from Rhodobacter sphaeroides with different quinones as QA. J. Am. Chem. Soc. 111: 3400-3412 Herbert SK, Han T, Vogelmann TC (2001) New applications of photoacoustics to the study of photosynthesis. Photosynth. Res. 66: 13-31 Hou HJM (2010) Structural and mechanistic aspects of Mn-oxo and Co-based compounds in water oxidation catalysis and potential application in solar fuel production. J. Integr. Plant Biol. 52: 704-711 Hou HJM (2011) Enthalpy, entropy, and voluem changes of electron transfer reactions in photosynthetic proteins, In: Application of thermodynamics to biological and material science, Mizutani Tadashi Ed., Intech, pp. 93-110. Hou HJM (2011) Manganese-based materials inspired by photosynthesis for water-splitting. Materials 4: 1693-1704 Hou HJM, Mauzerall D (2006) The A1-FX to FA/B Step in Synechocystis 6803 Photosystem I Is Entropy Driven. J. Am. Chem. Soc. 128: 1580-1586 Hou HJM, Mauzerall D (2011) Listening to PS II: Enthalpy, entrhopy and volume changes. J. Photochem. Photobiol. B 104: 357-365 Hou HJM, Sakmar TP (2010) Methodology of pulsed photoacoustics and its application to probe photosystems and receptors. Sensors 10: 5642-5667 Hou HJM, Shen G, Boichenko VA, Golbeck JH, Mauzerall D (2009) Thermodynamics of Charge Separation of Photosystem I in the menA and menB Null Mutants of Synechocystis sp. PCC 6803 Determined by Pulsed Photoacoustics. Biochemistry 48: 1829-1837 Hou JM, Boichenko VA, Wang YC, Chitnis PR, Mauzerall D (2001) Thermodynamics of electron transfer in oxygenic photosynthetic reaction centers: a pulsed photoacoustic study of electron transfer in photosystem I reveals a similarity to bacterial reaction centers in both volume change and entropy. Biochemistry 40: 7109-7116 Johnson TW, Shen G, Zybailov B, Kolling D, Reategui R, Beauparlant S, Vassiliev IR, Bryant DA, Jones AD, Golbeck JH, Chitnis PR (2000) Recruitment of a foreign quinone into the A1 site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J. Biol. Chem. 275: 85238530 Johnson TW, Zybailov B, Jones AD, Bittl R, Zech S, Stehlik D, Golbeck JH, Chitnis PR (2001) Recruitment of a foreign quinone into the A1 site of photosystem I. In vivo replacement of plastoquinone-9 by media-supplemented naphthoquinones in phylloquinone biosynthetic pathway mutants of Synechocystis sp. PCC 6803. J. Biol. Chem. 276: 3951239521 Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, Krauss N (2001) Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution. Nature 411: 909-917 Kamlowski A, Altenberg-Greulich B, Van der Est A, Zech SG, Bittl R, Fromme P, Lubitz W, Stehlik D (1998) The Quinone Acceptor A1 in Photosystem I: Binding Site, and Comparison to QA in Purple Bacteria Reaction Centers. J. Phys. Chem. B 102: 8278-8287

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Kanan M, Nocera DG (2008) In Situ Formation of an Oxygen-Evolving Catalyst in Neutral Water Containing Phosphate and Co2+. Science 321: 1072 - 1075 Lewis NS, Nocera DG (2006) Powering the planet: chemical challenges in solar energy utilization. Proc. Natl. Acad. Sci. U S A 103: 15729-15735 Losi A, Bedotti R, Viappiani C (1995) Time-Resolved Photoacoustics Determination of Intersystem Crossing and Singlet Oxygen Photosensitization Quantum Yields for 4,5',8Trimethylpsoralen. J. Phys. Chem. 99: 16162-16167 Malkin S (2000) The photoacoustic effect in leaves and its applications. Probing In: Probing Photosynthesis: Mechanism, Regulation & Adaptation, M Yunus, U Pathre, and P Mohanty Eds., Taylor & Francis, pp. 484-524 Mauzerall D (2006) Thermodynamics in photosystem I. In: Photosystem I: The Light-Driven Plastocyanin: Ferredoxin Oxidoreductase, J Golbeck ed., Springer, pp. 571-581 Nagy L, Kiss V, Brumfeld V, Malkin S (2001) Thermal and structural changes of photosynthetic reaction centers characterized by photoacoustic detection with a broad frequency band hydrophone. Photochem. Photobiol. 74: 81-87 Semenov AY, Vassiliev IR, van Der Est A, Mamedov MD, Zybailov B, Shen G, Stehlik D, Diner BA, Chitnis PR, Golbeck JH (2000) Recruitment of a foreign quinone into the A1 site of photosystem I. Altered kinetics of electron transfer in phylloquinone biosynthetic pathway mutants studied by time-resolved optical, EPR, and electrometric techniques.J. Biol. Chem. 275: 23429-23438 Semenov AY, Vassiliev IR, Van der Est A, Mamedov MD, Zybailov B, Shen G, Stehlik D, Diner BA, Chitnis PR, Golbeck JH (2000) Recruitment of a foreign quinone into the A1 site of photosystem I. Altered kinetics of electron transfer in phylloquinone biosynthetic pathway mutants studied by time-resolved optical, EPR, and electrometric techniques. J. Biol. Chem. 275: 23429-23438 Sharma V, Hudspeth ME, Meganathan R (1996) Gene 168: 43-48 Small JR, Libertini LJ, Small EW (1992) Analysis of photoacoustic waveforms using the nonlinear least squares method. Biophys. Chem. 42: 29-48 Tadashi M (2011) Application of Thermodynamics to Biological and Materials Science. Intech Zybailov B, van der Est A, Zech SG, Teutloff C, Johnson TW, Shen G, Bittl R, Stehlik D, Chitnis PR, Golbeck JH (2000) Recruitment of a foreign quinone into the A1 site of photosystem I. II. Structural and functional characterization of phylloquinone biosynthetic pathway mutants by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy. J. Biol. Chem. 275: 8531-8539

Chapter 20

Fuzzy Spheres Decays and Black Hole Thermodynamics

C.A.S. Silva
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51630

1. Introduction
A black hole is, by denition, a region in spacetime in which the gravitational eld is so strong that it precludes even light from escaping to innity. A black hole is formed when a body of mass M contracts to a size less than the so called gravitational radius r g = 2GM/c2 . (G is the Newtons gravitational constant, and c is the speed of light). The velocity required to leave the boundary of the black hole and move away to innity (the escape velocity) equals the speed of light. In this way, one easily concludes that neither signals nor particles can escape from the region inside the black hole since the speed of light is the limiting propagation velocity for physical signals. From the fact that no signals can escape from a black hole, while physical objects and radiation can fall into it, the surface bounding the black hole in spacetime (called the event horizon) is a lightlike surface. The term black hole" was introduced by Wheeler in 1967 although the theoretical study of these objects has quite a long history. The very possibility of the existence of such objects was rst discussed by Michell and Laplace within the framework of the Newtonian theory at the end of the 18th century [13]. In general relativity context, the problem arose within a year after the theory had been developed, i.e., after Schwarzschild (1916) obtained the rst exact (spherically symmetric) solution of Einsteins equations in vacuum. In particular, black hole developments in the last forty years have shown that black holes have thermodynamics properties like entropy and temperature, and as a consequence of the instability of the vacuum in strong gravitational elds, they are sources of quantum radiation [46]. String theory and loop quantum gravity, lately, showed that the origin of the black hole thermodynamics must be related with the quantum structure of the spacetime, bringing together the developments in black hole physics and the improvement of our understanding on the nature of the spacetime in quantum gravity regime [7, 8]. In this way, it is believed that black holes may play a major role in our attempts to shed some light on the quantum nature of the spacetime such as the role played by atoms in the early development of quantum mechanics.

2012 Silva, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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However the understanding of black hole thermodynamics in the semiclassical and furthermore in quantum regime has been a very difcult, and still unsolved problem. To explain the situation, it is known that, in statistical physics, entropy counts the number of accessible microstates that a system can occupy, where all states are presumed to occur with equal externally observable classical parameters: mass, electric charge, and angular momentum. All other information about the matter which formed a black hole disappears behind its event horizon, and therefore the nature of these microstates is obscure. Thus, the origin of the black hole entropy is not clear. Furthermore, in order to justify the name entropy, one must to explain also why the sum of the entropy of a black hole and the entropy of its vicinity is a non-decreasing function of time. In other words, why black holes obey the so called Generalized Second Law of thermodynamics (GSL). The situation becomes even worse if black hole evaporation is considered. Since black holes evaporate, one could expect, from black hole radiation, any information about the state which collapsed into the black hole. However, Hawking showed, through semiclassical arguments, that black hole radiation is thermal, and therefore does not carry any information about its initial state. In this situation, the matter that formed the black hole, which initially was in a pure state has evolved into a mixed state. This fact bring us a contradiction with quantum mechanics, where a pure state can only evolve into another pure state because of the unitarity of the evolution operator [4, 5, 9, 10]. In this context, a new phenomenon arises as one way to solve the drawbacks between black hole physics and quantum mechanics. This phenomenon is related with quantum gravity, and consists in a topology change of the spacetime, where a new topologically disconnected region arises inside the black hole, and information can be stored and preserved there. This scenario can be produced by the gravitational collapse, which would lead to a region of Planckian densities and curvature where quantum gravitational effects becomes important. Topology change must occur deep inside the black hole horizon, in a way that, it is entirely invisible to observers outside the black hole, which see the usual Hawking evaporation. In this situation, a complete state specication of the (now topologically non-trivial) universe requires a wavefunction which has a component on the new topologically disconnected region too. In this way, observers without access to this new region, have incomplete information about the universe as a whole. In this chapter, the black hole thermodynamics will be addressed in the context of topology change, as conceived for some classes of quantum spaces, called fuzzy spheres. It will be argued that a model based on the topology change of these fuzzy manifolds can be used to shed some light on the origin of the black hole entropy, including why black hole evaporation process obeys the GSL. In this sense, the selection rules will be addressed for the black hole area transitions in a black hole evaporation process driven by topology change. Moreover, the information loss problem will be discussed, including the possibility of some information about the black hole initial state could be recovered by an observer in our universe, where one can perform measures. This chapter is organized as follows. In the second section, the black hole thermodynamics will be addressed, introducing the laws of black hole mechanics and the Hawking effect. In the third section, the fuzzy sphere model and the topology change process for fuzzy spaces will be addressed. In the forth section, the relation between fuzzy spaces topology change and black hole thermodynamics will be addressed, where the selection rules for the black hole area

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transitions in the evaporation process are obtained. In the fth section, it will be investigated the obedience to GSL by the black hole evaporation in the fuzzy topology change approach. The sixth section is devoted to conclusions.

2. Black hole thermodynamics

Over the last forty years, black holes have been shown to have a number of surprising properties. These discoveries have revealed unforeseen relations between the otherwise distinct areas of general relativity, quantum physics and statistical mechanics. This interplay, in turn, led to a number of deep puzzles at the very foundations of physics. Some have been resolved while others remain open. The starting point of these fascinating developments remounts to the early 1970s, where a set of relations among neighboring black hole solutions were found, culminating in Bardeen, Carter, and Hawkings Four Laws of Black Hole Mechanics [11]. These laws dictate the behavior of black holes in equilibrium, under small perturbations away from equilibrium, and in fully dynamical situations. While they are consequences of classical general relativity alone, they have a close similarity with the laws of thermodynamics. The origin of this seemingly strange coincidence lies in quantum physics.

