The Basics of NMR

Chapter 1
INTRODUCTION

NMR
Spectroscopy
Units Review

NMR

Nuclear magnetic resonance, or NMR as it is abbreviated by scientists, is a phenomenon

which occurs when the nuclei of certain atoms are immersed in a static magnetic field
and exposed to a second oscillating magnetic field. Some nuclei experience this
phenomenon, and others do not, dependent upon whether they possess a property called
spin. You will learn about spin and about the role of the magnetic fields in Chapter 2, but
first let's review where the nucleus is.

Most of the matter you can examine with NMR is composed of molecules. Molecules are
composed of atoms. Here are a few water molecules. Each water molecule has one
oxygen and two hydrogen atoms. If we zoom into one of the hydrogens past the
electron cloud we see a nucleus composed of a single proton. The proton possesses a
property called spin which:

1. can be thought of as a small magnetic field, and

2. will cause the nucleus to produce an NMR signal.

Not all nuclei possess the property called spin. A list of these nuclei will be presented in
Chapter 3 on spin physics.

Spectroscopy

Spectroscopy is the study of the interaction of electromagnetic radiation with matter.

Nuclear magnetic resonance spectroscopy is the use of the NMR phenomenon to study
physical, chemical, and biological properties of matter. As a consequence, NMR
spectroscopy finds applications in several areas of science. NMR spectroscopy is
routinely used by chemists to study chemical structure using simple one-dimensional
techniques. Two-dimensional techniques are used to determine the structure of more
complicated molecules. These techniques are replacing x-ray crystallography for the
determination of protein structure. Time domain NMR spectroscopic techniques are used
to probe molecular dynamics in solutions. Solid state NMR spectroscopy is used to
determine the molecular structure of solids. Other scientists have developed NMR
methods of measuring diffusion coefficients.

The versatility of NMR makes it pervasive in the sciences. Scientists and students are
discovering that knowledge of the science and technology of NMR is essential for
applying, as well as developing, new applications for it. Unfortunately many of the
dynamic concepts of NMR spectroscopy are difficult for the novice to understand when
static diagrams in hard copy texts are used. The chapters in this hypertext book on NMR
are designed in such a way to incorporate both static and dynamic figures with hypertext.
This book presents a comprehensive picture of the basic principles necessary to begin
using NMR spectroscopy, and it will provide you with an understanding of the principles
of NMR from the microscopic, macroscopic, and system perspectives.

Units Review

Before you can begin learning about NMR spectroscopy, you must be versed in the
language of NMR. NMR scientists use a set of units when describing temperature,
energy, frequency, etc. Please review these units before advancing to subsequent chapters
in this text.

Units of time are seconds (s).

Angles are reported in degrees (o) and in radians (rad). There are 2 radians in 360o.

The absolute temperature scale in Kelvin (K) is used in NMR. The Kelvin temperature
scale is equal to the Celsius scale reading plus 273.15. 0 K is characterized by the
absence of molecular motion. There are no degrees in the Kelvin temperature unit.

Magnetic field strength (B) is measured in Tesla (T). The earth's magnetic field in
Rochester, New York is approximately 5x10-5 T.

The unit of energy (E) is the Joule (J). In NMR one often depicts the relative energy of a
particle using an energy level diagram.

The frequency of electromagnetic radiation may be reported in cycles per second or

radians per second. Frequency in cycles per second (Hz) have units of inverse seconds (s-
1
) and are given the symbols or f. Frequencies represented in radians per second (rad/s)
are given the symbol . Radians tend to be used more to describe periodic circular
motions. The conversion between Hz and rad/s is easy to remember. There are 2
radians in a circle or cycle, therefore

2 rad/s = 1 Hz = 1 s-1.

Power is the energy consumed per time and has units of Watts (W).
Finally, it is common in science to use prefixes before units to indicate a power of ten.
For example, 0.005 seconds can be written as 5x10-3 s or as 5 ms. The m implies 10-3. The
animation window contains a table of prefixes for powers of ten.

In the next chapter you will be introduced to the mathematical beckground necessary to
begin your study of NMR.

The Basics of NMR

Chapter 2
THE MATHEMATICS OF NMR

Exponential Functions
Trigonometric Functions
Differentials and Integrals
Vectors
Matrices
Coordinate Transformations
Convolutions
Imaginary Numbers
The Fourier Transform

Exponential Functions

The number 2.71828183 occurs so often in calculations that it is given the symbol e.
When e is raised to the power x, it is often written exp(x).
ex = exp(x) = 2.71828183x

Logarithms based on powers of e are called natural logarithms. If

x = ey

then

ln(x) = y,

Many of the dynamic NMR processes are exponential in nature. For example, signals
decay exponentially as a function of time. It is therefore essential to understand the nature
of exponential curves. Three common exponential functions are

y = e-x/t
 y = (1 - e-x/t)

y = (1 - 2e-x/t)

where t is a constant.

Trigonometric Functions

The basic trigonometric functions sine and cosine describe sinusoidal functions which
are 90o out of phase.

The trigonometric identities are used in geometric calculations.

Sin( ) = Opposite / Hypotenuse

Cos( ) = Adjacent / Hypotenuse
Tan( ) = Opposite / Adjacent
The function sin(x) / x occurs often and is called sinc(x).

Differentials and Integrals

A differential can be thought of as the slope of a function at any point. For the function

the differential of y with respect to x is

An integral is the area under a function between the limits of the integral.

An integral can also be considered a sumation; in fact most integration is performed by

computers by adding up values of the function between the integral limits.

Vectors

A vector is a quantity having both a magnitude and a direction. The magnetization from
nuclear spins is represented as a vector emanating from the origin of the coordinate
system. Here it is along the +Z axis.
In this picture the vector is in the XY plane between the +X and +Y axes. The vector
has X and Y components and a magnitude equal to
 ( X2 + Y2 )1/2

Matrices

A matrix is a set of numbers arranged in a rectangular array. This matrix has 3 rows and
4 columns and is said to be a 3 by 4 matrix.

To multiply matrices the number of columns in the first must equal the number of rows in
the second. Click sequentially on the next start buttons to see the individual steps
associated with the multiplication.

Coordinate Transformations

A coordinate transformation is used to convert the coordinates of a vector in one

coordinate system (XY) to that in another coordinate system (X"Y").

Convolution

The convolution of two functions is the overlap of the two functions as one function is
passed over the second. The convolution symbol is . The convolution of h(t) and g(t)
is defined mathematically as

The above equation is depicted for rectangular shaped h(t) and g(t) functions in this
animation.

Imaginary Numbers

Imaginary numbers are those which result from calculations involving the square root
of -1. Imaginary numbers are symbolized by i.

A complex number is one which has a real (RE) and an imaginary (IM) part. The real and
imaginary parts of a complex number are orthogonal.

Two useful relations between complex numbers and exponentials are

e+ix = cos(x) +isin(x)

and
e-ix = cos(x) -isin(x).

Fourier Transforms
The Fourier transform (FT) is a mathematical technique for converting time domain data
to frequency domain data, and vice versa.

The Basics of NMR

Chapter 3
SPIN PHYSICS

Spin
Properties of Spin
Nuclei with Spin
Energy Levels
Transitions
Energy Level Diagrams
Continuous Wave NMR Experiment
Boltzmann Statistics
Spin Packets
T1 Processes
Precession
T2 Processes
Rotating Frame of Reference
Pulsed Magnetic Fields
Spin Relaxation
Spin Exchange
Bloch Equations

Spin

What is spin? Spin is a fundamental property of nature like electrical charge or mass.
Spin comes in multiples of 1/2 and can be + or -. Protons, electrons, and neutrons possess
spin. Individual unpaired electrons, protons, and neutrons each possesses a spin of 1/2.

In the deuterium atom ( 2H ), with one unpaired electron, one unpaired proton, and one
unpaired neutron, the total electronic spin = 1/2 and the total nuclear spin = 1.

Two or more particles with spins having opposite signs can pair up to eliminate the
observable manifestations of spin. An example is helium. In nuclear magnetic
resonance, it is unpaired nuclear spins that are of importance.

Properties of Spin
When placed in a magnetic field of strength B, a particle with a net spin can absorb a
photon, of frequency . The frequency depends on the gyromagnetic ratio, of the
particle.
= B

For hydrogen, = 42.58 MHz / T.

Nuclei with Spin

The shell model for the nucleus tells us that nucleons, just like electrons, fill orbitals.
When the number of protons or neutrons equals 2, 8, 20, 28, 50, 82, and 126, orbitals are
filled. Because nucleons have spin, just like electrons do, their spin can pair up when the
orbitals are being filled and cancel out. Almost every element in the periodic table has an
isotope with a non zero nuclear spin. NMR can only be performed on isotopes whose
natural abundance is high enough to be detected. Some of the nuclei routinely used in
NMR are listed below.
Nuclei Unpaired Protons Unpaired Neutrons Net Spin (MHz/T)
1
H 1 0 1/2 42.58
2
H 1 1 1 6.54
31
P 1 0 1/2 17.25
23
Na 1 2 3/2 11.27
14
N 1 1 1 3.08
13
C 0 1 1/2 10.71
19
F 1 0 1/2 40.08

Energy Levels

To understand how particles with spin behave in a magnetic field, consider a proton.
This proton has the property called spin. Think of the spin of this proton as a magnetic
moment vector, causing the proton to behave like a tiny magnet with a north and south
pole.

