CHAPTER II

QUANTUM CHEMICAL CALCULATIONS AND NORMAL

COORDINATE ANALYSIS

Abstract

Two areas of computational methods are discussed with

necessary theoretical background. An overview of density functional

theory and the different types of basis sets are outlined. The

Hohenberg-Kohn Theorems were explained. Different types of

quantum mechanical force fields and the procedure of normal

coordinate analysis employed in interpreting the molecular vibration

spectra are discussed briefly. The procedure of performing Scaled

quantum chemical calculations using Molvib software is explained.

Natural bond orbital analysis and its importance is outlined.

 CHAPTER II

QUANTUM CHEMICAL CALCULATIONS AND NORMAL

COORDINATE ANALYSIS

2.1 INTRODUCTION

Normal Coordinate Analysis (NCA) plays an important role in

understanding vibrational properties of molecular structures at the

atomic level. To perform NCA, one must formulate an appropriate

potential model and calculate the second derivatives of the potential

with respect to the Cartesian coordinates. This process yields force

constant matrix. The eigen values and eigen vectors of this matrix

characterize the vibrational frequencies and displacement patterns of

each atom.

Theoretical approach to vibrational spectroscopy is possible by

the quantum chemical calculations. Quantum chemical calculations

are performed on a wide range of molecules using advanced

computer programs, with possibilities to make calculations of

molecules containing hundreds or thousands of atoms. Harmonic

force fields derived from quantum chemical calculations can provide

a valuable insight in peak assignments and also in calculating the IR

intensity and Raman activities and thus inculcating a complete a

vibrational analysis of a chosen molecule.

Nowadays sophisticated electron correlation calculations are

increasingly available and deliver force fields of high accuracy for

30
small polyatomic molecules. The scaled quantum mechanical force

fields are of comparable accuracy with the best purely theoretical

results. In addition, the scaling procedure fits the force field to

observed (anharmonic) frequencies. Thus, the reproduction of

observed spectra will be better with an SQM force field than with the

best harmonic force field.

2.1.1 Energy minimisation

Molecular mechanics deals with the change in the electronic

energy of the molecule due to bond stretching (Vb ), bond angle

bending (V ), out-of-plane bending (VO ), internal rotation (torsion)

about bonds (V ), interactions between different kinds of motions

(Vint ), Van der waals attractions and repulsion between non-bonded

atoms (Vvdw ) and electrostatic interactions between atoms (Ves ). The

sum of these contributions gives the potential energy V of the

molecule. It is often called the steric energy or strain energy for the

motion of atoms in the molecule. The mathematical form of this

energy function (also called potential energy surface) is given below.

k
V (XN ) = V
i =1
i ..... (2.1)

Where V represents the potential energy of the molecular

system, which is a function of the Cartesian coordinates of all atoms

denoted as XNs. The equation (2.1) can be written as

31
 V = Vb + V + V + VO + Ves + Vvdw + Vint .... (2.2)

The potential energy calculated by summing up the energies of

various interactions is a numerical value for a single conformation.

Energy minimization is usually performed by gradient optimization;

atoms are moved so as to reduce the net force on them. The energy

minimized structure has small forces on each atom and therefore serves

as an excellent starting point for molecular dynamics simulations.

2.2 COMPUTATIONAL CHEMISTRY

There are two broad areas within computational chemistry:

molecular mechanics and electronic structure theory. They both

perform the following basic type of calculation.

Computing the energy of a particular molecular structure

(physical arrangement of atoms or nuclei and electrons).

Performing geometry optimization which depends primarily on the

gradient of energy.

Computing the vibrational frequencies of molecules resulting from

interatomic motion within the molecule. These frequency

calculations may also predict other properties which depend on

second derivative of the energy.

2.2.1 Molecular mechanics

Molecular mechanics is a non quantum mechanical method of

computing molecular structures and properties that treats a

32
molecule as a flexible collection of atoms held together by chemical

bonds. The method minimizes the molecular potential energy, which

is generally calculated classically in terms of internal degrees of

freedom such as bond lengths, bond angles, dihedral angles, and

electrostatic and vanderwaals nonbonding interactions. The

molecular mechanics minimization depends on an empirically-based

parameterization scheme and is able to handle molecules with

thousands of atoms. There are different molecular mechanics

methods. Each one is characterized by its particular force field.

These classical force fields are based on empirical results, averaged

over a large number of molecules. Because of this extensive

averaging, the results can be good for standard systems; no force

field can be generally used for all molecular systems of interest.