2.1. The laws of black hole mechanics

1 - (Zeroth law) If the energy-momentum tensor T obeys the dominant energy condition, then the surface gravity is constant on the future event horizon H + . Although the surface gravity is dened locally on the horizon, it turns out that it is always constant over the horizon of a stationary black hole. This constancy is reminiscent of the Zeroth Law of Thermodynamics which states that the temperature is uniform everywhere in a system in thermal equilibrium. The zeroth law of black hole mechanics can be proved without eld equations or energy conditions [1215] assuming that the horizon is a Killing horizon (i.e. there is a Killing eld tangent to the null generators of the horizon) and that the black hole is either (i) static (i.e. stationary and time reection symmetric) or (ii) axisymmetric and t reection symmetric. Alternatively it can be proved (Hawking) assuming only stationarity together with Einsteins eld equations with the dominant energy condition for matter [16, 17]. 1 2 - (First law) If a stationary black hole of mass M, charge Q and angular momentum J, with future event horizon of surface gravity , electric potential H and angular velocity H , is perturbed such that it settles down to another black hole with mass M + dM, charge Q + dQ and angular momentum J + dJ, then, dM = dA + H dJ + H dQ . 8 (1)

The rst law relates nearby stationary black hole solutions of the Einsteins equation, and has been derived in many ways. If stationary matter (other than the electromagnetic eld) is present outside the black hole, then there are additional matter terms on the right hand side of the equation (1). The surface gravity evidently plays the hole of temperature. Although the quantities , H , and H are all dened locally on the horizon, they are always constant
1

Assuming also hyperbolic eld equations for matter, and analyticity of the spacetime, Hawking also shows that the event horizon must be a Killing horizon, and that the spacetime must be either static or axisymmetric.

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over the horizon of a stationary black hole (modulo some assumptions; see for example the assumptions above for ). 3 - (Second law) If T satises the weak energy condition, and assuming that the cosmic censorship hypothesis is true then the area of the future event horizon of an asymptotically at spacetime is a non-decreasing function of time: A 0 . (2)

4 - (Third law) It is impossible by any procedure to reduce the surface gravity to zero in a nite number of steps. 2 Bardeen, Carter, and Hawking noted that these laws closely parallel the ordinary laws of thermodynamics, with the horizon area playing the role of entropy and the surface gravity playing the role of temperature. But can one truly considers that this analogy is something more than a mere formal coincidence? The physical temperature of a black hole in classical general relativity is absolute zero. The existence of the event horizon prevents the black hole to emit anything, and it can be regarded as a perfect absorber, with absolute zero temperature. In this way, the identication of the surface gravity of a black hole with a temperature, in the context of the classical theory, is completely non-physical, and so the identication of the event horizon area with an entropy. This was the general view of most physicists before the discovery of the Hawking effect. The most notable exception was Bekenstein, who put forward the idea of a real physical connection between entropy and area of the event horizon, even before the work of Hawking. He also suggested a generalized second law for black holes: Generalized Second Law (GSL) : The sum of the black holes entropy and the entropy of matter outside black holes would never decrease" 1 Sout + (3) A 0. 8 The existence of black holes is not compatible with the ordinary second law of thermodynamics. If matter can fall into a black hole and disappear, the entropy of matter for the external observer decreases. However, the area of the event horizon increases. Bekenstein suggested that the generalized entropy S = Sout + A/8 does not decrease. A more detailed inspection of this suggestion shows that it is not consistent. One can considers a black hole immersed in a thermal bath at a temperature lower that c2 /G. Since the black hole will absorb part of the radiation without emitting anything, one has a heat ow from a cold thermal radiation to a hotter" black hole. This would disagree with the generalized second law because the loss of entropy from the thermal radiation would be greater than the increase in black hole entropy. An additional physical input is required to pass from a formal to a physical analogy. Some insights can be gained analyzing the dimension of the constant . A simple look unravels that, since S has the dimension of Boltzmanns constant k B . In this way, k B must
2

As in ordinary thermodynamics, there are a number of formulations of the third law, which are not strictly equivalent. The version given here is analogous to the Nernst form of the third law of thermodynamics.

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have dimensions of length squared. With the physical constants that one has in classical general relativity (i.e., Newtons constant G and the velocity of light c) it is not possible to form a constant (to be identied with k B ) with dimensions of length squared. The Plancks constant is necessary for that. From G, c and , one can form the Planck length lP = G . c3 (4)

2 With this fundamental length available (k B l P ), one can go further in the analogy and write

kB c

k B c3 A. G

(5)

The lesson of this brief discussion is that the input required to properly establish a physical analogy between black holes and thermodynamics involves considering quantum effects. This will be the topic of the next section.

2.2. The Hawking effect

In 1974, Hawking demonstrated that all black holes emit blackbody radiation [4]. The original derivation of the Hawking effect made direct use of the formalism for calculating particle creation in a curved spacetime. Hawking considered a classical spacetime describing gravitational collapse to a Schwarzschild black hole. A free (i.e., linear) quantum eld propagating in this background spacetime was considered, which is initially in its vacuum state prior to the collapse, and the particle content of the eld at innity at late times was computed. This calculation involves taking the positive frequency mode function corresponding to a particle state at late times, propagating it backwards in time, and determining its positive and negative frequency parts in the asymptotic past. Hawkings calculation revealed that at late times, the expected number of particles at innity corresponds to emission from a perfect black body (of nite size)

N
at the Hawking temperature

( + )

e2/ 1

(6)

, (7) 2k B where is a scattering coefcient sometimes called the gray-body factor since it indicates the emissivity of the black hole which is not that of a perfect blackbody. T=

It should be noted that this result relies only on the analysis of quantum elds in the region exterior to the black hole, and it does not make use of any gravitational eld equations. In this way, Hawkings calculation has two main ingredients: the rst is that the quantum mechanical vacuum is lled with virtual particle-antiparticle pairs that uctuate briey into and out of existence. Energy is conserved, so one member of each pair must have negative energy. 3 Normally, negative energy is forbidden - in a stable quantum eld theory, the vacuum must
3

To avoid a common confusion, note that either the particle or the antiparticle can be the negative-energy partner.

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be the lowest energy state - but energy has a quantum mechanical uncertainty of order /t, so a virtual pair of energy E can exist for a time of order /E. The second ingredient is the observation that, in general relativity, energy - and, in particular, the sign of energy - can be frame dependent. The easiest way to see this is to note that the Hamiltonian is the generator of time translations, and thus depends on ones choice of a time coordinate. 4 In this way, one can conclude that a black hole may radiate its energy at a temperature given by equation (7). This result makes the relation between the laws of black hole mechanics and the laws of thermodynamics to be more than a mere analogy. From the results above, one can attribute an entropy to black hole which is given by: S BH = A . 2 4l P (8)

Another interesting result is a consequence of the Stephan law. For a black hole with a horizon area A: dE 4 ATH , (9) dt where = 2 k4 /60 3 c2 . B Moreover, from the fact that E = Mc2 , and, for a Schwarzchild black hole: A = 4 another result is that MG c2
2

k B TH

c3 , GM

(10)

(11)

dE c4 2 2 . dt G M In this way, a Schwarzchild black hole possess a nite lifetime which is given by: G2 M3 . c4

(12)

(13)

One must therefore be careful about what one means by positive and negative energy for a virtual pair. In particular, consider the Schwarzschild scenario. Outside the event horizon, t is the usual time coordinate, measuring the proper time of an observer at innity. Inside the horizon, though, components of the metric change sign, and r becomes a time coordinate, while t becomes a spatial coordinate: an observer moving forward in time is one moving in the direction of decreasing r, and not necessarily increasing t. Hence an ingoing virtual particle that has negative energy relative to an external observer may have positive energy relative to an observer inside the horizon. The uncertainty principle can thus be circumvented: if the negative-energy member of a virtual pair crosses the horizon, it need no longer vanish in a time /E, and its positive-energy partner may escape to innity [18].

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3. Open questions
The results described in the previous sections provide a remarkably compelling case that stationary black holes are localized thermal equilibrium states of the quantum gravitational eld, and that the laws of black hole mechanics are simply the ordinary laws of thermodynamics applied to a system containing a black hole. Although no results on black hole thermodynamics have been subject to any experimental or observational tests, the theoretical foundation of black hole thermodynamics appears to be sufciently rm to provide a solid basis for further research and speculation on the nature of quantum gravitational phenomena. In this section, it will be briey discussed two key unresolved issues in black hole thermodynamics which may shed considerable further light upon quantum gravitational physics.

3.1. The origin of black hole entropy

From the results above, it is clear that black holes are really thermodynamical systems with an actual temperature and entropy. What remains to be understood is the meaning of this entropy in terms of statistical mechanics. It is known that in statistical physics, entropy counts the number of accessible microstates that a system can occupy, where all states are presumed to occur with equal probability. In the thermodynamical description, entropy S is related to the number of all consistent microscopic states N as S = k B lnN . (14) In analogy, it is expected that there might be a microscopic description of the black hole thermodynamics, too. However, it is also known that black holes can be completely characterized by only three externally observable classical parameters: mass, electric charge, and angular momentum. All other information about the matter which formed a black hole disappears behind its event horizon, and therefore the nature of these microstates is obscure. Then, what is the origin of the black hole entropy? It is widely believed that the black hole entropy might be related to a number of microscopic states. Since the microscopic description seems to require a quantum theory of gravity, detailed investigations of the black hole entropy should contribute a lot toward construction of the theory of quantum gravity. This is one among the several reasons why the origin of the black hole entropy needs to be understood at the fundamental level. Another question is related with GSL. In order to justify the name entropy, one must to explain also why S = Sbh + Sout is a non-decreasing function of time, in other words, why black holes obey a GSL. A strong motivation to investigate the black hole entropy is the so-called information loss problem, which will be addressed in the next section.