When the proton is placed in an external magnetic field, the spin vector of the particle
aligns itself with the external field, just like a magnet would. There is a low energy
configuration or state where the poles are aligned N-S-N-S and a high energy state N-
N-S-S.

Transitions

This particle can undergo a transition between the two energy states by the absorption of
a photon. A particle in the lower energy state absorbs a photon and ends up in the upper
energy state. The energy of this photon must exactly match the energy difference between
the two states. The energy, E, of a photon is related to its frequency, , by Plank's
constant (h = 6.626x10-34 J s).
E=h

In NMR and MRI, the quantity is called the resonance frequency and the Larmor
frequency.

Energy Level Diagrams

The energy of the two spin states can be represented by an energy level diagram. We
have seen that = B and E = h , therefore the energy of the photon needed to cause a
transition between the two spin states is
E=h B

When the energy of the photon matches the energy difference between the two spin states
an absorption of energy occurs.

In the NMR experiment, the frequency of the photon is in the radio frequency (RF) range.
In NMR spectroscopy, is between 60 and 800 MHz for hydrogen nuclei. In clinical
MRI, is typically between 15 and 80 MHz for hydrogen imaging.

CW NMR Experiment

The simplest NMR experiment is the continuous wave (CW) experiment. There are two
ways of performing this experiment. In the first, a constant frequency, which is
continuously on, probes the energy levels while the magnetic field is varied. The energy
of this frequency is represented by the blue line in the energy level diagram.

The CW experiment can also be performed with a constant magnetic field and a
frequency which is varied. The magnitude of the constant magnetic field is represented
by the position of the vertical blue line in the energy level diagram.

Boltzmann Statistics

When a group of spins is placed in a magnetic field, each spin aligns in one of the two
possible orientations.

At room temperature, the number of spins in the lower energy level, N+, slightly
outnumbers the number in the upper level, N-. Boltzmann statistics tells us that

N-/N+ = e-E/kT.

E is the energy difference between the spin states; k is Boltzmann's constant, 1.3805x10-23
J/Kelvin; and T is the temperature in Kelvin.
As the temperature decreases, so does the ratio N- /N+. As the temperature increases, the
ratio approaches one.

The signal in NMR spectroscopy results from the difference between the energy absorbed
by the spins which make a transition from the lower energy state to the higher energy
state, and the energy emitted by the spins which simultaneously make a transition from
the higher energy state to the lower energy state. The signal is thus proportional to the
population difference between the states. NMR is a rather sensitive spectroscopy since it
is capable of detecting these very small population differences. It is the resonance, or
exchange of energy at a specific frequency between the spins and the spectrometer, which
gives NMR its sensitivity.

Spin Packets

It is cumbersome to describe NMR on a microscopic scale. A macroscopic picture is

more convenient. The first step in developing the macroscopic picture is to define the
spin packet. A spin packet is a group of spins experiencing the same magnetic field
strength. In this example, the spins within each grid section represent a spin packet.

At any instant in time, the magnetic field due to the spins in each spin packet can be
represented by a magnetization vector.

The size of each vector is proportional to (N+ - N-).

The vector sum of the magnetization vectors from all of the spin packets is the net
magnetization. In order to describe pulsed NMR is necessary from here on to talk in
terms of the net magnetization.

Adapting the conventional NMR coordinate system, the external magnetic field and the
net magnetization vector at equilibrium are both along the Z axis.

T1 Processes

At equilibrium, the net magnetization vector lies along the direction of the applied
magnetic field Bo and is called the equilibrium magnetization Mo. In this configuration,
the Z component of magnetization MZ equals Mo. MZ is referred to as the longitudinal
magnetization. There is no transverse (MX or MY) magnetization here.

It is possible to change the net magnetization by exposing the nuclear spin system to
energy of a frequency equal to the energy difference between the spin states. If enough
energy is put into the system, it is possible to saturate the spin system and make MZ=0.

The time constant which describes how MZ returns to its equilibrium value is called the
spin lattice relaxation time (T1). The equation governing this behavior as a function of the
time t after its displacement is:
 Mz = Mo ( 1 - e-t/T1 )

T1 is therefore defined as the time required to change the Z component of magnetization

by a factor of e.

If the net magnetization is placed along the -Z axis, it will gradually return to its
equilibrium position along the +Z axis at a rate governed by T1. The equation governing
this behavior as a function of the time t after its displacement is:

Mz = Mo ( 1 - 2e-t/T1 )

The spin-lattice relaxation time (T1) is the time to reduce the difference between the
longitudinal magnetization (MZ) and its equilibrium value by a factor of e.

Precession

If the net magnetization is placed in the XY plane it will rotate about the Z axis at a
frequency equal to the frequency of the photon which would cause a transition between
the two energy levels of the spin. This frequency is called the Larmor frequency.

T2 Processes

In addition to the rotation, the net magnetization starts to dephase because each of the
spin packets making it up is experiencing a slightly different magnetic field and rotates at
its own Larmor frequency. The longer the elapsed time, the greater the phase difference.
Here the net magnetization vector is initially along +Y. For this and all dephasing
examples think of this vector as the overlap of several thinner vectors from the individual
spin packets.

The time constant which describes the return to equilibrium of the transverse
magnetization, MXY, is called the spin-spin relaxation time, T2.

MXY =MXYo e-t/T2

T2 is always less than or equal to T1. The net magnetization in the XY plane goes to zero
and then the longitudinal magnetization grows in until we have Mo along Z.

Any transverse magnetization behaves the same way. The transverse component rotates
about the direction of applied magnetization and dephases. T1 governs the rate of
recovery of the longitudinal magnetization.

In summary, the spin-spin relaxation time, T2, is the time to reduce the transverse
magnetization by a factor of e. In the previous sequence, T2 and T1 processes are shown
separately for clarity. That is, the magnetization vectors are shown filling the XY plane
completely before growing back up along the Z axis. Actually, both processes occur
simultaneously with the only restriction being that T2 is less than or equal to T1.
Two factors contribute to the decay of transverse magnetization.
1) molecular interactions (said to lead to a pure pure T2 molecular effect)
2) variations in Bo (said to lead to an inhomogeneous T2 effect
The combination of these two factors is what actually results in the decay of transverse
magnetization. The combined time constant is called T2 star and is given the symbol T2*.
The relationship between the T2 from molecular processes and that from inhomogeneities
in the magnetic field is as follows.

1/T2* = 1/T2 + 1/T2inhomo.

Rotating Frame of Reference

We have just looked at the behavior of spins in the laboratory frame of reference. It is
convenient to define a rotating frame of reference which rotates about the Z axis at the
Larmor frequency. We distinguish this rotating coordinate system from the laboratory
system by primes on the X and Y axes, X'Y'.

A magnetization vector rotating at the Larmor frequency in the laboratory frame appears
stationary in a frame of reference rotating about the Z axis. In the rotating frame,
relaxation of MZ magnetization to its equilibrium value looks the same as it did in the
laboratory frame.

A transverse magnetization vector rotating about the Z axis at the same velocity as the
rotating frame will appear stationary in the rotating frame. A magnetization vector
traveling faster than the rotating frame rotates clockwise about the Z axis. A
magnetization vector traveling slower than the rotating frame rotates counter-clockwise
about the Z axis .

In a sample there are spin packets traveling faster and slower than the rotating frame. As
a consequence, when the mean frequency of the sample is equal to the rotating frame, the
dephasing of MX'Y' looks like this.

Pulsed Magnetic Fields

A coil of wire placed around the X axis will provide a magnetic field along the X axis
when a direct current is passed through the coil. An alternating current will produce a
magnetic field which alternates in direction.

In a frame of reference rotating about the Z axis at a frequency equal to that of the
alternating current, the magnetic field along the X' axis will be constant, just as in the
direct current case in the laboratory frame.

This is the same as moving the coil about the rotating frame coordinate system at the
Larmor Frequency. In magnetic resonance, the magnetic field created by the coil passing
an alternating current at the Larmor frequency is called the B1 magnetic field. When the
alternating current through the coil is turned on and off, it creates a pulsed B1 magnetic
field along the X' axis.

The spins respond to this pulse in such a way as to cause the net magnetization vector to
rotate about the direction of the applied B1 field. The rotation angle depends on the length
of time the field is on, , and its magnitude B1.

=2 B1.

In our examples, will be assumed to be much smaller than T1 and T2.

A 90o pulse is one which rotates the magnetization vector clockwise by 90 degrees about
the X' axis. A 90o pulse rotates the equilibrium magnetization down to the Y' axis. In the
laboratory frame the equilibrium magnetization spirals down around the Z axis to the XY
plane. You can see why the rotating frame of reference is helpful in describing the
behavior of magnetization in response to a pulsed magnetic field.