2.2.2 Electronic structure methods

Electronic structure methods use the law of quantum mechanics

as the basis for their computations and used for molecular modeling

and the calculation of molecular properties. Quantum mechanics states

that the energy and other related properties of a molecule can be

obtained by solving the Schrodinger equation,

H = E ..... (2.3)

However, exact solutions to the Schrodinger equation are not

practical. Electronic structure methods are characterized by their

33
various mathematical approximations to their solutions. There are

two major classes of electronic structure methods:

Semi empirical methods use a simpler Hamiltonian than the

correct molecular Hamiltonian and use a parameter whose values

are adjusted to fit the experimental data. That means they solve an

approximate form of the Schrodinger equation that depends on

having approximate parameters available for the type of chemical

system in question. There is no unique method for the choice of

parameter. Ab initio force fields provide solutions to these problems.

Ab initio methods, use the correct Hamiltonian and does not use

experimental data other than the values of the fundamental

physical constants (i.e., c, h, mass and charges of electrons and

nuclei). Ab initio methods includes treatment of electron

correlation, lead to calculations of molecular geometries and

spectroscopic properties that are very close to experimental data.

2.3 AB INITIO METHODS

Ab initio quantum chemistry involves calculating molecular

properties using quantum chemistry based methods. A variety of Ab

initio methods exist and although these calculations are computationally

expensive, they allow chemists to make predictions of molecular

properties of new and existing compounds. The ever increasing level of

compute power available to researchers makes the application of Ab

initio methods more practical for larger molecular systems.

34
 Ab initio orbital molecular methods are useful to predict

harmonic force constants and frequencies of normal modes. The ab

initio methods first optimize the molecular geometry and then

evaluate the second derivative at the equilibrium positions usually

using analytical derivatives. Such methods provide reliable values for

harmonic vibrational frequencies for fairly large sized molecules.

Additionally such calculations can be used to predict barriers to

internal rotation as well as relative stabilities of different conformers.

The information obtained from structural parameters,

conformational stabilities, force constants, vibrational frequencies as

well as infrared and Raman band intensities gives significant

contributions to the field of vibrational spectroscopy.

Harmonic force constants in Cartesian coordinates can be

directly derived from ab initio calculations. These force constants can

be transformed to force constants in internal or symmetry

coordinates. Ab initio calculations followed by normal coordinate

analysis are very helpful in making reliable vibrational assignments.

Band intensities from ab initio studies are another important output.

Such band intensity data can also be very useful in making

vibrational assignments. Two principally different quantum

mechanical methods addressing the vibrational problems are namely

Hartree-Fock method and Density functional theory (DFT). Density

functional theory calculation has emerged in the past few years as

successful alternative to traditional Hartree-Fock method. The DFT

35
methods, particularly hybrid functional methods [64-67] have evolved

as a powerful quantum chemical tool for the determination of the

electronic structure of molecules. In the frame work of DFT approach,

different exchange and correlation functional are routinely used.

Among these, the Becke-3-Lee-Yang-Parr (B3LYP) combination [68-69]

is the most used since it proved its ability in reproducing various

molecular properties, including vibrational spectra. The combined use

of B3LYP functional and various standard basis sets, provide an

excellent compromise between accuracy and computational efficiency

of vibrational spectra for large and medium size molecules.

The vibrational frequencies calculated by applying DFT methods

are normally overestimated. This overestimation is due to the

neglect of electron correlation, anharmonicities and incomplete basis

sets.

This overestimation can be narrowed down by applying

empirical corrections called scaling, where the empirical scaling

factors are ranging from 0.8 to 1.0. The scaling factors depend both

on method and basis sets and they partially compensate for the

systemic errors in the calculation of frequencies. Global scaling or

uniform scaling, multiple scaling or selective scaling are some scaling

methods advocated to minimize the overestimation of the frequency

differences. Ab initio calculation could be performed using Gaussian

2009W Software package [70].

36
 If the quantum-mechanical force field is not corrected,

especially in the case of large deviations from the experimental

results, this omission can complicate the theoretical analysis of the

vibrational spectrum of a molecule and lead to errors in the

assignment of the experimental frequencies. Therefore, determining

empirical corrections to quantum mechanical force fields is

important. It is shown that among all the methods for empirically

correcting quantum mechanical force fields, the one with the best

physical basis is the modern version of the Pulay method [71-73].

A simple flow chart which explains the complete scheme of

calculation by quantum chemical methods is given below.