3.2. The information loss problem

Black holes can be completely characterized by only three externally observable classical parameters: mass, electric charge, and angular momentum. All other information about the matter which formed a black hole disappears behind the black hole event horizon, and therefore the nature of these microstates is obscure. Since black holes evaporate, one could

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expect, from the Hawking radiation, any information about the state which collapsed into the black hole. However, Hawking showed that this radiation is thermal, and therefore does not carry any information about the black hole initial state. That is to say, no information can escape from inside of the black hole horizon. In this situation, the matter that formed the black hole, which initially was in a pure state has evolved into a mixed state. But, it contradict our basic knowledge about quantum mechanics. There, a pure state can only evolve into another pure state because of the unitarity of the evolution operator U (U U = 1). This problem is known as the black hole information loss paradox. Some possibilities to solve this paradox have already been proposed. possibilities, one has Among these

i - The evolution is indeed non-unitary and the basics concepts of quantum mechanics must be revised [5, 19]. However, these proposal has difculties related with violation of energy conservation and the absence of an empty vacuum as the ground state [2023]. ii - The black hole radiation is not thermal and carries information. The problem is that a new physics is necessary, which is radically different from the one is known: concepts as locality and causality must be left, since matter behind the horizon has to inuence matter outside the horizon [2426]. iii - The information is stored in a stable black hole remnant [27]. The main problem with remnants is that, since the initial black hole could have been arbitrarily massive, the remnant must be capable of carrying an arbitrarily large amount of information (about M2 /M2 Planck bits, if the initial mass was M). This means that there must be an innite number of species of stable remnants, all with mass comparable to M Planck . Black hole remnants have appeared in several noncommutative approaches of black holes, including one where the fuzzy sphere model is used [2830]. iv - Information could be stored in a topological disconnected region which arises inside of the black hole [31]. Gravitational collapse leads to a region of Planckian densities and curvature where quantum gravitational effects can lead to a topology change process where a new topologically disconnected region (a baby universe) appears. Information about the black hole initial state can be stored there. It is possible, but not necessary, that information returns via quantum gravity tunneling after some long timescale. In this point, the baby universe ceases to exist, and the black hole evolution as seen by an observer outside the black hole is unitary. Topology change had been claim to be non-unitary and therefore to suffer from the same problems of the rst proposal. The other objection against topology change is the violation of cluster decomposition(locality) [31, 32]. In this chapter, the topology change approach will be addressed. The main idea present here is to see the black hole event horizon as a fuzzy sphere, and using its known quantum symmetries properties, nd out a topology change process to black holes, which is free of the problems related with unitarity and locality. If this is possible, a solution to the information loss paradox will be gotten. Moreover, this model, based on the topology change of a quantum manifold, is used to explain the origin of the black hole thermodynamics. It will be argued that this model can explain the origin of the black hole entropy, and why black holes obey a generalized second law of thermodynamics. In the following sections, all fundamental constants will be considered equals to one

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4. Fuzzy spaces topology change and black hole thermodynamics

4.1. The fuzzy sphere model
Fuzzy spheres consist in one of the most simplest example of noncommutative spaces and appear as vacuum solutions in Euclidean gravity [3335]. It is obtained when one quantizes the usual sphere S2 replacing the commutative algebra of functions on this manifold by the noncommutative algebra of matrices. It is known that any function dened on the usual sphere can be expanded in terms of the spherical harmonics Ylm as f ( x ) | S2 =
l =0 m= l

clm Ylm ( x ) ,

(15)

where clm are complex coefcients, and the product of these functions is commutative. The introduction of the noncommutative geometry is performed as one quantizes the coordinates x ( = 1, 2, 3) on S2 , through the transformation x x = J , with x x = r2 1 , (16) (17)

where J form the n-dimensional irreducible representation of the SU (2) algebra, whereas r is the fuzzy sphere radius, and r . (18) = N2 1 In this way, the coordinates on the fuzzy sphere S2 satisfy the following commutation relations F

[ x , x ] = i 1 x , /r

(19)

where has a dimension of / and plays here a role analogous to that played by Plancks constant in quantum mechanics. The fact that the coordinates x do not commute anymore implies that the points on the sphere are smeared out, and one has to substitute the idea of points for the idea of elementary (Planck) cells. A consequence of the process above is the introduction of a cutoff N on the expansion (15), in a way that it becomes f ( x ) | S2 =
F

(length)2 ,

l =0 m= l

clm Ylm ( x ) ,

(20)

In the context of black hole physics, the use of fuzzy spheres is mostly motivated by the Bekensteins limit [6], which says that the black hole entropy is nite and proportional to the event horizon area. Since fuzzy spheres, are obtained from quantization of a compact space, they are described by nite dimensional matrices, in a way that the number of independent states dened on the fuzzy sphere is limited, and the entropy associated with these states is nite, in agreement with the Bekensteins limit [28, 34, 3639].

where now Ylm ( x ) are matrices. In this way the function f ( x ) is replaced by a matrix ( N + 1) ( N + 1) in a way that its product becomes noncommutative. The commutative limit is given by 0 or N . /

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4.2. Fuzzy spheres and Hopf algebras

Another important feature of fuzzy spheres is its close relationship with Hopf algebras, which allow us to dene a linear operation (the coproduct of a Hopf algebra) on S2 and compose F two fuzzy spheres preserving algebraic properties intact. This operation produces a topology change process where a fuzzy sphere splits into two others [40], and can be used as a good mathematical model to black hole topology change [36, 37]. In order to dene a Hopf algebra, one has that a bi-algebra is a vector space A over a eld of scalars F which is both an algebra and a coalgebra in a compatible way. The algebra structure is given by F-linear maps m : A A A (the product) and : F A (the unit map), where xy : = m( x, y) and (1) = 1A. The coalgebra structure is likewise given by linear maps : A A A (the coproduct) and : A F (the counit map). One writes : A A, or sometimes A , to denote the identity map on A. The required properties are Associativity: m(m ) = m( m) : A A A A; Unity: m( ) = m( ) = : A A; Coassociativity: ( ) = ( ) : A A A A; Counity: ( ) = ( ) = : A A; A Hopf algebra is dened as a bi-algebra H together with a (necessarily unique) convolution inverse S for the identity map = H ; the map S is called the antipode of H. Fuzzy spaces possess quantum groups properties related with a Hopf algebra [40].5 To describe the fuzzy sphere topology change, one has that under the quantization procedure (16), functions dened on S2 are replaced by matrices on S2 [33]. In this way, let a matrix M F describing a wave function on S2 , the Hopf coproduct : S2 ( j) S2 (K ) S2 ( L ) acts on M F F F F as ( K,L) ( M ) =
1 ,2 ,m1 ,m2

CK,L,J;1,2 CK,L,J;m1,m2

(21)

M1 +2 ,m1 +m2 e1 m1 (K ) e2 m2 ( L ) ,
where Cs are the Clebsh-Gordan coefcients and ei m j s are basis for a matrix space dened on the fuzzy sphere [40]. The coproduct has the following properties: ( K,L) ( M ) = ( K,L) ( M ) , (22) ( K,L) ( MN ) = ( K,L) ( M ) ( K,L) ( N ) , (23) Tr ( K,L) ( M ) = Tr ( M ) ,
5

Actually, fuzzy spaces possess algebraic properties more general than a Hopf algebra. It is due to the fact that a coproduct of two different algebras is possible, whereas in an ordinary Hopf algebra only the coproduct of an algebra by itself is possible.

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Fuzzy Spheres Decays and Black Hole Thermodynamics 511 11

and

In this way, the coproduct preserves the Hermitian conjugation, the matrix product, the matrix trace, and the matrix inner product. These properties of the coproduct assure that (21) is a unitary process, and preserves the algebraic properties of the operators dened on the fuzzy sphere [36, 37, 40].

( K,L) ( M ), ( K,L)( N ) = M, N

(24)

4.3. Fuzzy spaces topology change and black hole thermodynamics

The basic assumptions in this chapter stay in the meaning of the eq. (21). This equation says that a wavefunction M S2 ( J ) splits into a superposition of wavefunctions on S2 (K ) S2 ( L ). F F F In this way, the information in M is divided between two regions of the spacetime, i.e, the two fuzzy spheres with spins K and L respectively. The following consequences are imminent: (i) If one use the fuzzy sphere Hilbert space as the ones of the black hole, the maximum of information about the black hole that an outside observer can obtain would be encoded in wave functions dened on the fuzzy sphere Hilbert space. (ii) One will nd out, through the Hopf coproduct , a topology change process for the black hole. In this process the information about the black hole initial state, will be divided into two spacetime regions. One of them is a fuzzy sphere with spin K, which will be considered as the original world and name it the main world. The other one is a fuzzy sphere with spin L which will be named the baby world. (iii) The process is unitary, in this way there is no information loss. However, since the baby world arises in the black hole interior, an observer in the main world can not access the degrees of freedom there. In this way, from his standpoint, the black hole will appear to evolve from a pure to a mixed state described by a density matrix . It enable us to dene an entropy, measured by the observer in the main world, associated to the black hole horizon. Now, in order to analyze how the topology change process drives the black hole evaporation, it will be necessary to investigate how the fuzzy topology change drives the black hole area transitions. It will be admitted that the selection rules for the black hole area transitions are the ones for the topology change. These rules are obtained from the eq. (21), when one traces over the degrees of freedom in the baby universe.
The splitting process (21) for a matrix M = | J, m J, m | with L = 1/2, and K = J 1/2 is given by:

(| J, m J, m |)

( K + mK +1)( K + mK +1) 2K +1

| K, m 1/2K, m 1/2 | | K, m + 1/2K, m + 1/2 | .

( K mK +1)( K mK +1) 2K +1

(25)

In that point, it still necessary to ensure that the splitting process above can be performed repeatedly, under identical circumstances, with statistically independent results to outside observers in different regions of spacetime. That is to say, it is necessary to ensure that locality

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is preserved in this process. In ordinary quantum eld theory these requirements are insured by the Cluster Decomposition Theorem. Cluster decomposition theorem The vacuum expectation value of a product of many operators - each of them being either in different regions A and B, where A and B are very separated - asymptotically equals to the expectation value of the product of the operators in A, times a similar factor from the region B. Consequently, sufciently separated regions behave independently. If A1 , ..., An are n operators each localized in a bounded region and one picks some subset of the n operators to translate xi into x i = xi + a,

lim M0 , A1 ( x1 ) A2 ( x2 ), ..., A j1 ( x j1 ) A j ( x ), ...An ( xn ), M0 j

(26)

= M0 , A1 ( x1 ) A2 ( x2 ), ..., A j1 ( x j1 ), M0
M0 , A j ( x j ), ...An ( xn ), M0 ,

where M0 represents the vacuum state. If one admits that (26) is valid for an outside observer is easy to see, from Eq. (24) that

lim ( M0 ), ( A1 ( x1 )) ( A2 ( x2 )), ..., ( A j1 ( x j1 )) ( A j ( x )), ..., ( An ( xn )), ( M0 ) j

= ( M0 ), ( A1 ( x1 )) ( A2 ( x2 )), ..., ( A j1 ( x j1 )), ( M0 )

( M0 ), ( A j ( x j )), ..., ( An ( xn )), ( M0 ) ,

(27)

where ( A j ( x j )) and ( A j ( x )) represent the splitting process in different points of spacetime. j The splitting process, then, occurs in a way that cluster decomposition is preserved and locality is not violated. From the equation (25), and from the fact that the splitting process (21) obeys cluster decomposition, in a way that different steps J J 1/2, in the black hole evaporation, are independent events, the probability amplitude for a n-steps transition is given by a Jn = 2J + 1 . 2J n + 1 (28)

Now, in order to analyze the black hole area transitions, it will be introduced a canonical ensemble in which our system (the BH) can occupy different area microstates. The idea of using these types of ensembles goes back to Krasnov [4143] and is, somehow, a necessity in the Loop Quantum Gravity formalism as the count of states is naturally done by using the horizon area instead of BH mass [44, 45]. In this framework, the probability amplitude for the BH evaporate is given by (29) a Jn = e A Jn , where is a temperature-like parameter dual to the black hole area [4648]. The probability amplitude (28) will be identied with (29), in a way that the value of the black hole area in the J-state will be written as A J = 1 ln(2J + 1) . (30)

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Fuzzy Spheres Decays and Black Hole Thermodynamics 513 13

Moreover, the density matrix describing the black hole quantum states can be written as = (1/Z )
Dim ( S2 ) F J =0

e A J | J J |= (1/Z )e A ,

(31)

where Z = Tre A is the partition function. The matrix in the eq. (31) satisfy the Bloch equation i where has been replaced by i/8. A = , 8 (32)