A 180o pulse will rotate the magnetization vector by 180 degrees. A 180o pulse rotates the
equilibrium magnetization down to along the -Z axis.

The net magnetization at any orientation will behave according to the rotation equation.
For example, a net magnetization vector along the Y' axis will end up along the -Y' axis
when acted upon by a 180o pulse of B1 along the X' axis.

A net magnetization vector between X' and Y' will end up between X' and Y' after the
application of a 180o pulse of B1 applied along the X' axis.

A rotation matrix (described as a coordinate transformation in #2.6 Chapter 2) can also be

used to predict the result of a rotation. Here is the rotation angle about the X' axis, [X',
Y', Z] is the initial location of the vector, and [X", Y", Z"] the location of the vector after
the rotation.

Spin Relaxation

Motions in solution which result in time varying magnetic fields cause spin relaxation.

Time varying fields at the Larmor frequency cause transitions between the spin states and
hence a change in MZ. This screen depicts the field at the green hydrogen on the water
molecule as it rotates about the external field Bo and a magnetic field from the blue
hydrogen. Note that the field experienced at the green hydrogen is sinusoidal.

There is a distribution of rotation frequencies in a sample of molecules. Only frequencies

at the Larmor frequency affect T1. Since the Larmor frequency is proportional to Bo, T1
will therefore vary as a function of magnetic field strength. In general, T1 is inversely
proportional to the density of molecular motions at the Larmor frequency.

The rotation frequency distribution depends on the temperature and viscosity of the
solution. Therefore T1 will vary as a function of temperature. At the Larmor frequency
indicated by o, T1 (280 K ) < T1 (340 K). The temperature of the human body does not
vary by enough to cause a significant influence on T1. The viscosity does however vary
significantly from tissue to tissue and influences T1 as is seen in the following molecular
motion plot.

Fluctuating fields which perturb the energy levels of the spin states cause the transverse
magnetization to dephase. This can be seen by examining the plot of Bo experienced by
the red hydrogens on the following water molecule. The number of molecular motions
less than and equal to the Larmor frequency is inversely proportional to T2.

In general, relaxation times get longer as Bo increases because there are fewer relaxation-
causing frequency components present in the random motions of the molecules.

Spin Exchange

Spin exchange is the exchange of spin state between two spins. For example, if we have
two spins, A and B, and A is spin up and B is spin down, spin exchange between A and B
can be represented with the following equation.
A( ) + B( ) A( ) + B( )

The bidirectional arrow indicates that the exchange reaction is reversible.

The energy difference between the upper and lower energy states of A and of B must be
the same for spin exchange to occur. On a microscopic scale, the spin in the upper energy
state (B) is emitting a photon which is being absorbed by the spin in the lower energy
state (A). Therefore, B ends up in the lower energy state and A in the upper state.

Spin exchange will not affect T1 but will affect T2. T1 is not effected because the
distribution of spins between the upper and lower states is not changed. T2 will be
affected because phase coherence of the transverse magnetization is lost during exchange.

Another form of exchange is called chemical exchange. In chemical exchange, the A and
B nuclei are from different molecules. Consider the chemical exchange between water
and ethanol.

CH3CH2OHA + HOHB CH3CH2OHB + HOHA

Here the B hydrogen of water ends up on ethanol, and the A hydrogen on ethanol ends up
on water in the forward reaction. There are four senarios for the nuclear spin, represented
by the four equations.

Chemical exchange will affect both T1 and T2. T1 is now affected because energy is
transferred from one nucleus to another. For example, if there are more nuclei in the
upper state of A, and a normal Boltzmann distribution in B, exchange will force the
excess energy from A into B. The effect will make T1 appear smaller. T2 is effected
because phase coherence of the transverse magnetization is not preserved during
chemical exchange.

Bloch Equations

The Bloch equations are a set of coupled differential equations which can be used to
describe the behavior of a magnetizatiion vector under any conditions. When properly
integrated, the Bloch equations will yield the X', Y', and Z components of magnetization
as a function of time.

The Basics of NMR

Chapter 4
NMR SPECTROSCOPY

Chemical Shift
Spin-Spin Coupling
The Time Domain NMR Signal
The Frequency Convention

Chemical Shift

When an atom is placed in a magnetic field, its electrons circulate about the direction of
the applied magnetic field. This circulation causes a small magnetic field at the nucleus
which opposes the externally applied field.

The magnetic field at the nucleus (the effective field) is therefore generally less than the
applied field by a fraction .

B = Bo (1-σ )

In some cases, such as the benzene molecule, the circulation of the electrons in the
aromatic orbitals creates a magnetic field at the hydrogen nuclei which enhances the Bo
field. This phenomenon is called deshielding. In this example, the Bo field is applied
perpendicular to the plane of the molecule. The ring current is traveling clockwise if you
look down at the plane.

The electron density around each nucleus in a molecule varies according to the types of
nuclei and bonds in the molecule. The opposing field and therefore the effective field at
each nucleus will vary. This is called the chemical shift phenomenon.

Consider the methanol molecule. The resonance frequency of two types of nuclei in this
example differ. This difference will depend on the strength of the magnetic field, Bo, used
to perform the NMR spectroscopy. The greater the value of Bo, the greater the frequency
difference. This relationship could make it difficult to compare NMR spectra taken on
spectrometers operating at different field strengths. The term chemical shift was
developed to avoid this problem.

The chemical shift of a nucleus is the difference between the resonance frequency of the
nucleus and a standard, relative to the standard. This quantity is reported in ppm and
given the symbol delta, .

δ = (ν - ν REF ) x106 / ν REF

In NMR spectroscopy, this standard is often tetramethylsilane, Si(CH3)4, abbreviated

TMS. The chemical shift is a very precise metric of the chemical environment around a
nucleus. For example, the hydrogen chemical shift of a CH2 hydrogen next to a Cl will be
different than that of a CH3 next to the same Cl. It is therefore difficult to give a detailed
list of chemical shifts in a limited space. The animation window displays a chart of
selected hydrogen chemical shifts of pure liquids and some gasses.

The magnitude of the screening depends on the atom. For example, carbon-13 chemical
shifts are much greater than hydrogen-1 chemical shifts. The following tables present a
few selected chemical shifts of fluorine-19 containing compounds, carbon-13
containing compounds, nitrogen-14 containing compounds, and phosphorous-31
containing compounds. These shifts are all relative to the bare nucleus. The reader is
directed to a more comprehensive list of chemical shifts for use in spectral interpretation.

Spin-Spin Coupling

Nuclei experiencing the same chemical environment or chemical shift are called
equivalent. Those nuclei experiencing different environment or having different chemical
shifts are nonequivalent. Nuclei which are close to one another exert an influence on each
other's effective magnetic field. This effect shows up in the NMR spectrum when the
nuclei are nonequivalent. If the distance between non-equivalent nuclei is less than or
equal to three bond lengths, this effect is observable. This effect is called spin-spin
coupling or J coupling.
Consider the following example. There are two nuclei, A and B, three bonds away from
one another in a molecule. The spin of each nucleus can be either aligned with the
external field such that the fields are N-S-N-S, called spin up , or opposed to the
external field such that the fields are N-N-S-S, called spin down . The magnetic field at
nucleus A will be either greater than Bo or less than Bo by a constant amount due to the
influence of nucleus B.

There are a total of four possible configurations for the two nuclei in a magnetic field.
Arranging these configurations in order of increasing energy gives the following
arrangement. The vertical lines in this diagram represent the allowed transitions
between energy levels. In NMR, an allowed transition is one where the spin of one
nucleus changes from spin up to spin down , or spin down to spin up .
Absorptions of energy where two or more nuclei change spin at the same time are not
allowed. There are two absorption frequencies for the A nucleus and two for the B
nucleus represented by the vertical lines between the energy levels in this diagram.

The NMR spectrum for nuclei A and B reflects the splittings observed in the energy level
diagram. The A absorption line is split into 2 absorption lines centered on A, and the B
absorption line is split into 2 lines centered on B. The distance between two split
absorption lines is called the J coupling constant or the spin-spin splitting constant and is
a measure of the magnetic interaction between two nuclei.

For the next example, consider a molecule with three spin 1/2 nuclei, one type A and two
type B. The type B nuclei are both three bonds away from the type A nucleus. The
magnetic field at the A nucleus has three possible values due to four possible spin
configurations of the two B nuclei. The magnetic field at a B nucleus has two possible
values.

The energy level diagram for this molecule has six states or levels because there are two
sets of levels with the same energy. Energy levels with the same energy are said to be
degenerate. The vertical lines represent the allowed transitions or absorptions of energy.
Note that there are two lines drawn between some levels because of the degeneracy of
those levels.

The resultant NMR spectrum is depicted in the animation window. Note that the center
absorption line of those centered at A is twice as high as the either of the outer two. This
is because there were twice as many transitions in the energy level diagram for this
transition. The peaks at B are taller because there are twice as many B type spins than A
type spins.