Graphical input of geometry (or)

Input files as recommended by Gaussian inc.

Ab initio geometry optimizations including offset

forces

Cartesian gradient, Force constant, Dipole moment

and polarisability derivatives

Transformation of force constants, Dipole moment

and polarisability derivatives, scaling of Frequencies,
Normal coordinates analysis

Theoretical frequencies, IR and Raman intensities in

the form of graphical display.

37
2.4 DENSITY FUNCTIONAL THEORY

The main objective of density functional theory is to replace the

manybody electronic wave function with the electronic density as

the basic quantity. Whereas the many-body wave function is

dependent on 3N variables, three spatial variables for each of the N

electrons, the density is only a function of three variables and is a

simpler quantity to deal with both conceptually and practically.

The most common implementation of density functional theory

is through the KohnSham method. Within the frame work at Kohn

Sham DFT, the intractable manybody problem of interacting

electrons in a static external potential is reduced to a tractable

problem of non-interacting electrons moving in an effective potential.

The effective potential includes the external potential and the effects

of the coulomb interactions between the electrons eg. the exchange

and correlation interactions. In many cases DFT with the local-

density approximation give quite satisfactory results, at relatively

less computational costs when compared to other ways of solving the

quantum mechanical many body problem.

2.4.1 Derivation and formalism of DFT

As usual in many-body electronic structure calculations, the

nuclei of the treated molecules or clusters are seen as fixed (the

Born-Oppenheimer approximation), generating a static external

potential V in which the electrons are moving. A stationary

38

electronic state is then described by wave functions ( r 1 ,..., r N )

fulfilling the manyelectron Schrodinger equation.

N 2 N

2
H = [T +V +U] = + V( r i ) + U( r i , r j ) = ..... (2.4)
E
i 2m i
i i< j

Where H is the electronic molecular Hamiltonian, N is the

number of electrons and U is the electron - electron interaction. The

operators T and U are so - called universal operators as they are the

same for any system, while V is system dependent or non-universal.

As one can see, the actual difference between a single particle

problem and the much more complicated manyparticle problem just

arises from the interaction term U. There are many sophisticated

methods for solving the many-body Schrodinger equation based on

the expansion of the wave function in Slater determinants. While the

simplest one is the Hartree-Fock method, more sophisticated

approaches are usually categorized as post-Hartree-Fock methods.

However, the problem with these methods is the huge computational

effort, which makes it virtually impossible to apply them efficiently to

larger, more complex systems.

Here DFT provides an appealing alternative, being much more

versatile as it provides a way to systematically map the manybody

problem, with U, onto a single-body problem without U. In DFT the

key variable is the particle density n( r ) which is given by,

39
 . . . . . . .

n(r ) = N d3 r2 d3 r3 ... d 3 rN * (r , r2 ..., rN )(r , r2 ..., rN ) (2.5)

Hohenberg and Kohn proved in 1964 [74] that the relation

expressed above can be reversed, i.e. to given ground state

density n0 ( r ) it is in principle to calculate the corresponding ground

state wavefunction 0 ( r 1 ,... rN ) . In other words, 0 is a unique

functional of n0 , i.e.

0 = 0 [n0 ] ..... (2.6)

and consequently all other ground state observables O are also

functionals of n0

O [n0 ] = 0 [n0 ] O 0 [n0 ] . ..... (2.7)

From this follows, in particular, that also the ground state

energy is a functional of n0

E0 = E[n0 ] = 0 [n0 ]T + V + U 0 [n0 ..... (2.8)

]

where the contribution of the external potential 0 [n0 ] V 0 [n0 ] can

be written explicitly in terms of the density.

V[n] = V( r )n( r )d3r ..... (2.9)

The functions T[n] and U[n] are called universal functions while V[n]

is obviously non universal, as it depends on the system under

study. Having specified a system, i.e. V is known, one then has to

minimize the functional,

40


E[n] = T[n] +U[n] + V ( r )n( r )d 3r ..... (2.10)

with respect to n( r ), assuming one has got reliable expressions for

T[n] and U[n]. A successful minimization of the energy functional will

yield the ground state density n0 , and thus all other ground state

observables.

The variational problem of minimizing the energy functional

E[n] can be solved by applying the Lagrangian method of

undetermined multipliers, which was done by Kohn and Sham in

1965 [75]. The functional in the equation (2.10) can be written as a

fictitious density functional of a non-interacting system.