The equation (32) will govern the transitions between black hole area states. It must be used when working in the Euclidean continuation of the black hole, supplementing the Wheeler-DeWitt equation, where plays the role of a sort of dimensionless internal time associated with the horizon [4648]. Moreover, = i E , where E is the Euclidian angle. Regularity of the Euclidean manifold at the horizon imposes a xed Euclidean angle given by E = 2. In this way, at the horizon = 1/4. From the equation (30), and the results above, the entropy S = Tr (ln ) = ln (2J + 1), associated for an outside observer to black hole is given by S= A , 4 (33)

which corresponds to the Bekenstein-Hawking formula. The logarithmic dependence of the black hole area spectrum on J, in the expression (30), tell us that the decrease in the horizon area is continuous at large values of J, and discrete to small values of J, when the black hole approaches the Planck scale. The black hole area spectrum is showed in the gure (1).
BH Area 15

10

Figure 1. The black hole area spectrum for topology change approach

In this way, if one models a black hole horizon by a fuzzy sphere and consider its quantum symmetry properties, a topological change process which can be used to solve the black hole

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information loss paradox is obtained. In this process a black hole event horizon, modeled by a fuzzy sphere with spin J , splits into two others. The fuzzy sphere splitting can be used to describe a black hole evaporation process in which information about the black hole initial state is divided between two topologically disconnected regions: the main and the baby world. Nor unitarity or locality is broken in the evolution of the whole system. On the other hand, an observer in the main world sees the topology change process occurs in a non-unitary way, due to the impossibility of access the degrees of freedom in the baby world. It is possible, but not necessary, that information returns via quantum gravity tunneling at the nal stages of black hole evaporation. In this point, the baby universe ceases to exist, and the black hole evolution as seen by an observer outside the black hole is unitary. In the next section it will seen how the selection rules, inherited from the topology change process, will bring essential consequences to the way how entropy is emitted by black holes. One has that Hawkings radiation is known semi-classically to be continuous. However, the Hawking quanta of energy are not able to hover at a xed distance from the horizon since the geometry of the horizon has to uctuate, once quantum gravitational effects are included. Thus, one suspects a modication of the black hole radiation when quantum geometrical effects are taken into account. As will be seen in the next section, a possible modication on the description of the black hole emission process occurs at the nal stages of black hole evaporation, where its area spectrum becomes discrete.

4.4. Entropy emitted during the evaporation process

It is known that the entropy of a system measures ones lack of information about its actual internal conguration. Suppose that everything one knows about the internal conguration of the system is that it may be found in any of a number of states, with probability pn for the nth state. Then the entropy associated with the system is given by Shannons well-known relation S = pn lnpn [4952].

The probability for a black hole to emit a specic quantum should be given by the expression (28), in which one must yet include a gray-body factor (representing a scattering of the quantum off the spacetime curvature surround the black hole). Thus, the probability pn to the black hole goes n steps down in the area ladder is proportional to (n ) e 4 . Moreover, the discrete area spectrum (30) implies a discrete line emission from a quantum black hole. To gain some insight into the physical problem, it will be considered a simple toy model suggested by Hod [53, 54]. To begin with, it is well known that, for massless elds, ( M ) approaches 0 in the low-frequency limit, and has a high-frequency limit of 1. A rough approximation of this effect can be archived by introducing a low frequency cutoff at some = c [55]. That is, ( ) = 0 for < c , and ( ) = 1 otherwise, where = M [5658]. The ratio R =| Srad /S BH | of entropy emission rate from the quantum black hole to the rate of black hole entropy decrease is given by:
s i=1 n=1 C (n )e A Jn

2J

A Jn 4

R=

ln C (n )e
A Jn 4

A Jn 4

s i=1 n=1 C (n )e

2J

A Jn 4

(34)

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Fuzzy Spheres Decays and Black Hole Thermodynamics 515 15

where C is a normalization factor, dened by the normalization condition:

i =1 n =1

C(n)e

Ns 2J

A Jn 4

=1 .

(35)

For the effective number of particle species emitted ( Ns ), it will be taken into account the various massless modes emitted. Here, Ns will be considered as Ns = 2J + 1 for 2J + 1 < 112 , 112 for 2J + 1 112 .

In this way Ns is upper limited by the number of modes of massless particles in nature which make the dominant contribution to the black-hole spectrum (the 1/2, 3/2, 5/2 neutrino modes, the 1 and 2 photon modes, and the 2 and 3 graviton modes [53, 54, 5658]), and by the size of the fuzzy sphere Hilbert space. In the gure (2), R has been plotted down taking c 0.2 (the location of the peak in the total power spectrum [5658]). With this frequency cutoff, the minimal non-null value to the quantum number J, in order to have = 0, is J = 6.0. In this point, the black hole must evaporate completely. From the graphic for R, one has that the non-unitary evolution of the black hole geometry in the main world, due to the topology change process, imposes obedience to a second law of thermodynamics on the black hole evolution process, since R is ever larger than (or equal) to unity. The value of R approaches the value of 1.3 at the large J limit in agreement with known Zureks semiclassical results [55]
R 1.2 1.0 0.8 0.6 0.4 0.2 J

500

1000

1500

Figure 2. The ratio of entropy emission rate from the quantum black hole to the rate of black hole entropy decrease.

It is important to notice that the entropy emitted from the black hole decreases as the area spacing increases. The entropy of the radiation should be maximal in the semiclassical limit where the black hole can be in any area state, and the various transitions have almost the same probabilities. On the other hand, in the quantum limit, only special values are allowed to the black hole area, and then only special transitions are allowed. In this way, the entropy of the radiation emitted by the black hole becomes smaller. The striking consequence of this

516 16 Thermodynamics Fundamentals and Its Application in Science

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is the possibility that, since the black hole radiation becomes less and less entropic as the evaporation process takes place, some information about the black hole initial state could leak out from its interior and be accessible to an observer in our universe, where measures can be performed. The possibility of information leakage from a black hole with a discrete area spectrum is already pointed out by Hod [53, 54]

5. Remarks and conclusions

It has been argued that a model based on the topology change of a quantum manifold can be used to shed some light on the problems of the origin of black hole entropy and information loss. In this approach, black hole entropy is generated because of the non-unitary evolutions of the main world geometry due to the topology change process in black hole interior. To do this, the process of emission of quanta of radiation by black holes has been putted in connection with topology changes in the quantum manifold which is assumed to describe the horizon (the fuzzy sphere). Nor unitarity or locality is broken in the evolution of the whole system in topology change approach in a way that no information is lost. Moreover, from the topology change model, the selection rules for the black hole area transitions have been obtained. In this way, an expression for the probability amplitudes of black hole transitions has been derived. From them, an understanding of the Bekenstein-Hawking formula for black hole entropy is provided. The topology change approach gives us a relation of states to points that brings together the black hole entropy and our standard concept of entropy as the logarithm of the number of microstates. Through the study of the black hole evaporation process, an area spectrum, which is continuous in the semiclassical limit, and becomes discrete as the black hole approaches the Planck scale has been obtained. In order to investigate the inuences of the area spectrum shape to the black hole emission, the ratio R between the rates of entropy emission and black hole entropy decrease has been calculated. At rst, R is found to be larger than 1, showing that the considered mechanism is able to produce a generalized second law. Then, R approach 1 as the black hole shrinks to the Planck scale, and the area spectrum becomes discrete. These results point to a possible information leak out from black hole, since its radiation becomes less and less entropic as the black hole evaporates, and could alleviate the information problem for an observer outside the black hole. Since the possible information leakage would occurs more strongly in the quantum gravity limit, it would not require radical modications in the laws of physics above the Planck scale. The task of found an appropriate quantum mechanism for information leakage remains.

Acknowledgements
The author thanks to Instituto Federal de Educao, Cincia e Tecnologia da Paraba - Campus Campina Grande, for the nancial support.

Author details
C.A.S.Silva Instituto Federal de Educao Cincia e, Tecnologia da Paraba, Campus Campina Grande, Rua Tranquilino Coelho Lemos, 671, Jardim Dinamrica I, Campina Grande, Paraba, Brazil

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Fuzzy Spheres Decays and Black Hole Thermodynamics 517 17

6. References
[1] I.D. Barrow, I. Silk, The left hand of creation, Basic Books, Nova York (1983). [2] W. Israel, 300 years of gravity (S.W. Hawking e W. Israel), Cambridge Univ. Press, Cambridge (1983), p. 199. [3] I.D. Novikov, Black holes and the universe, Cambridge Univ. Press, Cambridge (1990). [4] S.W. Hawking, Commun.Math.Phys. 43 (1975) 199. [5] S.W. Hawking, Phys.Rev.D 14 (1976) 2460. [6] J.D. Bekenstein, Lett. Nuovo Cim. 4 (1972) 737. [7] A. Strominger and C. Vafa, Phys. Lett. B 379 (1996) 99. [8] A. Ashtekar, J. Baez, A. Corichi, and K. Krasnov, Phys. Rev. Lett. 80, (1998) 904. [9] J. Preskill, hepth/9209058 preprint (1992). [10] D.N. Page, hepth/9305040 preprint (1993). [11] J. M. Bardeen, B. Carter and S. W. Hawking, Commun. Math. Phys. 31 (1973) 161. [12] B. Carter, Phys. Rev. Lett. 26, (1971) 331 [13] B. Carter, Black hole equilibrium states, in Black Holes, eds. C. DeWitt and B.S. DeWitt, Gordon and Breach, (1973) [14] B. Carter, Overview: stationary and static equilibrium, in Gravitation and Astrophysics, Plenum Press (1987). [15] I. Rcz and R.M. Wald, gr-qc/9507055 (1995). [16] S.W. Hawking, Commun. Math. Phys. 25, 152 (1972). [17] S.W. Hawking and G.F.R. Ellis, The Large Scale Structure of Spacetime, Cambridge University Press, (1973). [18] S. Carlip, Physics of black hole: a guided tour, ed. E. Papantonopoulos Springer, (2009), 89. [19] S.W. Hawking, Commun. Math. Phys. 87 (1982) 395. [20] D.J. Gross, Nucl. Phys. B 236 (1984) 349. [21] J.R. Ellis, J.S. Hagelin, D.V. Nanopoulos, M. Srednicki, Nucl. Phys. B 241 (1984) 381. [22] T. Banks, L. Susskind, M.E. Peskin, Nucl. Phys. B 244 (1984) 125. [23] A. Strominger, hep-th/9410187 (1994). [24] D.N. Page, Phys. Rev. Lett. 44 (1980) 301. [25] G.t Hooft, Nucl. Phys. B 256 (1985) 727. [26] S.B. Giddings, Mod. Phys. Lett. A 22 (2007) 2949. [27] Y. Aharonov, A. Casher, S. Nussinov, Phys. Lett. B 191 (1987) 51. [28] B.P. Dolan, JHEP 0502 (2005) 008. [29] P. Nicolini, hep-th/08071939 (2008). [30] K. Nozari, S. Hamid Mehdipour, Class. Quantum Grav. 25 (2008) 175015. [31] S.D.H. Hsu, Phys.Lett.B 664 (2007) 67. [32] L. Susskind, hep-th/9405103 preprint (1994). [33] J. Madore, Class.Quant.Grav. 9 (1992) 69. [34] M. M. Sheikh-Jabbari, Phys. Lett. B 642 (2006) 119. [35] Y. Abe and V. P. Nair Phys. Rev. D 68 (2003) 025002 [36] C.A.S. Silva, Phys.Lett.B 677 (2009) 318. [37] C.A.S. Silva, R.R. Landim, Europhys. Lett. 96 (2011) 10007. [38] G. t Hooft, Class. Quant. Grav. 13 (1996) 1023. [39] P.A. Zizzi, Mod. Phys. Lett. A 20 (2005), 645. [40] A.P. Balachandran, S. Krko Int.J.Mod.Phys.A 19 (2004) 3395. glu, [41] K.V. Krasnov, Phys. Rev. D 55 (1997) 3505.