The complexity of the splitting pattern in a spectrum increases as the number of B nuclei
increases. The following table contains a few examples.

Configuration Peak Ratios

A 1
 AB 1:1
AB2 1:2:1
AB3 1:3:3:1
AB4 1:4:6:4:1
AB5 1:5:10:10:5:1
AB6 1:6:15:20:15:6:1

This series is called Pascal's triangle and can be calculated from the coefficients of the
expansion of the equation

(x)n

where n is the number of B nuclei in the above table.

When there are two different types of nuclei three bonds away there will be two values
of J, one for each pair of nuclei. By now you get the idea of the number of possible
configurations and the energy level diagram for these configurations, so we can skip to
the spectrum. In the following example JAB is greater JBC.

The Time Domain NMR Signal

An NMR sample may contain many different magnetization components, each with its
own Larmor frequency. These magnetization components are associated with the nuclear
spin configurations joined by an allowed transition line in the energy level diagram.
Based on the number of allowed absorptions due to chemical shifts and spin-spin
couplings of the different nuclei in a molecule, an NMR spectrum may contain many
different frequency lines.

In pulsed NMR spectroscopy, signal is detected after these magnetization vectors are
rotated into the XY plane. Once a magnetization vector is in the XY plane it rotates about
the direction of the Bo field, the axis. As transverse magnetization rotates about the Z
axis, it will induce a current in a coil of wire located around the X axis. Plotting current
as a function of time gives a sine wave. This wave will, of course, decay with time
constant T2* due to dephasing of the spin packets. This signal is called a free induction
decay (FID). We will see in Chapter 5 how the FID is converted into a frequency
domain spectrum. You will see in Chapter 6 what sequence of events will produce a
time domain signal.

The Frequency Convention

Transverse magnetization vectors rotating faster than the rotating frame of reference are
said to be rotating at a positive frequency relatve to the rotating frame (ν ). Vectors
rotating slower than the rotating frame are said to be rotating at a negative frequency
relative to the rotating frame (-ν ).
It is worthwhile noting here that in most NMR spectra, the resonance frequency of a
nucleus, as well as the magnetic field experienced by the nucleus and the chemical shift
of a nucleus, increase from right to left. The frequency plots used in this hypertext book
to describe Fourier transforms will use the more conventional mathematical axis of
frequency increasing from left to right.

The Basics of NMR

Chapter 5
FOURIER TRANSFORMS

Introduction
The + and - Frequency Problem
The Fourier Transform
Phase Correction
Fourier Pairs
The Convolution Theorem
The Digital FT
Sampling Error
The Two-Dimensional FT

Introduction

A detailed description of the Fourier transform ( FT ) has waited until now, when you
have a better appreciation of why it is needed. A Fourier transform is an operation which
converts functions from time to frequency domains. An inverse Fourier transform ( IFT )
converts from the frequency domain to the time domain.

Recall from Chapter 2 that the Fourier transform is a mathematical technique for
converting time domain data to frequency domain data, and vice versa.

The + and - Frequency Problem

To begin our detailed description of the FT consider the following. A magnetization

vector, starting at +x, is rotating about the Z axis in a clockwise direction. The plot of Mx
as a function of time is a cosine wave. Fourier transforming this gives peaks at both +
and - because the FT can not distinguish between a + and a - rotation of the vector
from the data supplied.
A plot of My as a function of time is a -sine function. Fourier transforming this gives
peaks at + and - because the FT can not distinguish between a positive vector rotating
at + and a negative vector rotating at - from the data supplied.

The solution is to input both the Mx and My into the FT. The FT is designed to handle two
orthogonal input functions called the real and imaginary components.

Detecting just the Mx or My component for input into the FT is called linear detection.
This was the detection scheme on many older NMR spectrometers and some magnetic
resonance imagers. It required the computer to discard half of the frequency domain data.

Detection of both Mx and My is called quadrature detection and is the method of detection
on modern spectrometers and imagers. It is the method of choice since now the FT can
distinguish between + and - , and all of the frequency domain data be used.

The Fourier Transform

An FT is defined by the integral

Think of f( ) as the overlap of f(t) with a wave of frequency .

This is easy to picture by looking at the real part of f( ) only.

Consider the function of time, f( t ) = cos( 4t ) + cos( 9t ).

To understand the FT, examine the product of f(t) with cos( t) for values between 1
and 10, and then the summation of the values of this product between 1 and 10 seconds.
The summation will only be examined for time values between 0 and 10 seconds.

=1
=2
=3
=4
=5
=6
=7
=8
 =9
=10
f( )

The inverse Fourier transform (IFT) is best depicted as an summation of the time domain
spectra of frequencies in f( ).

Phase Correction

The actual FT will make use of an input consisting of a REAL and an IMAGINARY part.
You can think of Mx as the REAL input, and My as the IMAGINARY input. The resultant
output of the FT will therefore have a REAL and an IMAGINARY component, too.

Consider the following function:

f(t) = e-at e-i2 t

In FT NMR spectroscopy, the real output of the FT is taken as the frequency domain
spectrum. To see an esthetically pleasing (absorption) frequency domain spectrum, we
want to input a cosine function into the real part and a sine function into the imaginary
parts of the FT. This is what happens if the cosine part is input as the imaginary and the
sine as the real.

To obtain an absorption spectrum as the real output of the FT, a phase correction must be
applied to either the time or frequency domain spectra. This process is equivalent to the
coordinate transformation described in Chapter 2

If the above mentioned FID is recorded such that there is a 45o phase shift in the real and
imaginary FIDs, the coordinate transformation matrix can be used with = - 45o. The
corrected FIDs look like a cosine function in the real and a sine in the imaginary.

Fourier transforming the phase corrected FIDs gives an absorption spectrum for the real
output of the FT. This correction can be done in the frequency domain as well as in the
time domain.

NMR spectra require both constant and linear corrections to the phasing of the Fourier
transformed signal.

=m +b

Constant phase corrections, b, arise from the inability of the spectrometer to detect the
exact Mx and My. Linear phase corrections, m, arise from the inability of the spectrometer
to detect transverse magnetization starting immediately after the RF pulse.
In magnetic resonance, the Mx or My signals are displayed. A magnitude signal might
occasionally be used in some applications. The magnitude signal is equal to the square
root of the sum of the squares of Mx and My.

Fourier Pairs

To better understand FT NMR functions, you need to know some common Fourier pairs.
A Fourier pair is two functions, the frequency domain form and the corresponding
time domain form. Here are a few Fourier pairs which are useful in NMR. The amplitude
of the Fourier pairs has been neglected since it is not relevant in NMR.

Constant value at all time

Real: cos(2 t), Imaginary: -sin(2 t)

Comb Function (A series of delta functions separated by T.)

Exponential Decay: e-at for t > 0.

A square pulse starting at 0 that is T seconds long.

Gaussian: exp(-at2)

Convolution Theorem

To the magnetic resonance scientist, the most important theorem concerning Fourier
transforms is the convolution theorem. The convolution theorem says that the FT of a
convolution of two functions is proportional to the products of the individual Fourier
transforms, and vice versa.

If f( ) = FT( f(t) ) and h( ) = FT( h(t) )

then f( ) g( ) = FT( g(t) f(t) ) and f( ) g( ) = FT( g(t) f(t) )

It will be easier to see this with pictures. In the animation window we are trying to find
the FT of a sine wave which is turned on and off. The convolution theorem tells us that
this is a sinc function at the frequency of the sine wave.

Another application of the convolution theorem is in noise reduction. With the

convolution theorem it can be seen that the convolution of an NMR spectrum with a
Lorentzian function is the same as the Fourier Transform of multiplying the time domain
signal by an exponentially decaying function.

The Digital FT
In a nuclear magnetic resonance spectrometer, the computer does not see a continuous
FID, but rather an FID which is sampled at a constant interval. Each data point making up
the FID will have discrete amplitude and time values. Therefore, the computer needs to
take the FT of a series of delta functions which vary in intensity.

Sampling Error

The wrap around problem or artifact in a nuclear magnetic resonance spectrum is the
appearance of one side of the spectrum on the opposite side. In terms of a one
dimensional frequency domain spectrum, wrap around is the occurrence of a low
frequency peak which occurs on the high frequency side of the spectrum.

The convolution theorem can explain why this problem results from sampling the
transverse magnetization at too slow a rate. First, observe what the FT of a correctly
sampled FID looks like. With quadrature detection, the spectral width is equal to the
inverse of the sampling frequency, or the width of the green box in the animation
window.

When the sampling frequency is less than the spectral width, wrap around occurs.

The Two-Dimensional FT

The two-dimensional Fourier transform (2-DFT) is an FT performed on a two

dimensional array of data.

Consider the two-dimensional array of data depicted in the animation window. This
data has a t' and a t" dimension. A FT is first performed on the data in one dimension and
then in the second. The first set of Fourier transforms are performed in the t' dimension to
yield an f' by t" set of data. The second set of Fourier transforms is performed in the t"
dimension to yield an f' by f" set of data.