Es [n] = s [n] Ts + Vs s [n] . ..... (2.11)

Where Ts denotes the noninteracting kinetic energy and Vs is

an external effective potential in which the particles are moving.

Obviously, ns ( r ) n( r ) if Vs chosen to be

Vs = V + U + (T Ts )

Thus, one can solve the so-called Kohn-Sham equations of this

auxiliary non-interacting system

2 2
+Vs ( r )i ( r ) =i i ( r ). ..... (2.12)

2m

Which yields the orbitals i that reproduces the density n( r ) of

the original many-body system.

41
 N 2
n( r ) ns ( r ) = i ( r )
i

The effective single-particle potential Vs can be written in more

detail as
.
e 2 ns (r ') 3 .
Vs =V + . . d r ' +Vxc [ns ( r )] ..... (2.13)
r r '

where the second term of equations (2.13) denotes, Hartree term

describing the electron Coulomb repulsion, while the last term VXC is

called the exchange correlation potential. Here, VXC includes all the

many-particle interactions. Since the Hartree term and VXC depend

on n( r ) , which depends on the i , which in turn depend onVs , the

problem of solving the Kohn-Sham equation has to be done in a self-

consistent (i.e., iterative) way. Usually one starts with an initial guess

for n( r ) , then calculated the corresponding Vs and solves the Kohn-

Sham equations for the i . From these values a new density can be

calculated and the whole process is started again. This procedure is

then repeated until convergence is reached.

2.4.2 Application of DFT

Kohn-Sham theory can be applied in several distinct ways

depending on what is being investigated. In molecular calculations, a

huge variety of exchangecorrelation functions have been developed

for chemical applications. A popular functional widely used is B3LYP

[68,69,76] which is a hybrid method in which the DFT exchange

42
functional, is combined with the exchange functional from Hartree

Fock theory. These hybrids functional carry adjustable parameters

which are generally fitted to a training set of molecules.

2.5 BASIS SET

Gaussian 2003 and other ab initio electronic structure

programs use Gaussian type atomic functions as basis functions. A

basis set is the mathematical description of the orbitals within a

system (which in turn combine to approximate the total electronic

wave functions) used to perform theoretical calculation. Larger basis

sets more accurately approximate the orbitals by imposing fewer

restrictions on the location of the electron in space. Each unique

pairing of method with basis set represents a different approximation

to the Schrodinger equation. In the true quantum mechanical

picture, electrons have a finite probability of existing anywhere in

space; this limit corresponds to the infinite basis set expansion.

When molecular calculations are performed, it is common to

use basis composed of a finite number of atomic orbitals, centered at

each atomic nucleus within the molecule. Initially, these atomic

orbitals were typically Slater orbital, which corresponded to a set of

functions which decayed exponentially with distance from the nuclei,

These Slater-type orbitals could be approximated as linear

combinations of Gaussian orbitals. It is easier to calculate overlap

and other intergrals with Gaussian basis functions and this led to

huge computational savings. Of the many basis sets composed of

43
Gaussian-type orbitals (GTOs), the smallest are called minimal basis

sets and they typically composed of the minimum number of basis

functions required to represent all the electrons on each atom.

2.5.1 Minimal basis sets

A common naming convention for minimal basis set is STO-

XG, where X in an integer. This X value represents the number of

Gaussian primitive functions comprising a single basis functions. In

these basis sets, the same number of Gaussian primitives comprises

core and valence orbitals. Minimal basis sets typically give rough

results that are insufficient for research quality publication, but are

much cheaper than their larger counter parts. The commonly used

minimal basis sets are STO-2G, STO-3G, STO-6G, STO-3G*(polarized

version of STO-3G)

2.5.2 Split valence Basis sets

The first way that a basis set can be made larger is to increase

the number of basis functions per atom. The notation for these split-

valance basis sets is typically X-YZg. In this case, X represents the

number of primitive Gaussians comprising each core atomic orbital

basis function. The Y and Z indicate that the valance orbitals are

composed of two basis functions each, the first one composed of a

linear combination of Y primitive Gaussian functions, the other

composed of a linear combination of Z primitive Gaussian functions.

In this case, the presence of two numbers after the hypens implies

that this basis set is a split valance. Split valence basis sets, such as

44
3-21G and 6-31G, have two (or more) sizes of basis function for each

valence orbital for example; hydrogen and carbon are represented as

H :1s,1s'

C :1s,1s ', 2s, 2s ', 2 p x, 2 px ', 2 py , 2 py ', 2 pz , 2 pz '

Where, the primed and unprimed orbitals differ in size. Similarly,

triple zeta basis sets, like 6-311G, use three sizes of contracted

functions for each orbital type.