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[42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58]

K. V. Krasnov, Gen. Rel. Grav. 30 (1998) 53. K. V. Krasnov, Class. Quant. Grav. 16 (1999) 563. A. Ashtekar, J. C. Baez and K. Krasnov, Adv. Theor. Math. Phys. 4 (2000) 1. J. Fernando Barbero G. and E.J.S. Villasenor, gr-qc/1106.3179 preprint (2011). S. Massar, R. Parentani , Nucl.Phys.B 575 (2000) 333. M. Banados, C. Teitelboim, J. Zanelli, Phys.Rev.Lett. 72 (1994) 957. Steven Carlip, Claudio Teitelboim, Class.Quant.Grav. 12 (1995) 1699. C.E. Shannon and W. Weaver, The mathematical theory of communications, University of Illinois Press, Urbana (1949). E.T. Jaynes, Phys.Rev. 106 (1957) 620. E.T. Jaynes, Phys.Rev. 108 (1957) 171. J. D. Bekenstein, Phys. Rev. D 7 (1973) 2333. S. Hod, Phys.Rev.D 61 (2000) 124016. S. Hod, Phys. Lett. A 299, (2002) 144. W. H. Zurek, Phys. Rev. Lett. 49 (1982) 1683. D.N. Page, Phys.Rev.D 13 (1976) 198. D.N. Page, Phys.Rev.D 14 (1976) 3260. D.N. Page, Phys.Rev.D 16 (1977) 2402.

Chapter 21

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis

Hui-Zhen Fu and Yuh-Shan Ho
Additional information is available at the end of the chapter http://dx.doi.org/10.5772/48360

1. Introduction
Thermodynamics is the study of energy and its transformation (Holman, 1985). This subject has evolved since the beginning of the eighteenth century (Look & Saucer, 1982). Most studies of thermodynamics are primarily concerned with two forms of energy: heat and work (Holman, 1985; Keizer, 1985; Rosakis et al., 2000). Thermodynamics advanced dramatically in the 1960s and 1970s, primarily in the area of critical phenomena (Callen, 1985). In recent years, thermodynamic research has been conducted in more systems, such as corn-ethanol biofuel cycle (Patzek, 2004), lipid-peptide interactions (Seelig, 2004), DNA structural motifs (SantaLucia & Hicks, 2004), and glass-forming substances (Ngai, 2000). Bibliometrics, as a measure of scientific performance, has been widely applied to research evaluation for a long period (Saracevi & Perk, 1973; Luukkonen, 1990; Friedberg, 2000). It has been employed to evaluate various researches, for example biology (Sainte-Marie 2010), desalination research (Tanaka & Ho, 2011), solid waste research (Fu et al., 2010), acupuncture research (Han & Ho, 2011), and global climate change (Li et al., 2011). In exited bibliometric analyses, the analyzed aspects usually covering languages (Alfaraz & Calvino, 2004; Chiu & Ho, 2007; Ferrara, 2011), annual publication outputs (Chiu & Ho, 2007; Tsay, 2008), journals (Schubert et al., 1989; Tsay, 2008), categories (Moed et al., 1995; Yamazaki, 1994), and contributing countries and institutions (Schubert et al., 1989; Chiu & Ho, 2007; Tanaka & Ho, 2011; Li et al., 2011). In recent years, author keywords which could provide a reasonably detailed picture of the articles subject (Garfield, 1990), have been quantitatively analyzed to figure out the research emphases and trends (Chiu & Ho, 2007; Fu et al., 2010; Li
2012 Fu and Ho, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

520 Thermodynamics Fundamentals and Its Application in Science

et al., 2011). To analyze these aspects, the common evaluation indicators number of publications and their publication share were utilized (Schubert et al., 1989; Rehn et al., 2007). Impact factor was introduced by Garfield and Sher (1963) to help select additional source journals using the recent citations received from other journals, and has been also widely used to rank and evaluate journals (Garfield, 1996; Moed, 2002). In particular, the five indicators including total, independent, collaborative, first author, and corresponding author articles have been recently used to compare the publication performance of countries and institutions in the researched of Japanese lung cancer (Ho et al., 2010), solid waste research (Fu et al., 2010), desalination research (Tanaka & Ho, 2011), acupuncture research (Han & Ho, 2011), global climate change (Li et al., 2011), and estuary pollution (Sun et al., 2012). In addition, rankings are useful indicators, especially in terms of institutions and researchers in urgent demand by politics (Weingart, 2003). These indicators including number of publication, publication share, impact factor, rankings, and five newly indicators were utilized for the evaluation of thermodynamics research. The aim of this study was to systematically evaluate not only the publication characteristics of languages, annual publication outputs, journals and Web of Science categories, and national and inter-institutional contributors, but also the research emphases and trends by author keywords to obtain an overview of thermodynamic research during the period from 1991 to 2010.

2. Methodology
2.1. Data collection
Documents used in this study were derived from the Science Citation Index Expanded (SCIExpanded) database of the Web of Science, the Thomson Reuters. According to Journal Citation Reports (JCR), it indexes 8,073 journals with citation references across 174 scientific disciplines in 2010. The data was collected on November 20 in 2011, and the detail data collection process is illustrated in Fig. 1. Firstly, thermodynamics related keywords including thermodynamic, thermodynamics, free energy change, enthalpy change, and entropy change were searched in terms of topic (including four parts: title, abstract, author keywords, and KeyWords Plus) within the publication year limitation from 1991 to 2010 based on SCI-Expanded. Total 157,140 documents were therefore found out. However, these 157,140 documents contained the documents not closely relating to thermodynamics which was searched only in terms of KeyWords Plus which providing search terms extracted from the titles of papers cited in each new article listed in Current Contents (Garfield, 1990). To efficiently obtain the characteristics of thermodynamics, this study only focused on the documents (50,865) with searching keywords in front page which including three parts: title, abstract, and author keywords, while the documents where searching keywords only appeared in KeyWords Plus were excluded. These documents consists of 19 document types, where articles (41,245) dominants with a percentage of 81%, followed by proceedings paper (4,860; 10%), meeting abstract (1,787; 3.5%), and review (1,407; 2.8%).

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 521

Finally, the journal articles (41,245) were extracted from the 50,865 documents for subsequent analyses.
Topic = thermodynamic or thermodynamics or free energy change or enthalpy change or entropy change Lemmatization = off Year published = 1991-2010 thermodynamic, thermodynamics, free energy change, enthalpy change, and entropy change in front page (title, abstract, and author keywords) Document type = article

Web of Science SCI-Expanded

157140 documents

50865 documents 41245 articles

Figure 1. Data collection process for searching thermodynamic related research

2.2. Analyzing structure

The analyzing aspects were divided into five sections from different angles. To be specific, the analytic structure of analytic structure of bibliometric analysis of thermodynamic research is presented in Fig. 2. The first section dealt with the basic information covering the distribution of languages and annual production. The second section revealed the performance of productive journals and Web of Science categories. Then national contributors countries and institutional contributors institutions were analyzed in the following third and fourth sections. Finally, recent research emphases and trends were examined by the frequency of author keywords.

Figure 2. Analytic structure of bibliometric analysis of thermodynamic research

522 Thermodynamics Fundamentals and Its Application in Science

2.3. Indicators and acronyms

The indicators displayed in Fig. 2 for detail analysis are explained in Table 1. As for the section of national and institutional contributors, some newly indicators (CP, SP, FP, and RP) were employed to evaluate the performance of countries/territories and institutions. The institutions and countries/territories contributions were identified by the appearance of at least one author in the publications. Collaboration type was determined by the addresses of the authors. The articles were classified by four types for country/territory and institution. (1) The term single country article was assigned if the researchers addresses were from the same country. The term single institution article was assigned if the researchers addresses were from the same institution. (2) The term internationally collaborative article was designated to those articles that were coauthored by researchers from multiple countries. The term inter-institutionally collaborative article was assigned if authors were from different institution. (3) The term first author article was assigned if the first author was from the country/territory or institution for analysis. (4) The term corresponding author article was assigned if the corresponding author was from the country/territory or institution for analysis. In addition, the acronyms used in the following analysis were listed in Table 2. Abbreviation Indicators TP Number of scientific publications by the analyzed unit (document type, language, year, journal, Web of Science category, country/territory, institution, or author keyword) % Number of papers of an actor (document type, language, journal, country/territory, institution, or author keyword) as a share of the total number of articles %C Number of articles of internationally collaborative articles or interinstitutionally collaborative articles as a share of the number of articles of an actor (country/territory or institution) IF Impact factor reported in Journal Citation Reports 2010 SP Number of single country articles or single institution articles CP Number of internationally collaborative articles or inter-institutionally collaborative articles FP Number of first author articles RP Number of corresponding author articles R Rankings of number of articles (TP, SP, CP, RP, or FP) by countries or institutions
Table 1. Explanation of the abbreviations used in subsequent analysis

3. Results and discussion

3.1. Language and publication outputs
There are 41,245 articles with 17 languages used. English which had 38,976 articles (94%) is the most frequently used language in thermodynamic research. The other languages used in more than 100 articles were Russian (863), Chinese (156), French (151), Japanese (147), and

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 523

Full Name Canada, France, Germany, Italy, Japan, Russia, the UK, and the USA G8 Canada, France, Germany, Italy, Japan, the UK, and the USA Chinese Academy of Sciences Russian Academy of Sciences Central South University Naval University of Engineering calculation of phase diagram
Table 2. Introduction of the acronyms used in subsequent analysis

Acronyms G7 CAS RAS CSU NUE CALPHAD

German (146). Some other languages that were less used were as follows: Spanish, Portuguese, Polish, Czech, Korean, Ukrainian, Croatian, Hungarian, Slovak, Serbo-Croatian, and Romanian. The high proportion of English also appears in other research areas, such as 94% of desalination research (Tanaka & Ho, 2011), and 93% in acupuncture research (Han & Ho, 2011). Non-English language publications considerably dilute the the measured impact of published articles (van Raan, 2005).