The 2-DFT is required to perform state-of-the-art MRI. In MRI, data is collected in the
equivalent of the t' and t" dimensions, called k-space. This raw data is Fourier
transformed to yield the image which is the equivalent of the f' by f" data described
above.

The Basics of NMR

Chapter 6
PULSE SEQUENCES

Introduction
The 90-FID Sequence
The Spin-Echo Sequence
The Inversion Recovery Sequence

Introduction

You have seen in Chapter 5 how a time domain signal can be converted into a frequency
domain signal. In this chapter you will learn a few of the ways that a time domain signal
can be created. Three methods are presented here, but there are an infinite number of
possibilities. These methods are called pulse sequences. A pulse sequence is a set of RF
pulses applied to a sample to produce a specific form of NMR signal.

The 90-FID Sequence

In the 90-FID pulse sequence, net magnetization is rotated down into the X'Y' plane with
a 90o pulse. The net magnetization vector begins to precess about the +Z axis. The
magnitude of the vector also decays with time.

A timing diagram is a multiple axis plot of some aspect of a pulse sequence versus time.
A timing diagram for a 90-FID pulse sequence has a plot of RF energy versus time and
another for signal versus time.

When this sequence is repeated, for example when signal-to-noise improvement is

needed, the amplitude of the signal after being Fourier transformed (S) will depend on T1
and the time between repetitions, called the repetition time (TR), of the sequence. In the
signal equation below, k is a proportionality constant and is the density of spins in the
sample.

S = k ( 1 - e-TR/T1 )

The Spin-Echo Sequence

Another commonly used pulse sequence is the spin-echo pulse sequence. Here a 90o
pulse is first applied to the spin system. The 90o degree pulse rotates the magnetization
down into the X'Y' plane. The transverse magnetization begins to dephase. At some
point in time after the 90o pulse, a 180o pulse is applied. This pulse rotates the
magnetization by 180o about the X' axis. The 180o pulse causes the magnetization to at
least partially rephase and to produce a signal called an echo.

A timing diagram shows the relative positions of the two radio frequency pulses and the
signal.

The signal equation for a repeated spin echo sequence as a function of the repetition time,
TR, and the echo time (TE) defined as the time between the 90o pulse and the maximum
amplitude in the echo is
 S = k ( 1 - e-TR/T1 ) e-TE/T2

The Inversion Recovery Sequence

An inversion recovery pulse sequence can also be used to record an NMR spectrum. In
this sequence, a 180o pulse is first applied. This rotates the net magnetization down to the
-Z axis. The magnetization undergoes spin-lattice relaxation and returns toward its
equilibrium position along the +Z axis. Before it reaches equilibrium, a 90o pulse is
applied which rotates the longitudinal magnetization into the XY plane. In this example,
the 90o pulse is applied shortly after the 180o pulse. Once magnetization is present in the
XY plane it rotates about the Z axis and dephases giving a FID.

Once again, the timing diagram shows the relative positions of the two radio frequency
pulses and the signal.

The signal as a function of TI when the sequence is not repeated is

S = k ( 1 - 2e-TI/T1 )

It should be noted at this time that the zero crossing of this function occurs for TI = T1
ln2.

The Basics of NMR

Chapter 7
NMR HARDWARE

Hardware Overview
Magnet
Field Lock
Shim Coils
Sample Probe
RF Coils
Gradient Coils
Quadrature Detector
Digital Filtering
Safety

Hardware Overview
The graphics window displays a schematic representation of the major systems of a
nuclear magnetic resonance spectrometer and a few of the major interconnections. This
overview briefly states the function of each component. Some will be described in detail
later in this chapter.

At the top of the schematic representation, you will find the superconducting magnet of
the NMR spectrometer. The magnet produces the Bo field necessary for the NMR
experiments. Immediately within the bore of the magnet are the shim coils for
homogenizing the Bo field. Within the shim coils is the probe. The probe contains the RF
coils for producing the B1 magnetic field necessary to rotate the spins by 90o or 180o. The
RF coil also detects the signal from the spins within the sample. The sample is positioned
within the RF coil of the probe. Some probes also contain a set of gradient coils. These
coils produce a gradient in Bo along the X, Y, or Z axis. Gradient coils are used for for
gradient enhanced spectroscopy (See Chapter 11.), diffusion (See Chapter 11.), and NMR
microscopy (See Chapter 11.) experiments.

The heart of the spectrometer is the computer. It controls all of the components of the
spectrometer. The RF components under control of the computer are the RF frequency
source and pulse programmer. The source produces a sine wave of the desired frequency.
The pulse programmer sets the width, and in some cases the shape, of the RF pulses. The
RF amplifier increases the pulses power from milli Watts to tens or hundreds of Watts.
The computer also controls the gradient pulse programmer which sets the shape and
amplitude of gradient fields. The gradient amplifier increases the power of the gradient
pulses to a level sufficient to drive the gradient coils.

The operator of the spectrometer gives input to the computer through a console terminal
with a mouse and keyboard. Some spectrometers also have a separate small interface for
carrying out some of the more routine procedures on the spectrometer. A pulse sequence
is selected and customized from the console terminal. The operator can see spectra on a
video display located on the console and can make hard copies of spectra using a printer.

The next sections of this chapter go into more detail concerning the magnet, lock, shim
coils, gradient coils, RF coils, and RF detector of nuclear magnetic resonance
spectrometer.

Magnet

The NMR magnet is one of the most expensive components of the nuclear magnetic
resonance spectrometer system. Most magnets are of the superconducting type. This is a
picture of a 7.0 Tesla superconducting magnet from an NMR spectrometer. A
superconducting magnet has an electromagnet made of superconducting wire.
Superconducting wire has a resistance approximately equal to zero when it is cooled to a
temperature close to absolute zero (-273.15o C or 0 K) by emersing it in liquid helium.
Once current is caused to flow in the coil it will continue to flow for as long as the coil is
kept at liquid helium temperatures. (Some losses do occur over time due to the
infinitesimally small resistance of the coil. These losses are on the order of a ppm of the
main magnetic field per year.)

The length of superconducting wire in the magnet is typically several miles. This wire is
wound into a multi-turn solenoid or coil. The coil of wire is kept at a temperature of 4.2K
by immersing it in liquid helium. The coil and liquid helium are kept in a large dewar.
This dewar is typically surrounded by a liquid nitrogen (77.4K) dewar, which acts as a
thermal buffer between the room temperature air (293K) and the liquid helium. A cross
sectional view of the superconducting magnet, depicting the concentric dewars, can be
found in the animation window.

The following image is an actual cut-away view of a superconducting magnet. The

magnet is supported by three legs, and the concentric nitrogen and helium dewars are
supported by stacks coming out of the top of the magnet. A room temperature bore hole
extends through the center of the assembly. The sample probe and shim coils are located
within this bore hole. Also depicted in this picture is the liquid nitrogen level sensor, an
electronic assembly for monitoring the liquid nitrogen level.

Going from the outside of the magnet to the inside, we see a vacuum region followed by
a liquid nitrogen reservoir. The vacuum region is filled with several layers of a reflective
mylar film. The function of the mylar is to reflect thermal photons, and thus diminish
heat from entering the magnet. Within the inside wall of the liquid nitrogen reservoir, we
see another vacuum filled with some reflective mylar. The liquid helium reservoir comes
next. This reservoir houses the superconducting solenoid or coil of wire.

Taking a closer look at the solenoid it is clear to see the coil and the bore tube extending
through the magnet.

Field Lock

In order to produce a high resolution NMR spectrum of a sample, especially one which
requires signal averaging or phase cycling, you need to have a temporally constant and
spatially homogeneous magnetic field. Consistency of the Bo field over time will be
discussed here; homogeneity will be discussed in the next section of this chapter. The
field strength might vary over time due to aging of the magnet, movement of metal
objects near the magnet, and temperature fluctuations. Here is an example of a one line
NMR spectrum of cyclohexane recorded while the Bo magnetic field was drifting a very
significant amount. The field lock can compensate for these variations.

The field lock is a separate NMR spectrometer within your spectrometer. This
spectrometer is typically tuned to the deuterium NMR resonance frequency. It constantly
monitors the resonance frequency of the deuterium signal and makes minor changes in
the Bo magnetic field to keep the resonance frequency constant. The deuterium signal
comes from the deuterium solvent used to prepare the sample. The animation window
contains plots of the deuterium resonance lock frequency, the small additional magnetic
field used to correct the lock frequency, and the resultant Bo field as a function of time
while the magnetic field is drifting. The lock frequency plot displays the frequency
without correction. In reality, this frequency would be kept constant by the application of
the lock field which offsets the drift.

On most NMR spectrometers the deuterium lock serves a second function. It provides the
=0 reference. The resonance frequency of the deuterium signal in many lock solvents is
well known. Therefore the difference in resonance frequency of the lock solvent and
TMS is also known. As a consequence, TMS does not need to be added to the sample to
set =0; the spectrometer can use the lock frequency to calculate =0.