2.5.3 Polarized basis sets

The most common addition to minimal basis sets is the

addition of polarization functions, denoted by an asterisk*, indicating

that d function added to heavy atom. Two asterisks, **, indicate that

polarization functions are also added to light atoms (hydrogen and

helium). When polarization is added to this basis set, a p-function is

added to the basis set. This adds some additional needed flexibility

within the basis set, effectively allowing molecular orbitals involving

the hydrogen atoms to be more asymmetric about the hydrogen.

Similarly, d-type functions can be added to a basis set with valence

p-orbitals and f-functions to a basis set with d-type orbitals and so

on. The precise notation indicates exactly which and how many

functions are added to the bases set, such as (d, p).Some of the

commonly used polarized basis sets are

6-31G(d) or 6-31G*

6-31G(d,p) or 6-31G**

45
2.5.4 Diffuse functions

Another common addition to basis sets is the addition of

diffuse functions, denoted by a plus sign, +. (i.e., diffuse functions

added to heavy atoms), Two plus signs indicated that diffuse

functions are also added to light atoms (hydrogen and helium). Basis

set with diffuse functions are important for systems where electrons

are relatively far from the nucleus: molecules with lone pairs, anions

and other systems with significant negative charge, systems in their

excited states, systems with low ionization potentials, descriptions of

absolute acidities. They allow orbitals to occupy a larger region of

space. Some of the commonly used diffuse functions are

A 6-31+G(d) or 6-31+G*(i.e 6-31G(d) basis set with diffuse

functions added to heavy atoms).

A 6-31+G(d,p) or 6-31+G**(i.e 6-31G(d,p) basis set with diffuse

functions added to heavy atoms).

Even larger basis sets are now practical for many systems,

such basis sets add multiple polarization function per atom to the

triple zeta basis set.

Examples :

6-311+G(2d, 2p) - Put 2d functions on heavy atoms (plus diffuse

functions), and 2p functions on hydrogens.

6-311+G (2df, 2pd) - Put 2d functions and 1f function on heavy

atoms (plus diffuse functions), and 2p functions and 1d function

on hydrogen

46
 6-311+G (3df, 3pd) - Put 3d functions and 1f function on heavy

atoms, and 3p functions and 1d function on hydrogens, as well as

diffuse functions on both

These basis sets are useful for describing the interactions between

electrons in electron correlation method; they are not generally

needed for HartreeFock calculations.

2.6 SCALING OF FORCE FIELDS

SQM, the method of scaled quantum mechanical force fields

[77] is a pragmatic approach to the ab initio based determination of

molecular force fields. Its basis idea is a to use relatively low level ab

initio calculations using small basis sets and combine them with

experimental information in the form of an empirical adjustment,

scaling of the calculated force constants. SQM force fields are of

comparable accuracy with the best purely theoretical results.

Quantum mechanical methods yield harmonic force constants.

On the other hand, the observed frequencies are anharmonic, but it

is possible to calculate the harmonic frequencies of small molecules

from the observed vibrational spectra. The frequencies that are

calculated on the basis of quantum mechanical force fields usually

differ appreciably from the observed frequencies. This is partly due to

the neglect of anharmoncity and party due to approximate nature of

the quantum mechanical methods. The scaling procedure fits the

force field to observed (anharmonic) frequencies; therefore the scale

factors correct, as far as possible, the anharmonicity. Thus, the

47
reproduction of observed spectra may be better with SQM force than

with the best harmonic field.

The basic features of SQM are as follows:

(1) For the reference geometry, rather than using the theoretical

geometry of the quantum chemical method applied, the ideal

choice would be the best experimental geometry. This

eliminates a major part of the short comings of the HF method

in predicting potential surfaces [78-80]. In practice, a reliable

equilibrium structure is not always available and theoretical

geometry is corrected based on experience on small molecules.

(2) Scaling of force constants was proposed to account for the

deviation of the calculated and the observed frequencies and

was first attempted by Blom and Altona [81]. They scaled the

diagonal internal force constants with different scale factors

but used the same scale factors for the cross terms. Later on

pulay et al. [76] introduced a formula for the scaling of a force

constants fij :

f ij = S i S j fij ..... (2.14)

where the symbol Si and Sj denote the scale factors for the

diagonal force constants fii and fjj. Pulays method makes it

possible to calculate scale factors that are transferable between

similar molecules if suitable internal coordinates are chosen.