Figure 3. The growth trend of articles in thermodynamic research

524 Thermodynamics Fundamentals and Its Application in Science

Journal Russian Journal of Physical Chemistry A Journal of Alloys and Compounds

TP (%) 827 (2.0) 768 (1.9)

IF 0.503 2.134

Web of Science category (rankings by IF) physical chemistry (114/127) physical chemistry (63/127); multidisciplinary materials science (50/225); metallurgy & metallurgical engineering (5/76) condensed matter physics (13/68) atomic, molecular & chemical physics (7/33) thermodynamics (3/51); physical chemistry (46/127) analytical chemistry (33/73); physical chemistry (71/127) biochemistry & molecular biology (120/286) physical chemistry (32/127) thermodynamics (5/51); physical chemistry (61/127); chemical engineering (24/135) thermodynamics (16/51); physical chemistry (81/127)

Physical Review B Journal of Chemical Physics Journal of Chemical Thermodynamics Thermochimica Acta Biochemistry Journal of Physical Chemistry B Fluid Phase Equilibria

741 (1.8) 716 (1.7) 697 (1.7) 652 (1.6) 601 (1.5) 584 (1.4) 483 (1.2)

3.774 2.920 2.794 1.899 3.226 3.603 2.253

CALPHAD-Computer Coupling of Phase Diagrams and Thermochemistry Physical Review E Journal of Colloid and Interface Science Journal of Chemical and Engineering Data Surface Science Journal of Solution Chemistry Journal of Molecular Biology Journal of the American Chemical Society Physical Review D Physical Review Letters

450 (1.1)

1.429

444 (1.1) 411 (1.0) 400 (1.0) 382 (0.93) 360 (0.87) 339 (0.82) 317 (0.77) 278 (0.67) 262 (0.64)

2.352 3.066 2.089 2.010 1.335 4.008 9.019 4.964 7.621

fluids & plasmas physics (8/31); mathematical physics (4/54) physical chemistry (40/127) multidisciplinary chemistry (44/147); chemical engineering (28/135) physical chemistry (69/127); condensed matter physics (19/68) physical chemistry (85/127) biochemistry & molecular biology (86/286) multidisciplinary chemistry (11/147) astronomy & astrophysics (8/55); particles & fields physics (5/27) multidisciplinary physics (5/80)

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 525

Journal Langmuir

TP (%) 242 (0.59)

IF 4.268

Web of Science category (rankings by IF) multidisciplinary chemistry (24/147); physical chemistry (29/127); multidisciplinary materials science (26/225)

Table 3. Characteristics of top 20 journals with the most articles in thermodynamics

The thermodynamic research revealed a growth trend through the study period, especially in recent years. The number of articles has been climbing up from 1991 to 2010 in Fig. 3. According to the annual growth rate, it can be divided into two stages: 1991-2003 and 20042010. In the first stage, the growth rate was 48 articles per year from 1,412 in 1991 to 1,988 in 2003, while in the second stage the growth rate has risen four-fold to 203 articles per year from 2,169 in 2004 to 3,410 in 2010.

3.2. Journals and Web of Science categories 3.2.1. Journals

The total articles (41,245) were published in 2,434 sources among 150 Web of Science categories. Table 3 lists the top 20 journals with the greatest number of articles. The impact factors of these journals were also exhibited as reputation of a journal attached much attention by the authors and editors (van Raan, 2001). Approximately 24% of the articles resided in these 20 journals. Russian Journal of Physical Chemistry A (IF = 0.523) which was founded in 1930, published the most articles (827; 2.0%). Its former was Zhurnal fizicheskoi khimii (1930-1999) and Russian Journal of Physical Chemistry (1999-2006). Articles published in this journal concern chemical thermodynamics and thermochemistry (http://www.maik.ru/cgiperl/journal.pl?name=physcha&page=main) which is closely related to the topic of this study. Among the total institutions (1,004) contributing to Russian Journal of Physical Chemistry A, 831 institutions (83%) belonged to Russia while only 173 institutions (17%) belonged to other countries. Following three journals: Journal of Alloys and Compounds (IF = 2.134), Physical Review B (IF = 3.774), and Journal of Chemical Physics (IF = 2.920), all had the more than 700 articles. However, the journal which had the highest IF (9.019) was Journal of the American Chemical Society in the category of multidisciplinary chemistry which was ranked 17th. Physical Review Letters in multidisciplinary physics category was ranked 19th in the list and ranked 2nd in terms of IF (7.621). Furthermore, of these 2,434 sources, 1,828 (75%) sources only contained less than 10 articles; 519 (21%) sources contained 11-100 articles, 60 (2.5%) sources contained 101-200 articles; 20 (0.82%) sources contained 201-600 articles; and seven sources (0.28%) contained more than 600 articles, accounting for 11 percent of the total articles. The trends of the annual publication outputs of the top core seven journals are displayed in Fig. 4. The curves of these seven journals (Russian Journal of Physical Chemistry A, Journal of Alloys and Compounds, Physical Review B, Journal of Chemical Physics, Journal of Chemical Thermodynamics, and Thermochimica Acta Biochemistry) had been interlacing in the study period. However, after 2008, Journal of Alloys and Compounds which published 108 articles in 2009 and 70 articles in 2010 showed its domination in the thermodynamic field.

526 Thermodynamics Fundamentals and Its Application in Science

Figure 4. The trends of top seven journals with more than 600 articles

3.2.2. Web of Science categories

As for category analysis, excluding the 84 articles without subject category information, the remained 41,161 articles were analyzed. The most common category was physical chemistry (10,295; 25%), followed distantly by other categories. A half of the above top 20 journals are assigned to the category of physical chemistry. Within the total 150 Web of Science categories, 92 categories (61%) published articles less than 100 articles; 40 categories (27%) published 101-1000 articles; 12 categories (8.0%) published 1,001-3,000 articles; only six categories (4.0%) published more than 3,000 articles. The six core categories including physical chemistry, multidisciplinary materials science, multidisciplinary chemistry, metallurgy & metallurgical engineering, chemical engineering, and biochemistry & molecular biology, took the majority of the total articles with a great percentage of 55%. As illustrated in Fig. 5, these categories showed greater growth rates in recent years than those in 1990s. These trends were similar to the above trends of annual total publication outputs. The articles of position 1st category of physical chemistry which contained 127 journals increased from 390 in 1991 to 777 in 2010. The 2nd position category of multidisciplinary materials science which included 225 journals increased six-fold from 70 in 1991 to 423 in 2010.

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 527

Figure 5. The trends of top seven Web of Science categories with more than 3000 articles

3.3. National contributors 3.3.1. Global geographical distribution

Excluding 263 articles without any author address information on the Web of Science, the 40,982 articles originated from 128 countries. Articles originating from England, Scotland, Northern Ireland, and Wales were reclassified as being from the United Kingdom (UK) (Chiu & Ho, 2005). Articles from Hong Kong were included in the ones from China. The geographical global distribution of thermodynamic research is shown in Fig. 6. According to their production, the 128 countries were divided into five parts. Particularly, 81 countries (63%) belonged to the first part of 1-100 articles; 36 countries (28%) belonged to the second part of 101-1,000 articles; seven countries (Japan, France, India, Italy, UK, Spain, and Canada) belonged to the third part of 1,001-3,000 articles; three countries (China, Russia, and Germany) belonged to the fourth part of 3,001-5,000 articles; and only one country (USA) which totally published 9,161 articles, belonged to the fifth part of 5,001-10,000 articles. Although there were only 11 countries which published more than 1,000 articles, these 11 countries produced 77% articles. The majority of articles originated from a small number of particular countries. Furthermore, five continents contributed to the thermodynamics

528 Thermodynamics Fundamentals and Its Application in Science

research differently. Europe with 42 countries published the most articles 22,969 (56%); Asia with 42 countries published the second most articles 13,163 (32%); and America with sixteen countries published the third most articles 12,333 (30%). Africa, and Oceania two continents made much less contributions, and the quantity of them were 933 (2.3%), and 667 (1.6%), respectively. It is noticeable that Europe is taking the leading position of thermodynamic research. Asia was seeing a striking increase to catch up with Europe in terms of scientific output (Friedberg, 2000; von Bubnoff, 2005).

Figure 6. Global geographical distribution of thermodynamics research outputs

3.3.2. Characteristics of top 20 countries/territories

With respect to international collaboration, 33,234 (81%) were independent publications and 7,748 (19%) were internationally collaborative publications. The collaboration rate was a little greater than that of other areas, such as 14% biosorption technology for water treatment (Ho, 2008), 16% of desalination research (Tanaka & Ho, 2011), 16% of solid waste research (Fu et al., 2010), and 14% of acupuncture research (Han & Ho, 2011). Table 4 shows the characteristics of the top 20 productive countries. The eight major industrialized countries G8, ranked in the top 11 in Table 4, had 59% over the investigation period. Similarly, the seven major industrialized countries G7 the USA, Germany, the UK, Japan, France, Canada, and Italy accounted for a significant proportion exited in many researches (Li et al., 2009; He, 2009; Fu et al., 2010; Wang et al., 2010). The USA dominated, ranking 1st in independent and collaborative articles, as well as first author and corresponding author articles. Total 1,421 contributing institutions (13%) were affiliated with USA, followed by China (824 institutions, 7.7%), and Russia (792 institutions, 6.5%). The 2nd position China, the 7th position India, and the 19th position Iran had low percentages of collaboration less than 20%. It was not coincident that China emerged as a leading nation in science production (Zhou & Leydesdorff, 2006; Zhou & Leydesdorff, 2008). In most fields, the USA had the quantity (number of papers) lead, although the China has made dramatic strides to overtake the USA, except the biomedical field and some aspects of environmental science (Kostoff, 2008).

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 529

Country USA China Russia Germany Japan France India Italy UK Spain Canada Poland Netherlands Brazil Ukraine Switzerland Sweden South Korea Iran Australia

IN 1,421 824 792 724 580 792 652 390 315 210 192 171 145 196 229 111 106 176 173 106

TP TP R (%) 9,162 1 (22) 4,652 2 (11) 3,792 3 (9.3) 3,421 4 (8.3) 2,804 5 (6.8) 2,515 6 (6.1) 2,201 7 (5.4) 1,858 8 (4.5) 1,797 9 (4.4) 1,487 10 (3.6) 1,446 11 (3.5) 934 12 (2.3) 741 13 (1.8) 733 14 (1.8) 720 15 (1.8) 690 16 (1.7) 645 17 (1.6) 632 18 (1.5) 587 19 (1.4) 566 20 (1.4)

SP R (%) 1 (20) 2 (12) 3 (9.1) 6 (5.5) 4 (6.3) 7 (4.1) 5 (5.7) 8 (3.6) 9 (2.5) 11 (2.5) 10 (2.5) 12 (1.6) 18 (1.1) 14 (1.5) 15 (1.4) 21 (0.93) 19 (1.1) 17 (1.3) 13 (1.5) 23 (0.79)

CP R (%) 1 (33) 5 (10) 6 (10) 2 (21) 7 (9.0) 3 (15) 15 (3.8) 8 (8.6) 4 (12) 9 (8.4) 10 (7.8) 11 (5.1) 13 (4.7) 19 (3.1) 18 (3.1) 12 (4.9) 16 (3.5) 22 (2.5) 32 (1.0) 14 (3.9)

FP R (%) 1 (19) 2 (11) 3 (8.2) 4 (6.3) 5 (5.8) 7 (4.6) 6 (5.1) 8 (3.8) 9 (3.0) 10 (2.9) 11 (2.7) 12 (1.7) 17 (1.3) 13 (1.5) 14 (1.4) 19 (1.2) 20 (1.2) 16 (1.3) 15 (1.4) 21 (1.0)

RP R (%) 1 (18) 2 (11) 3 (8.6) 4 (6.2) 5 (5.8) 7 (4.5) 6 (5.0) 8 (3.8) 9 (2.9) 10 (2.8) 11 (2.6) 12 (1.7) 19 (1.2) 13 (1.5) 14 (1.4) 18 (1.2) 20 (1.1) 16 (1.4) 15 (1.4) 21 (1.0)

%C 28 17 20 47 25 46 13 36 53 44 42 42 50 33 34 55 42 31 14 54

IN: Number of institutions.