Shim Coils

The purpose of shim coils on a spectrometer is to correct minor spatial inhomogeneities

in the Bo magnetic field. These inhomogeneities could be caused by the magnet design,
materials in the probe, variations in the thickness of the sample tube, sample
permeability, and ferromagnetic materials around the magnet. A shim coil is designed to
create a small magnetic field which will oppose and cancel out an inhomogeneity in the
Bo magnetic field. Because these variations may exist in a variety of functional forms
(linear, parabolic, etc.), shim coils are needed which can create a variety of opposing
fields. Some of the functional forms are listed in the table below.
Shim Coil Functional Forms
Shim Function
Z0
Z
Z2
Z3
Z4
Z5
X
XZ
XZ2
X2Y2
XY
Y
YZ
YZ2
XZ3
X2Y2Z
YZ3
XYZ
 X3
Y3

By passing the appropriate amount of current through each coil a homogeneous Bo

magnetic field can be achieved. The optimum shim current settings are found by either
minimizing the linewidth, maximizing the size of the FID, or maximizing the signal from
the field lock. On most spectrometers, the shim coils are controllable by the computer. A
computer algorithm has the task of finding the best shim value by maximizing the lock
signal.

Sample Probe

The sample probe is the name given to that part of the spectrometer which accepts the
sample, sends RF energy into the sample, and detects the signal emanating from the
sample. It contains the RF coil, sample spinner, temperature controlling circuitry, and
gradient coils. The RF coil and gradient coils will be described in the next two sections.
The sample spinner and temperature controlling circuitry will be described here.

The purpose of the sample spinner is to rotate the NMR sample tube about its axis. In
doing so, each spin in the sample located at a given position along the Z axis and radius
from the Z axis, will experience the average magnetic field in the circle defined by this Z
and radius. The net effect is a narrower spectral linewidth. To appreciate this
phenomenon, consider the following examples.

Picture an axial cross section of a cylindrical tube containing sample. In a very

homogeneous Bo magnetic field this sample will yield a narrow spectrum. In a more
inhomogeneous field the sample will yield a broader spectrum due to the presence of
lines from the parts of the sample experiencing different Bo magnetic fields. When the
sample is spun about its z-axis, inhomogeneities in the X and Y directions are averaged
out and the NMR line width becomes narrower.

Many scientists need to examine properties of their samples as a function of temperature.

As a result many instruments have the ability to maintain the temperature of the sample
above and below room temperature. Air or nitrogen which has been warmed or cooled is
passed over the sample to heat or cool the sample. The temperature at the sample is
monitored with the aid of a thermocouple and electronic circuitry maintains the
temperature by increasing or decreasing the temperature of the gas passing over the
sample. More information on this topic will be presented in Chapter 8.

RF Coils

RF coils create the B1 field which rotates the net magnetization in a pulse sequence.
They also detect the transverse magnetization as it precesses in the XY plane. Most RF
coils on NMR spectrometers are of the saddle coil design and act as the transmitter of
the B1 field and receiver of RF energy from the sample. You may find one or more RF
coils in a probe.

Each of these RF coils must resonate, that is they must efficiently store energy, at the
Larmor frequency of the nucleus being examined with the NMR spectrometer. All NMR
coils are composed of an inductor, or inductive elements, and a set of capacitive
elements. The resonant frequency, , of an RF coil is determined by the inductance (L)
and capacitance (C) of the inductor capacitor circuit.

RF coils used in NMR spectrometers need to be tuned for the specific sample being
studied. An RF coil has a bandwidth or specific range of frequencies at which it
resonates. When you place a sample in an RF coil, the conductivity and dielectric
constant of the sample affect the resonance frequency. If this frequency is different from
the resonance frequency of the nucleus you are studying, the coil will not efficiently set
up the B1 field nor efficiently detect the signal from the sample. You will be rotating the
net magnetization by an angle less than 90 degrees when you think you are rotating by 90
degrees. This will produce less transverse magnetization and less signal. Furthermore,
because the coil will not be efficiently detecting the signal, your signal-to-noise ratio will
be poor.

The B1 field of an RF coil must be perpendicular to the Bo magnetic field. Another

requirement of an RF coil in an NMR spectrometer is that the B1 field needs to be
homogeneous over the volume of your sample. If it is not, you will be rotating spins by a
distribution of rotation angles and you will obtain strange spectra.

Gradient Coils

The gradient coils produce the gradients in the Bo magnetic field needed for performing
gradient enhanced spectroscopy, diffusion measurements, and NMR microscopy. The
gradient coils are located inside the RF probe. Not all probes have gradient coils, and not
all NMR spectrometers have the hardware necessary to drive these coils.

The gradient coils are room temperature coils (i.e. do not require cooling with cryogens
to operate) which, because of their configuration, create the desired gradient. Since the
vertical bore superconducting magnet is most common, the gradient coil system will be
described for this magnet.

Assuming the standard magnetic resonance coordinate system, a gradient in Bo in the Z

direction is achieved with an antihelmholtz type of coil. Current in the two coils flow in
opposite directions creating a magnetic field gradient between the two coils. The B field
at the center of one coil adds to the Bo field, while the B field at the center of the other
coil subtracts from the Bo field.
The X and Y gradients in the Bo field are created by a pair of figure-8 coils. The X axis
figure-8 coils create a gradient in Bo in the X direction due to the direction of the current
through the coils. The Y axis figure-8 coils provides a similar gradient in Bo along the Y
axis.

Quadrature Detector

The quadrature detector is a device which separates out the Mx' and My' signals from the
signal from the RF coil. For this reason it can be thought of as a laboratory to rotating
frame of reference converter. The heart of a quadrature detector is a device called a
doubly balanced mixer. The doubly balanced mixer has two inputs and one output. If the
input signals are Cos(A) and Cos(B), the output will be 1/2 Cos(A+B) and 1/2 Cos(A-B).
For this reason the device is often called a product detector since the product of Cos(A)
and Cos(B) is the output.

The quadrature detector typically contains two doubly balanced mixers, two filters, two
amplifiers, and a 90o phase shifter. There are two inputs and two outputs on the device.
Frequency and o are put in and the MX' and MY' components of the transverse
magnetization come out. There are some potential problems which can occur with this
device which will cause artifacts in the spectrum. One is called a DC offset artifact and
the other is called a quadrature artifact.

Digital Filtering

Many newer spectrometers employ a combination of oversampling, digital filtering, and

decimation to eliminate the wrap around artifact. Oversampling creates a larger spectral
or sweep width, but generates too much data to be conveniently stored. Digital filtering
eliminates the high frequency components from the data, and decimation reduces the size
of the data set. The following flowchart summarizes the effects of the three steps by
showing the result of performing an FT after each step.

Let's examine oversampling, digital filtering, and decimation in more detail to see how
this combination of steps can be used to reduce the wrap around problem.

Oversampling is the digitization of a time domain signal at a frequency much greater than
necessary to record the desired spectral width. For example, if the sampling frequency, fs,
is increased by a factor of 10, the sweep width will be 10 times greater, thus eliminating
wraparound. Unfortunately digitizing at 10 times the speed also increases the amount of
raw data by a factor of 10, thus increasing storage requirements and processing time.

Filtering is the removal of a select band of frequencies from a signal. For an example of
filtering, consider the following frequency domain signal. Frequencies above fo could
be removed from this frequency domain signal by multipling the signal by this
rectangular function. In NMR, this step would be equivalent to taking a large sweep
width spectrum and setting to zero intensity those spectral frequencies which are farther
than some distance from the center of the spectrum.
Digital filtering is the removal of these frequencies using the time domain signal. Recall
from Chapter 5 that if two functions are multiplied in one domain (i.e. frequency), we
must convolve the FT of the two functions together in the other domain (i.e. time). To
filter out frequencies above fo from the time domain signal, the signal must be convolved
with the Fourier transform of the rectangular function, a sinc function. (See Chapter 5.)
This process eliminates frequencies greater than fo from the time domain signal. Fourier
transforming the resultant time domain signal yields a frequency domain signal without
the higher frequencies. In NMR, this step will remove spectral components with
frequencies greater than +fo and less than -fo.

Decimation is the elimination of data points from a data set. A decimation ratio of 4/5
means that 4 out of every 5 data points are deleted, or every fifth data point is saved.
Decimating the digitally filtered data above, followed by a Fourier transform, will reduce
the data set by a factor of five.

High speed digitizers, capable of digitizing at 2 MHz, and dedicated high speed
integrated circuits, capable of performing the convolution on the time domain data as it is
being recorded, are used to realize this procedure.

Safety

There are some important safety considerations which one should be familiar with before
using an NMR spectrometer. These concern the use of strong magnetic fields and
cryogenic liquids.

Magnetic fields from high field magnets can literally pick up and pull ferromagnetic
items into the bore of the magnet. Caution must be taken to keep all ferromagnetic items
away from the magnet because they can seriously damage the magnet, shim coils, and
probe. The force exerted on the concentric cryogenic dewars within a magnet by a large
metal object stuck to the magnet can break dewars and magnet supports. The kinetic
energy of an object being sucked into a magnet can smash a dewar or an electrical
connector on a probe. Small ferromagnetic objects are just as much a concern as larger
ones. A small metal sliver can get sucked into the bore of the magnet and destroy the
homogeneity of the magnet achieved with a set of shim settings.