48
 (3) For systematic calculations, the same basis set should be used

consistently.

2.7. COMPUTATIONAL PROCEDURE

Molvib [82] is a program used for the calculation of classical

molecular force fields. This program can be used for the scaling of

vibrational force fields by treating the scale factors as ordinary force

constants. They can thus be calculated from a least squares fit of the

calculated and observed frequencies.

To perform the scale factor calculations, the program needs the

atomic coordinates, and the Cartesian force constants from an ab

initio calculation. An auxiliary program (Rdarch) is used to extract

these data from the archive part of the output file of ab initio

calculations. In addition, this program can also extract the dipole

derivatives and the polarization derivatives, which are needed for

intensity calculations.

Molvib will convert the Gaussian force constants, which are

expressed in atomic units, into the units used by the program. Since

the optimal values of the scale factors usually are less than 1, it is

good to start with an initial calculation, where all the scale factors

have been set to 1, and check whether Molvib can reproduce the

frequencies calculated by the ab initio program.

In Molvib, three methods are available for the scale factor

calculations. Two of them are based on Pulays method, which was

described earlier. A strict application of this method would mean that

49
the non-diagonal terms in the potential energy will depend non-

linearly on the scale factors.

2V = si f ii qi qi + si s j f ij qi q j ..... (2-15)
i i j i

In the simplest method, the factor si s j that occurs in front of

the non-diagonal force constant will therefore be fixed during the

iteration, which means that the calculation has to be repeated. In

this case, the frequency fit usually converges in four or five

iterations, and often just a few repetitions are necessary. The initial

values for the scale factors are set to 1.

One can also use a variant of this method, where the scale

factors associated with the non-diagonal force constants are updated

during each iteration, but this produces usually a large number of

non-zero F-matrix elements. On the other hand, the calculation need

not be repeated and is thus easier to use than the first method.

Lastly, it is also possible to use individual scale factors for the

non-diagonal force constants. In this case, scale factors should be

associated both with diagonal and non-diagonal terms. Similar ideas

have been proposed by Blom and Altona [81]. However, too many

different scales should not be used; but instead group similar factors

together, so that the total number of scale factors is less than about

10. Too many scale factors can also give rise to large correlations.

The scale factors are calculated from a least squares fit of the

observed vibrations in a similar way as the force constants.

50
2.7.1. Intensity calculations in molvib

The integrated molar absorption coefficient Ak of the kth

vibrational mode Qk can be expressed as

2 2
1 N A
Ak =
4 0 3c 2
Qk
= 974.86277
Qk
[km / mol ]
g g

where the dipole derivatives are expressed in units of eu-1/2

(summations is over the components of degenerate vibrations)

The components of the derivatives are found from [83]
Qk

i i u ,k
=
Qk x m

where are the Cartesian dipole derivatives, obtained from the
x

Gaussian archive coordinates file. The transition moments are also

calculated from the dipole derivatives with respect to the normal

coordinates.

In a similar way the polarisability derivatives with respect to

the normal Qk are found from the Cartesian polarisability derivatives

[84].

ij ij u ,k
=
Qk x m

The mean polarisability is calculated from

= 13 11 + 22 + 33
k Qk Qk Qk

and the anisotropy is found from

51


2

2 2
2
r = 1
2 22 + 11 33 + 22 33
11 Q
Qk
Q Qk Qk
Qk
k
k

2 2
2


+ 6 12 + 13 + 23


Q Q
k k
Qk

The Raman activity can then be expressed as

4
a
0 (45 2 + 2 ) = 0.0784163 (45 2 + 2 ),

and the depolarization degree as

3 2
=
45 + 4 2

Molvib expresses the infrared and Raman intensities in the

same units as the Gaussian program.

2.7.2 Gauss View

Gauss View is an affordable, full-featured graphical user

interface for Gaussian 09. Guass view includes an advanced

Molecule Builder. It can be used to rapidly sketch in molecules and

examine them in three dimensions.

Gauss views Gaussian Calculation Setup window allows to set

up Gaussian 09 jobs in a simple and straightforward manner.

Gauss View can graphically display a variety of Gaussian

calculation results, including the following:

Optimized molecular structures Molecular orbitals

52
Atomic charges

53
 Electron density surfaces from any computed density

Electrostatic potential surfaces

NMR shielding density

Animation of the normal modes corresponding to vibrational

frequencies

2.7.3 Gaussian Program

Exploring Chemistry with Electronic structure Methods serves

as an introduction to the capabilities of and procedures for this

variety of computational chemistry. This work was developed using

the Gaussian series of computational chemistry. This work was

developed using the Gaussian series of computational chemistry

programs for all of its specific examples and exercises (specially

Gaussian 09).