Table 4. Characteristics of the top 20 productive countries/territories

Besides, the 9th position UK, the 13th position Netherlands, the 16th position Switzerland, and the 20th position Australia had high cooperation rates no less than 50%. It was also reported that international collaboration in both within and outside the European Communities played an increasing role for European scientific literature (Narin et al., 1991; Glnzel, 1999). South Korea and Iran had higher rankings in terms of FP and RP than that of TP, while Netherlands and Sweden had lower rankings in terms of FP and RP. Moreover, from the above languages analysis, except English, the popular languages (Russian, Chinese, French, Japanese, and German) were just the mother tongue of the top five countries China, Russia, Germany, Japan, and France except the USA. The excellent performance of these countries was consistent with the results of language analysis.

3.3.3. Comparison of top six countries

The comparison of top six countries with the most articles in 2010 is illustrated in Fig. 7. The USA hold the trump card based on the total number of articles in the study period, but did not have the highest growth rate. China which was ranked 1st according to the 2010 production had the highest growth rate of 32 articles per year, and surpassed the USA in 2009, following distantly by other countries. USA, India, and Russia had the lower growth

530 Thermodynamics Fundamentals and Its Application in Science

rate of 10 - 13 articles per year. The following Germany and France had the growth rate of 6.3 and 5.9 articles per year. Particularly, Russia experienced a sharply increase in the first three year from 6 articles in 1991 to 174 articles in 1993, may due to its large fund for recovery of the politic reason (Goodman, 1993; Webb, 1994). The Russian annual output grew from 1980 to 1990, but fell after the dissolution of the USSR in late 1991; from 1994 there has been an inconsistent partial recovery, and by 2000 the annual output had approximately regained its 1980 value (Wilson & Markusova, 2004). It seems that the recovery time of Russian thermodynamic research was shorter.

Figure 7. Trends of top six countries with most articles in 2010

3.3.4. Comparison of China and USA

In order to compare the most productive country in 1991-2010, the USA and the most active country in 2010, China, annual number of articles and citations per publication (CPP) of both were presented in Fig. 8. Total citations were collected on November 20 in 2011 from web of Science. From the above analysis, China experienced a high grow rate and got ahead of the USA in 2009 and kept on top in 2010. However, in terms of CPP, the mean number of China was 7.1 which was much less than that of the USA (23). The annual CPP of the USA showed a declined trend in 1991-2010, ranging from 53 in 1991 to 2.8 in 2010. Except the year

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 531

of 1993, the annual CPP of China fluctuated ranging 6.2-11 in 1991-2006, and decreased after 2007 down to 1.9 in 2010. Both countries indicated declines as for annual CPPs, which can be attributed to that it needs time to accumulate their citations (Picknett & Davis, 1999). The outstanding performance of Chinas CPP in 1993 might be owned to the two highly cited articles of a series by the same authors. They were thermodynamics of molecular recognition by cyclodextrins. 1. calorimetric titration of inclusion complexation of naphthalenesulfonates with -, -, and -cyclodextrin: enthalpy entropy compensation (Inoue et al., 1993a) with 344 citations and thermodynamics of molecular recognition by cyclodextrins. calorimetric titration of inclusion complexation with modified -cyclodextrins. enthalpy-entropy compensation in host-guest complexation: from ionophore to cyclodextrin and cyclophane(Inoue et al., 1993b) with 198 citations, respectively. Furthermore, the most frequently cited article was a modified UNIFAC model. 2. present parameter matrix and results for different thermodynamic properties (Gmehling et al., 1993) with 727 citations. Although this article was published by authors from Germany only, it was also assigned to China according to its address record from Web of Science, because one of the authors had permanent address of China. It is a bias of address information for articles from Web of Science. Chinas CPP in 1993 were still high (CPP = 20) without these highest citations articles. Likewise, the well performance of the USAs CPP in 1991 can be ascribed to the top cited article protein folding and association: insights from the interfacial and thermodynamic

Figure 8. Comparison of USA and China by number of articles and citations per publication

532 Thermodynamics Fundamentals and Its Application in Science

properties of hydrocarbons which was published in 1991 (Nicholls et al., 1991) and received 4,999 citations. Most scientific publications from China have a lower citation impact than the world average and have a lower citation rate than expected (Glnzel et al., 2002). It is suggested that Chinas science needs to move from the quantitative expansion phase in nowadays to a rising quality phase (Jin & Rousseau, 2005). In general, China showed a high growth rate in recent years and dominant now in annual production, but still needs to make efforts on increasing their citations in thermodynamics.

3.4. Institutional contributors 3.4.1. Characteristics of top 20 institutions

After examining the national contributors, the characteristics of institutional contributors institutions were identified. Of 40,982 articles from 10,696 institutions in 128 countries, 16,628 (41%) were inter-institutionally collaborative publications, and 24,354 (59%) were independent publications. The percentage of collaboration among institutions was much higher than that among countries (19%). The inter-institutional collaboration rate was usually greater than international collaboration rates (Fu et al., 2010; Han & Ho, 2011; Li et al., 2011; Tanaka &Ho, 2011). The number of articles of institutions was smaller than the country, and it was reported that the collaboration was more likely to happen when the size of actors was small (Narin et al., 1991). Nevertheless, the inter-institutional collaboration rate (41%) of thermodynamic research was observed to be lower than that of many other fields, such as 62% of global climate change (Li et al., 2011), 53% in atmospheric simulation (Li et al., 2009), 44% in solid waste research (Fu et al., 2010), and 53% of acupuncture research (Han &Ho, 2011). Four institutions in the USA and Japan, three in China, two each in Russia, and one each in Sweden, Ukraine, UK, India, France, and Italy were ranked in the top 20 productive institutions (16%) as shown in Table 5. It is worth noting that the Russian Academy of Sciences ranked 1st and Chinese Academy of Sciences ranked 2nd are both integrated research centers and made up of many relatively independent institutions distributed throughout their country. At present, the publications of these institutions were pooled as one heading, and publications divided into branches would result in different rankings. A bias appeared because national research institutions might have many branches in different cities, for example the CAS (Li et al., 2009), the RAS (Li et al., 2009), and Indian Institute of Technology (Tanaka & Ho, 2011). RAS founded the most productive thermodynamic journal of Russian Journal of Physical Chemistry A. In particular, 228 articles (28%) were contributed by RAS, and 117 articles (14%) were contributed by Moscow Lomonosov State University in Russia based on the total articles (817 articles with author information) of Russian Journal of Physical Chemistry A during 1991-2010. With the exception of these two institutions, the most productive institution is Moscow Lomonosov State University in Russia (425; 1.0%), followed by Tohoku University in Japan (335; 0.82%), and Centre National de la Recherche Scientifique in France (313; 0.76%). However, a bias would appear in the analysis of institutions which was used by different names in their publications. It is strongly recommended that an international identity number for all institutions when authors published their paper with an institution as affiliation in a Web of Science-listed journal (Chiu &Ho, 2007).

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 533

Institution Russian Academy of Sciences, Russia Chinese Academy of Sciences, China Moscow Lomonosov State University, Russia Tohoku University, Japan Centre National de la Recherche Scientifique, France University of Tokyo, Japan University of Science and Technology Beijing, China Royal Institute of Technology, Sweden Pennsylvania State University, USA Central South University, China University of Wisconsin-Madison, USA Indian Institute of Technology, India University of California, USA Osaka University, Japan Massachusetts Institute of Technology, USA University of Cambridge, UK Polish Academy of Sciences, Poland National Research Council, Italy National Academy of Sciences of Ukraine, Ukraine Kyoto University, Japan

TP 1,604 720 425 335 313 280 265 261 256 247 245 242 241 240 222 220 219 208 201 200

TP R (%) 1 (3.9) 2 (1.8) 3 (1.0)

SP R (%) 1 (3.7) 3 (0.92) 2 (0.93)

CP R (%) 1 (4.2) 2 (3.0) 5 (1.2) 4 (1.3) 3 (1.4)

FP R (%) 1 (3.0) 2 (1.1) 3 (0.75) 8 (0.46)

RP R (%) 1 (3.1) 2 (1.1)

% C 43 69

3 (0.80) 47 7 (0.45) 62

4 (0.82) 10 (0.52) 5 (0.76) 23 (0.34) 6 (0.68) 7 (0.65)

11 (0.41) 13 (0.39) 73 6 (0.46) 5 (0.47) 6 (0.45) 50 5 (0.48) 52

6 (0.57) 11 (0.84) 9 (0.53) 14 (0.82)

8 (0.64) 14 (0.45) 9 (0.62)

7 (0.91) 12 (0.41) 11 (0.40) 58 9 (0.45) 10 (0.43) 45 4 (0.50) 6 (0.46) 4 (0.52) 50 8 (0.44) 33

5 (0.58) 19 (0.69)

10 (0.60) 11 (0.51) 18 (0.74) 12 (0.59) 4 (0.67) 42 (0.48)

11 (0.60) 14 (0.45) 15 (0.81) 14 (0.41) 18 (0.37) 55 13 (0.59) 18 (0.39) 15 (0.54) 8 (0.88) 16 (0.39) 22 (0.33) 61

14 (0.59) 16 (0.41) 11 (0.84) 17 (0.37) 15 (0.38) 58 8 (0.55) 35 (0.53) 10 (0.42) 11 (0.40) 40 8 (0.88) 22 (0.34) 24 (0.33) 66 6 (1.1) 52 (0.20) 58 (0.19) 87 9 (0.43) 31

16 (0.54) 29 (0.30) 18 (0.51) 166 (0.11) 19 (0.49)

17 (0.53) 24 (0.33) 13 (0.83) 22 (0.34) 21 (0.35) 63

7 (0.57) 80 (0.37) 12 (0.41)

20 (0.49) 18 (0.39) 27 (0.63) 18 (0.36) 17 (0.37) 53

Table 5. Characteristics of the top 20 productive institutions.

More independent institutions might lead to more first author articles and corresponding author articles or vice versa. Some institutions which had low collaboration rates no more than 40% usually had a higher rank in FP and RP. For example, the 12th place Indian Institute of Technology in India with the low collaboration rate of 33% ranked 6th in FP and 8th in RP; the 15th position Massachusetts Institute of Technology in USA with the low collaboration rate of 40% ranked 10th in FP and 11th in RP; the 19th position National Academy of Sciences of Ukraine in Ukraine with the low collaboration rate of 31% ranked 12th in FP and 9th in RP. On the other hand, some institutions which had high collaboration rates more than 70% were ranked lower in the rankings of FP and RP. For example, the 5th position Centre National de la Recherche Scientifique in France with the high collaboration rate of 73% ranked 11th in FP and 13th in RP; the 18th position National Research Council in Italy with the high collaboration rate of 87% ranked 52th in FP and 58th in RP.

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3.4.2. Comparison of top seven institutions

To identify the growth trends of active institutions in recent years, the trends of top seven productive institutions with most articles in 2010 are shown in Fig. 9. The most productive institution - RAS had an overwhelming majority in the total articles, and CAS was just down by three articles in 2010, following distantly by the other institutions. CAS as the Chinas highest academic institution in natural sciences played an active role in terms of scientific outputs in recent years as the exponentially growth scientific production in China (Li et al., 2009; Fu et al., 2010; Tanaka &Ho, 2011; Fu et al., 2011; Li et al., 2011).