There are additional concerns regarding the effect of magnetic fields on electronic
circuitry, specifically pacemakers. An individual with a pacemaker walking through a
strong magnetic field can induce currents in the pacemaker circuitry which will cause it
to fail and possibly cause death. A person with a pacemaker must not be able to
inadvertently stray into a magnetic field of five or more Gauss. Although not as important
as a pacemaker, mechanical watches and some digital watches will also be affected by
magnetic fields. Magnetic fields of approximately 50 Gauss will erase credit cards and
magnetic storage media.

The liquid nitrogen and liquid helium used in NMR spectrometers are at a temperature of
77.4 K and 4.2 K respectively. These liquids can cause frostbite, which is not a concern
unless you are filling the magnet. If you are filling the magnet or if you are operating the
spectrometer, suffocation is another concern you need to be aware of. If the magnet
quenches, or suddenly stops being a superconductor, it will rapidly boil off all its
cryogens, and the nitrogen and helium gasses in a confined space can cause suffocation.

The Basics of NMR

Chapter 8
PRACTICAL CONSIDERATIONS

Introduction
Sample Preparation
Sample Probe Tuning
Determining a 90 Degree Pulse
Field Shimming
Phase Cycling
1-D Hydrogen Spectra
Integration
SNR Improvement
Variable Temperature
Troubleshooting
Cryogen Fills
Unix Primer

Introduction

In previous chapters, you have learned the basic theory of nuclear magnetic resonance.
This chapter emphasizes some of the spectroscopic techniques. While some of these may
be easy for you to understand based on the simple theory you have learned in previous
chapters, there may be specific points discussed which are less obvious because they are
based on theories not presented in this hypertext book.

When comparing two NMR spectra, always keep in mind the subtle differences in the
way the spectra were recorded. One obvious example is the effect of field strength. As
the Bo field increases in magnitude (i.e. 1.5T, 4.7T, 7T) the signal-to-noise ratio generally
increases. The shape of the spectrum may also change. For example, consider the
hydrogen NMR spectrum from three coupled nuclei A, B, and C with the following
chemical shifts and J coupling constants.

Nuclei (ppm)
 A 1.89
B 2.00
C 2.08
Interaction J (Hz)
AB 4
BC 8

Compare the 100 MHz and 400 MHz NMR spectra. The spectral lines from the B type
spins are colored red. You can see how easy it would be to make the wrong choice as to
the structure of the molecule based on the 100 MHz spectrum, although the chance of
error might be reduced if you had further information, eg. the relative areas under the
peaks. This topic is described in a later section of this chapter.

Sample Preparation

NMR samples are prepared by dissolving an analyte in a deuterium lock solvent. Several
deuterium lock solvents are available . Some of these solvents will readily absorb
moisture from the atmosphere and give water signal in your spectrum. It is therefore
advisable to keep bottles of these solvents tightly capped when not in use.

Most routine high resolution NMR samples are prepared and run in 5 mm glass NMR
tubes. Always fill your NMR tubes to the same height with lock solvent. This will
minimize the amount of magnetic field shimming required. The animation window
depicts a sample tube filled with solvent such that it fills the RF coil.

The concentration of your sample should be great enough to give a good signal-to-noise
ratio in your spectrum, yet minimize exchange effects found at high concentrations.
The exact concentration of your sample in the lock solvent will depend on the sensitivity
of the spectrometer. If you have no guidelines for a specific spectrometer, use one drop of
analyte for liquids and one or two crystals for solid samples.

The position of spectral absorption lines can be solvent dependent. Therefore, if you are
comparing spectra or trying to identify an unknown sample by comparison to reference
spectra, use the same solvent. The hydrogen NMR spectrum of ethanol is a good example
of this solvent dependence. Compare the positions of the CH3, CH2, and OH absorption
lines in a hydrogen NMR spectrum of ethanol in the lock solvents CDCl3 and D2O .
Notice also that the relative peak heights are not the same in the two spectra. This is
because the linewidths are not equal. The area under a peak, not the height of a peak, is
proportional to the number of hydrogens in a sample. This point will be emphasized later
in this chapter.

Variations in the polarity and dielectric constant of the lock solvent will also effect the
tuning of the probe. The correction of these effects are covered in the next section of this
chapter on sample probe tuning.
Sample Probe Tuning

Variations in the polarity and dielectric constant of the lock solvent will affect the probe
tuning. For this reason the probe should be tuned whenever the lock solvent is changed.
Tuning the probe entails adjusting two capacitors on the RF probe. One capacitor is
called the matching capacitor and the other the tuning capacitor. The matching capacitor
matches the impedance of the loaded probe to that of the 50 Ohm cable coming from the
spectrometer. The tuning capacitor changes the resonance frequency of the RF coil.

Most spectrometers have a probe tuning mode of operation. This mode of operation
presents a display of reflected power vs. frequency on the screen. The goal is to adjust the
display so that the reflected power from the probe is zero at the resonance frequency of
the nucleus you are examining.

As the polarity and dielectric constant of the lock solvent changes, so does the bandwidth
of the RF probe. This is significant because it affects the amount of RF power needed to
produce a 90 degree pulse. The larger the bandwidth, the more power is needed to
produce the 90 degree rotation.

Determinining a 90o Pulse

As pointed out in the previous section of this chapter, changes in the polarity and
dielectric constant of the lock solvent affect the bandwidth of the RF probe which in turn
affects the amount of RF power needed to produce a 90 degree rotation. Most NMR
spectrometers will not allow you to change the RF power, but they will permit you to
change the pulse length. Therefore, if the bandwidth of the RF probe increases, you will
need to increase the RF pulse width to produce a 90 degree pulse.

To determine the pulse width needed to produce a 90 degree pulse, you should perform
the following experiment using a sample which has a single absorption line and a
relatively short T1. Record a series of spectra with incrementally longer RF pulse widths.
Fourier transform the time domain signals and plot these lines as a function of pulse
width. The peak height should vary sinusoidally with increasing pulse width. The 90
degree pulse width will be the first maximum. The 180 degree pulse width will be the
first zero crossing. Many spectrometers have routines which will automatically record the
data necessary to produce these plots.

You should also be aware of the effect of varying the width of the RF pulse on the
distribution of frequencies being delivered to your sample. Recall from the discussion of
the convolution theorem in Chapter 5 that the Fourier pair of a sine wave which is turned
on and off is a sinc function centered at the frequency of the sine wave. When you
apply an RF pulse of width t in the time domain, you apply a distribution of frequencies
to your sample. Not all of these frequencies will have sufficient B1 magnitude to produce
a 90 degree rotation. The range of frequencies from the center of the distribution to the
first zeros in the distribution is +/- 1/t. As your pulse width increases, the width of the
distribution of frequencies in your pulse decreases. If the distribution is too narrow, you
may not be applying the desired rotation to the entire sample.

Field Shimming

The purpose of shimming a magnet is to make the magnetic field more homogeneous and
to obtain better spectral resolution. Shimming can be performed manually or by computer
control. It is not the intent of this section to teach you a step-by-step procedure for
shimming, but to present you with the basic theory so that you can, with the aid of your
NMR instruction manual, shim your magnet. The reader is encouraged to write down or
save the current shim settings before making changes to any of the current shims coil
settings.

Broad lines, asymmetric lines, and a loss of resolution are indications that a magnet needs
to be shimmed. The shape of an NMR line is a good indication of which shim is
misadjusted. Consider a single narrow NMR line. If we zoom in on this line we might see
the following shape. . The following series of spectra depict the appearance of this
spectral line in the presence of various inhomogeneities.

Shim Spectrum
Z2
Z3
Z4
X, Y, ZX, or ZY
XY or X2-Y2

In general, asymmetric lineshapes result from mis-adjusted even-powered Z shims. This

can be seen by looking at the shape of a Z2 shim field. As you go further away from the
center of the sample in the +Z or -Z direction, the field increases, giving more
components of the spectral line at higher fields. The higher the power of the Z
inhomogeneity, the further away the asymmetry is from the center of the line.

Symmetrically broadened lines are from mis-adjusted odd-powered Z shims. Consider

the shape of the Z3 shim field. The top of the sample (+Z) is at a higher field, resulting
in higher field spectral components, while the bottom (-Z) is at a lower field, giving more
lower field spectral components. Transverse shims (X,Y) will cause large first order or
second order spinning sidebands when the sample is spun. The shape of these
inhomogeneities cause the sample, when it is spun, to experience a periodic variation in
the magnetic field. Those shims (XY or X2-Y2) causing a spinning sample to experience
two variations per cycle will create second order spinning sidebands.

Phase Cycling
There are a few artifacts of the detection circuitry which may appear in your spectrum if
you record a single FID and Fourier transform it. Phase cycling is the technique used to
eliminate these artifacts. The artifact will be introduced first, followed by the technique
used to eliminate it.