Gaussian is capable of predicting many properties of molecules

and reactions including the following

Gaussian is capable of predicting many properties of molecules

and reactions including the following

Molecular energies and structures

Energies and structures of transition states

Bond and reaction energies

Molecular orbitals

Multiple moments

54
 Atomic charges and electrostatic potentials

Vibrational frequencies

IR and Raman spectra

NMR properties

Polarizabilities and hyperpolarizabilities

Thermochemical properties

Reaction pathways

Computations can be carried out on systems in the gas phase

or in solution, and in their ground state or in an excited state.

Gaussian can serve as a powerful tool for exploring areas of chemical

interest like substituent effects, reaction mechanisms, potential

energy surfaces, and excitation energies.

2.8. NORMAL COORDINATE ANALYSIS

The procedures outlined by Wilson et al., [24,85] Nakamoto et

al. [7] and Colthub et al. [9] have been applied in the present

investigations for the treatment of normal coordinates analysis of

aromatic and heterocyclic compounds.

2.8.1 Structure of molecule

Usually the structure of the molecule is available from x-ray

studies or electron diffraction studies. In case the structure is not

available it is assumed and the molecular parameters from the

related systems are transferred.

55
2.8.2 Classification of normal modes

By applying Group theory, the point group symmetry of the

molecule and normal modes of vibrations are classified according to

the irreducible representations. Further these vibrations are

distributed to various symmetry species to which they belong.

Applying IR and Raman selection rules, the number of genuine

vibrations under each species is determined.

2.8.3 Internal coordinates and symmetry coordinates

Internal coordinates are the changes in bond lengths and bond

angles. The symmetry coordinates are constructed from the internal

coordinates and they should be normalized and orthogonalised.

If R is a column matrix consisting of the internal coordinates

and r is the column matrix of the Cartesian coordinates, then

R = Br

where B is the transformation matrix of the order (3n-6)*3N, N

being the number of atoms in the molecule. If U is the orthogonal

transformation matrix and S is a column matrix of the symmetric

coordinates, then

S = UR

2.8.4 Potential energy matrix

The potential energy V of a molecule is the harmonic

approximation and is given by the expression,

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 2V = f ij ri j
ij

where fij are the force constants. This equation can be written in the

matrix form as,

2V = R FR

which becomes interms of symmetric coordinates as,

2V = S FS

where,

F = U FU

R, S and U are the transposes of R,S and U-matrices respectively

2.8.5 Kinetic energy matrix

The kinetic energy can be expressed in the form

2T = S G 1 S

S i

where S is the derivative of the jth internal coordinate G 1 is
t

the inverse kinetic energy matrix obtained from B - matrix

G = BM 1 B

where M 1 is a inverse diagonal matrix of masses of the atoms of the

molecule.

2.8.6 Secular equations

After evaluation the elements of potential and kinetic energy

matrices, the secular equation is to be solved for evaluating the

potential energy constants.

FG E = 0

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 In the above equation E is the unit matrix and is a diagonal

matrix and it is related to the frequencies as

k = 4C 2 v k2

2.8.7 Force constant refinement process

It is very difficult to solve the unsymmetrical FG matrix in the

secular equation. Cyvins Wmatrix method is followed to overcome

this difficulty. The G matrix is factorised into a non singular matrix

such that

G = PP

method introduces several non-vanishing off-diagonal elements in

the F matrix which are useful in calculating interaction force

constants.

where

P is an upper triangular matrix

P is a lower triangular matrix

A trial F matrix is set up by transferring the force constants

from the molecules of similar environment and by diagonalising the

W-Matrix.

W = PFP

and the values are obtained.

The process of successive approximation is continued till all

the calculated frequencies are in good agreement with the observed

values. This method introduces several non-vanishing off-diagonal

58
elements in the F matrix which are useful in calculating interaction

force constants.

2.8.8 Computation of L Matrix

L Matrix is obtained from the force field by factorising the

symmetrised G- matrix into a product of triangular matrices T

and T

G = PP

G = LL

but L = PO

where O is an orthogonal matrix

The secular equation GF E = 0 can be written in the form

LFL =
P O FPO =
O(PFP)O =
OWO =
Here is a diagonal matrix containing eigen values of and

P FP is already defined. The O - matrix is obtained by diagonalising

the W-matrix so as to give the elements of matrix.