Figure 9. Trends of top seven institutions with most articles in 2010

Although three universities in China including Central South University, Naval University of Engineering, and SiChuan University just ranked 10th, 39th, and 43rd of total articles from 1991 to 2010, but they had high rankings (3rd, 4th, and 7th) with respect to the number of articles in 2010. The growth rates of the top institutions differed from each other. Particularly, based on the last decade (2001-2010), CAS showed the highest growth rate of 7.2 articles per year; CSU and NUE showed the growth rate of 4 5 articles per year. The other four institutions, RAS, Moscow Lomonosov State University, University of Science and Technology Beijing, and SiChuan University showed the growth rate of 1 2 articles

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 535

per year. About 14% percent articles in RAS were published in Russian Journal of Physical Chemistry A which was founded by RAS. It was interesting that the top three institutions (CAS, CSU, and NUE) with the greatest growth rates were all in China. CSU was established in 2000 by merging three separate universities: Hunan Medical University, Changsha Railway University, and Central South University of technology, and was involved in 985 Project and 211 Project which were supported by Chinese government to promote the development and reputation of the Chinese higher education system (http://iecd.csu.edu.cn/en-US/ColumnS.aspx?cid=12). Moreover, CSU hold one SCI journal named Transactions of Nonferrous Metals Society of China which published 11% thermodynamic related articles of CSU in the study period. Another institution, NUE ranks as a military university of higher learning subjected to the leadership of the Central Military Commission and the Party Committee of the PLA Navy, and is listed as one of the five comprehensive universities in the armed forces and the army 2110 project that enjoys the priority in development. It falls into the category of key national university specializing in engineering (http://english.chinamil.com.cn/site2/special-reports/2007-06/21/content_853791.htm).

3.5. Research emphases and trends

Bibliometric analysis of author keywords has been only observed in recent years (Chiu &Ho, 2007; Wang et al., 2010; Li et al., 2011). It tried to find the research emphases and trends by quantitatively analyzing the frequency of author keywords. Excluding some articles without author keywords information, 23,458 articles (57%) with records of author keywords in the SCI-Expanded database were analyzed. There were 45,182 author keywords listed by authors, 43,930 (97%) keywords were used no more than ten times, which indicated that thermodynamic research involved diverse scientific literature and a wide disparity in research focuses (Chuang et al., 2007). Only 74 (0.16%) author keywords were used no less than 100 times, suggesting that the mainstream research in thermodynamics was considered to focus on a small field. Four five-year intervals (19911995, 1996-2000, 2001-2005, and 2006-2010) were employed to obtain the trends of these author keywords as well as minimize the year-to-year fluctuations. The top 30 author keywords (accounting for 37% of the total articles) in the latest interval 2006-2010 are listed in Table 6. Except the author keywords thermodynamics, thermodynamic properties, thermodynamic parameters, and thermodynamic related to searching keywords, the three most frequently used author keywords were kinetics (883; 3.8%), adsorption (736; 3.1%), and phase diagram (545; 2.3%). Thermodynamics and kinetics were related to one another in ways, and were both commonly used to describe process (Kocks et al., 1975; Astumian, 1997; Ho & Ofomaja, 2005). Adsorption was a widely applied process, for example in environmental science (Wang et al., 2010; Wang et al., 2011; Chuang et al., 2011). The term phase diagram is a type of chart used to obtaining thermodynamic data at equilibrium (Kleppa, 1952; Svirbely, 1954).

536 Thermodynamics Fundamentals and Its Application in Science

Author keywords thermodynamics thermodynamic properties kinetics adsorption thermodynamic parameters thermodynamic phase diagram entropy thermodynamic modeling thermodynamic analysis heat capacity calorimetry phase diagrams CALPHAD solubility enthalpy thermodynamic property density functional theory isothermal titration calorimetry thermodynamic stability isotherm equation of state density molecular dynamics free energy phase equilibria biosorption AB initio calculations phase transition nonequilibrium thermodynamics
N/A: Not Available

TP 5,943 1,577 883 736 778 503 545 548 338 385 533 503 260 186 325 373 212 158 177 265 120 316 178 172 163 228 101 121 158 190

1991-2010 R (%) 1 (25) 2 (6.7) 3 (3.8) 5 (3.1) 4 (3.3) 9 (2.1) 7 (2.3) 6 (2.3) 13 (1.4) 11 (1.6) 8 (2.3) 9 (2.1) 17 (1.1) 25 (0.79) 14 (1.4) 12 (1.6) 20 (0.90) 36 (0.67) 28 (0.75) 16 (1.1) 60 (0.51) 15 (1.3) 27 (0.76) 29 (0.73) 33 (0.69) 19 (1.0) 72 (0.43) 59 (0.52) 36 (0.67) 24 (0.81)

1991-1995 R (%) 1 (31) 2 (5.5) 6 (2.5) 11 (1.5) 3 (2.6) 26 (1.0) 21 (1.2) 8 (2.0) 165 (0.27) 12 (1.5) 3 (2.6) 5 (2.5) 26 (1.0) N/A 10 (2.0) 8 (2.0) 59 (0.59) 1288 (0.045) 1288 (0.045) 38 (0.77) 1288 (0.045) 7 (2.4) 29 (1.0) 165 (0.27) 165 (0.27) 32 (0.86) N/A N/A 52 (0.64) 23 (1.1)

1996-2000 R (%) 1 (25) 2 (8.4) 8 (2.2) 10 (1.9) 3 (3.5) 15 (1.3) 6 (2.3) 7 (2.2) 56 (0.50) 14 (1.7) 5 (2.7) 4 (3.0) 31 (0.68) 782 (0.068) 16 (1.3) 9 (1.9) 64 (0.45) 415 (0.11) 108 (0.34) 16 (1.3) 565 (0.09) 13 (1.7) 41 (0.59) 31 (0.68) 52 (0.52) 25 (0.83) N/A 170 (0.25) 58 (0.47) 27 (0.81)

2001-2005 R (%) 1 (23) 2 (5.9) 3 (3.6) 6 (2.5) 4 (3.2) 10 (2.1) 9 (2.1) 7 (2.5) 16 (1.3) 12 (1.3) 5 (2.8) 8 (2.2) 25 (0.83) 35 (0.66) 13 (1.3) 11 (1.7) 25 (0.83) 56 (0.53) 31 (0.70) 13 (1.3) 231 (0.18) 13 (1.3) 60 (0.51) 47 (0.61) 51 (0.59) 18 (1.2) 431 (0.11) 147 (0.26) 60 (0.51) 39 (0.64)

2006-2010 R (%) 1 (25) 2 (6.7) 3 (4.8) 4 (4.4) 5 (3.5) 6 (2.7) 7 (2.7) 8 (2.4) 9 (2.2) 10 (1.8) 11 (1.7) 12 (1.7) 13 (1.5) 14 (1.3) 14 (1.3) 16 (1.3) 17 (1.2) 18 (1.1) 19 (1.1) 20 (1.0) 21 (1.0) 21 (1.0) 23 (0.94) 24 (0.93) 25 (0.92) 26 (0.91) 27 (0.89) 27 (0.89) 29 (0.86) 30 (0.85)

Table 6. The most frequently used 30 author keywords in 2006-2010

Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 537

In particular, there were also some emerging hotspots in thermodynamics recently. Some author keywords including the 3rd adsorption, the 9th thermodynamic modeling, the 14th CALPHAD, the 17th thermodynamic property, the 18th density functional theory, the 19th isothermal titration calorimetry, the 20th thermodynamic stability, the 21st isotherm, the 25th free energy, the 27th biosorption, and the 28th AB initio calculations in the list showed the increasing trends during the study period. It is noticeable that CALPHAD, biosorption, and AB initio calculations increased rapidly from zero articles in 1991-1995 into the top 30 rankings in 2006-2010. CALPHAD was firstly used as the author keyword of the article entitled compilation of CALPHAD formation enthalpy data - Binary intermetallic compounds in the COST507 Gibbsian database in 1998 (Fries & Jantzen, 1998). However, CALPHAD method had been used as the author keyword of the article titled thermodynamic study on the Ag-Sb-Sn system in 1996 (Oh et al., 1996). The first article which employed biosorption as author keyword was titled determination of the equilibrium, kinetic and thermodynamic parameters of the batch biosorption of nickel(II) ions onto Chlorella vulgaris in Process Biochemistry in 2002 (Aksu, 2002). Biosorption as a process for water treatment received increasing attention in recent years (Ho, 2008). As for AB initio calculations, it was originally utilized as author keywords of the article an AB initio study of structures and energetics of copper sulfide clusters in 1996 (Dehnen et al., 1996). Similarly, density functional theory, isothermal titration calorimetry, and isotherm grew fast from the 1288th (only one article) in 19911995 to 18th, 19th, and 21st in 2006-2010. The article targeting at density functional theory could be found in 1994 and it was entitled density-functional theory as thermodynamics (Nagy & Parr, 1994). Thermodynamical interpretation of the density functional theory for an electronic ground state was developed (Nagy & Parr, 1994). The following article which utilized density functional theory as author keyword was published in 1999. For the phrase isothermal titration calorimetry, the article which used it as author keyword appeared in 1995, and it was titled comparative thermodynamic analyses of the Fv, Fab* and Fab fragments of anti-dansyl mouse monoclonal-antibody (Shimba, 1995). However, it should be noticed that there was a bias that all these analysis were based on the data (57%) with author keywords information from SCI-Expanded.

4. Conclusion
Except the dominant language English, Russian, Chinese, French, Japanese and German were the most common languages. Above all, the growth process of annual thermodynamic scientific outputs can be divided into two stages, and the annual growth rate of the second stage 2004-2010 was four times of that in the first stage 1991-2003. Secondly, Russian Journal of Physical Chemistry was the most productive journal, and then Journal of Alloys and Compounds and Journal of Chemical Physics. The most common category was found to be physical chemistry. Thirdly, the global geographic distribution discovered that Europe took the leading position, following by Asia, America, Africa and Oceania. In particular, the eight major industrialized countries (G8: Canada, France, Germany, Italy, Japan, Russia, the UK, and USA) played a prominent role with more than a half contribution, especially the USA.

538 Thermodynamics Fundamentals and Its Application in Science

However, China experienced the greatest growth rate, and surpassed the USA in 2009 in terms of annual production, but needs to enhance its quality of publications. China and India had low collaboration rates while the UK, Netherlands, and Switzerland in Europe with a smaller size had high collaboration rates. In general, the thermodynamic research presented a higher international collaboration rate but a lower inter-institutional collaboration rate in comparison with other fields. Russian Academy of Sciences and Chinese Academy of Sciences took the leading position of institutions, following distantly by Tohoku University in Japan, and Centre National de la Recherche Scientifique in France. It was also revealed that the institutions with lower collaboration rates usually published greater proportion of first author articles and corresponding author articles, and vice versa. Finally, by analyzing the latest most frequently used author keywords, it was concluded that the items thermodynamic properties, kinetics, adsorption, thermodynamic parameters, phase diagram, and entropy are the traditional research hotspots and will continue being the emphases in the foreseeable future. CALPHAD, density functional theory, isothermal titration calorimetry, isotherm, biosorption, and AB initio calculations, as the quickly increasing concernings, are the newly thermodynamic research hotspots.

Author details
Hui-Zhen Fu1, Yuh-Shan Ho1,2,* 1Department of Environmental Sciences, Peking University, Peoples Republic of China 2Trend Research Centre, Asia University, Taiwan

5. References
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*

Corresponding Author

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