2.8.9 Potential energy distribution.

In order to get the complete and accurate picture of the normal

modes of vibrations, the potential energy distribution (PED) has to be

calculated in the present investigation using the relation

Fii L2ia
PED=
a

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where

Fii is the potential energy constant

Lia is the L matrix element and

a is equal to 4 2 c 2 va2

2.9. OTHER MOLECULAR PROPERTIES

2.9.1 Natural Bond Orbital Analysis

Natural bond orbital (NBO) analysis provides the most accurate

possible natural Lewis structure picture of P, because all orbital

details are mathematically chosen to include the highest possible

percentage of the electron density. A useful aspect of the NBO method

is that it gives information about interactions in both filled and virtual

orbital spaces that could enhance the analysis of intra and inter-

molecular interactions.

The second-order Fock matrix was carried to evaluate the

donoracceptor interactions in the NBO analysis [86]. The

interactions result in a loss of occupancy from the localized NBO of

the idealized Lewis structure into an empty non-Lewis orbital. For

each donor (i) and acceptor (j), the stabilization energy E(2) associated

with the delocalization i j is estimated as

..... (2-16)

where qi is the donor orbital occupancy, si and sj are diagonal

elements and F(i,j) is the off diagonal NBO Fock matrix element.

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Natural bond orbital analysis provides an efficient method for

studying intra- and inter-molecular bonding and interaction among

bonds, and also provides a convenient basis for investigating charge

transfer or conjugative interaction in molecular systems.

Some electron donor orbital, acceptor orbital and the

interacting stabilization energy resulted from the second-order

micro- disturbance theory are reported [87,88]. NBO analysis has

been performed on the molecule at the DFT/B3LYP/6-31** level in

order to elucidate the intra-molecular, rehybridization and

delocalization of electron density within the molecule. Delocalization

of electron density between occupied Lewis-type (bond or lone pair)

NBO orbitals and formally unoccupied (anti-bond or Rydberg) non-

Lewis NBO orbitals correspond to a stabilizing donoracceptor

interaction.

2.9.2. THERMODYNAMICAL PROPERTIES

Thermo dynamical parameters like total energy, zero point

vibrational energy, rotational constant, entropy and dipolemoment

have been calculated using DFT and B3LYP/ 6-31G** basis set.

2.9.3.HOMO-LUMO ANALYSIS

Both the highest occupied molecular orbital (HOMO) and the

lowest unoccupied molecular orbital (LUMO) are the main orbital

taking part in chemical reaction. The HOMO and LUMO energy gap

60
calculated by B3LYP/6-31G** method implies an electron density

transfer. The HOMO energy characterizes the ability of electron

giving, the LUMO characterizes the ability of electron accepting, and

the gap between HOMO and LUMO characterizes the molecular

chemical stability. The energy gap between the HOMOs and LUMOs

is a critical parameter in determining molecular electrical transport

properties because it is a measure of electron conductivity. There

are lot of applications available for the use of HOMO-LUMO energy

gap as a quantum chemical descriptor. A large HOMOLUMO gap

implies high stability for the molecule in the sense of its lower

reactivity in chemical reactions.

2.9.4. MOLECULAR ELECTROSTATIC POTENTIAL

Electrostatic potential maps, also known as electrostatic

potential energy maps, or molecular electrical potential surfaces,

illustrate the charge distributions of molecules three dimensionally.

These maps allow us to visualize variably charged regions of a

molecule. Knowledge of the charge distributions can be used to

determine how molecules interact with one another. It

simultaneously displays the molecular shape, size, and charge

distribution, as well as reactive sites of a molecule. The first step

involved in creating an electrostatic potential map is collecting a very

specific type of data: electrostatic potential energy. An advanced

computer program calculates the electrostatic potential energy at a

61
set distance from the nuclei of the molecule. Electrostatic potential

energy is fundamentally a measure of the strength of the nearby

charges, nuclei and electrons, at a particular position.

2.9.5 NMR SPECTRAL ANALYSIS

The NMR spectra calculations were performed using the

Gaussian 09 [70] program package. DFT methods treat the electronic

energy as a function of the electron density of all electrons

simultaneously and thus include electron correlation effect. The

B3LYP method allows calculating the shielding constants with the

proper accuracy, and the GIAO method is one of the most common

approaches for calculating nuclear magnetic shielding tensors.

62