Electronic amplifiers often have small offsets in their output when no signal is being put
in. This is referred to as the DC offset of the amplifier. A DC offset in the time domain is
equivalent to a peak at zero frequency in the frequency domain. If there is an FID on
top of a DC offset, its Fourier transform will have an additional peak at zero frequency in
the spectrum. This picture has been simplified by presenting only the real part of the
signal.

The DC offset could be eliminated by spending thousands of dollars on better quality

amplifiers. Alternatively, the artifact can be removed by taking an FID recorded with a 90
degree pulse applied along +X' , an FID recorded with a 90 degree pulse applied along
-X' (note the phase change in the FID) , multiplying the FID recorded with a 90 degree
pulse along -X' by -1 , adding the two FIDs, and Fourier transforming. This process
only costs a little extra time and a few extra lines of computer code.

Another type of artifact is caused by having unequal gains on the real and imaginary
outputs of the quadrature detector. For a Fourier transform to produce a proper spectrum,
it requires true real and imaginary inputs. When the inputs are equal in amplitude, there
are no negative frequency artifacts in the spectrum. If the two inputs are different, the
negative frequency components of a signal do not cancel. You can tell a negative
frequency artifact because it appears to be the mirror image (but smaller) of a peak from
the opposite sign end of the spectrum.

Negative frequency artifacts can be removed by recording an FID with Mx or the real
signal (My or the imaginary signal) from channel 1 (2) of the quadrature detector.
Another FID is recorded with Mx or the real signal (My or the imaginary signal) from
channel 2 (1) of the quadrature detector. The two FIDs are then averaged. As a result,
the amplitude of the real and imaginary inputs to the FT are equal, so when the FIDs are
Fourier transformed, there are no negative frequency artifacts.

The averaging described above can be achieved by applying a 90 degree pulse about +X
and a 90 degree pulse about +Y, and adding the two resulting FIDs together. To eliminate
all possible errors from different combinations of these types of pulses, phase cycling is
applied. Phase cycling adds together eight FIDs recorded with the following phases to
eliminate all the possible quadrature artifacts.

1-D Hydrogen Spectra

There are several parameters, in addition to the ones already discussed in this chapter,
which must be set before a spectrum can be recorded. These include the width of the
spectrum, number of data points in the spectrum, and the receiver gain. Some of these are
automatically set to default values on some spectrometers. You are encouraged to refer to
Chapter 5 for a deeper appreciation of the significance of these parameters.

Once an FID is recorded and Fourier transformed, the resultant spectrum must be phased
so that all the absorption lines are positive. You are encouraged to review Chapter 5 for
an explanation of the need to phase correcting a spectrum. There are various automatic
and manual phase correction algorithms on most NMR spectrometers.

Here are a few examples of simple hydrogen NMR spectra to demonstrate the capabilities
of NMR spectroscopy. As you become more knowledgeable about NMR, you will learn
the relationship between peak locations, peak splitting, and molecular structure in NMR
spectra.

Molecule Formula Solvent Spectrum

cyclohexane C6H12 CDCl3
benzene C6H6 CDCl3
toluene C6H5CH3 CDCl3
ethyl benzene C6H5CH2CH3 CDCl3
acetone CH3(C=O)CH3 CDCl3
methyl ethyl ketone CH3(C=O)CH2CH3 CDCl3
water H2O D2O
ethanol CH3CH2OH CDCl3
ethanol CH3CH2OH D2O
1-propanol CH3CH2CH2OH CDCl3
2-propanol (CH3)2CHOH CDCl3
t-butanol (CH3)3COH CDCl3
2-butanol CH3CH2CH(OH)CH3 CDCl3
pyridine C5H5N CDCl3

Integration

In addition to chemical shift and spin-spin coupling information, there is one additional
piece of information which the chemist can use in determining the structure of a molecule
from an NMR spectrum. This information is the relative area of absorption peaks in the
spectrum. Here an absorption peak is defined as the family of peaks centered at a
particular chemical shift. For example, if there is a triplet of peaks at a specific chemical
shift, the number is the sum of the area of the three. The rule is that peak area is
proportional to the number of a given type of spins in the molecule and in the sample. An
example should help you understand this relationship.

Consider the methyl ethyl ketone (CH3CH2(C=O)CH3) molecule and its hydrogen NMR
spectrum. When the -CH2- ( = 2.25 ppm), -CH3 ( = 2.0 ppm), and CH3- ( = 0.9 ppm)
peaks are integrated we get the following spectrum. The areas under the three types of
peaks on this spectrometer are 26:39:39. Dividing each number by 13, we obtain a 2:3:3
ratio which is proportional to the number of -CH2- to -CH3 to CH3- hydrogens.

There are a few assumptions which were made in presenting this rule.

• The T1 and T2 values of all the spins are equal.

• There is no spin decoupling being performed.
• The signal-to-noise ratio is good.
• There is no sloping baseline in the spectrum.

Spin decoupling will be discussed in Chapter 9.

You may correct for a sloping baseline by performing a baseline correction to the
spectrum. A poor signal-to-noise ratio may be improved by performing signal averaging,
discussed next.

SNR Improvement

The signal-to-noise ratio (SNR) of a spectral peak is the ratio of the average height of the
peak to the standard deviation of the noise height in the baseline. Often spectroscopists
approximate this quantity as the average peak height divided by the amplitude of the
noise in the baseline. The signal to noise ratio may be improved by performing signal
averaging. Signal averaging is the collection and averaging together of several spectra.
The signals are present in each of the averaged spectra so their contribution to the
resultant spectrum add. Noise is random so it does not add, but begins to cancel as the
number of spectra averaged increases. The signal-to-noise improvement from signal
averaging is proportional to the square root of the number of spectra (N) averaged.
SNR N1/2

Because of the need to perform phase cycling, you will need to have the number of
averages equal to a multiple of the minimum number of phase cycling steps. Compare the
results of averaging together the following number of spectra of a very dilute solution of
methyl ethyl ketone.

N N1/2 Spectrum
1 1.00
8 2.83
16 4.00
80 8.94
800 28.28

Variable Temperature
Many NMR spectrometers have the ability to control the temperature of the sample in the
probe. A schematic representation of the variable temperature hardware on an NMR
spectrometer is depicted in the animation window. All of these spectrometers permit
you to set the temperature to values above room temperature by just entering the desired
temperature. You should be careful not to exceed the maximum temperature allowable
for your probe because doing so will melt adhesives and components in the probe.
Controlling the temperature below room temperature requires the use of hardware to cool
the gas flowing over the sample. If this gas is air, it must be dry air to avoid condensation
of water on the sample. Once the sample and probe have been cooled or heated, you
should slowly return the probe to room temperature. Do not expose a cold probe to the
moist atmosphere; condensation will result.

Troubleshooting

By now you may realize that an NMR spectrometer is a complex piece of instrumentation
with many sub systems which must be functioning properly in order to record a useable
NRM spectrum. The intent of this section is to provide you with a systematic method of
identifying a problem with the spectrometer. Once a problem is identified, you are not
necessarily expected to be able to solve it, but you will at least be able to describe the
steps you took to diagnose the problem when speaking to a system administrator or a
service representative from the manufacturer of your spectrometer. Click on this icon to
start the diagnosis process in the animation window.

Cryogen Fills

Superconducting magnets require liquid nitrogen (N2) and liquid Helium (He). Because it
is difficult to make a perfect dewar to hold these cryogens, they need to be periodically
replenished. Liquid nitrogen is typically filled every 7 to 10 days and liquid helium every
200 to 300 days. Cryogen fills must be performed correctly to avoid injury to you and the
magnet. The injuries to you from cryogenic liquids were described in Chapter 7. Injury to
a magnet could include breaking a seal on a dewar or quenching a magnet. Both forms of
magnet injuries are repairable, but at the least entail recharging the magnet; at the most,
they can entail replacing the magnet.

When filling the magnet with liquid nitrogen, you must be sure not to exceed the
recommended fill pressure and rate for your magnet. If your magnet has two liquid
nitrogen ports, one should be used for filling and the other for venting the boil-off
gaseous nitrogen and overfill liquid nitrogen. A piece of tubing is typically placed on the
vent port to direct the overfill liquid nitrogen away from the magnet seals, probe, and
electronics. It is highly recommended that your liquid nitrogen tanks be made of non-
magnetic stainless steel.

Liquid helium fills are typically a two-person operation. Because they are done so
infrequently, it is good to review the process before each fill. The fill requires a supply
dewar of liquid helium, a special liquid helium transfer line, and a tank of pure
compressed helium gas. Liquid helium is transferred from the liquid helium supply
dewar up through the transfer line, into the helium dewar of the magnet.

The transfer line goes into the top of the liquid helium supply dewar, but should never
rest on the bottom of the dewar. The bottom of the dewar may contain frozen water,
oxygen, and nitrogen which will be forced into your magnet if the transfer line touches
the bottom during the transfer process. The compressed helium gas, mentioned earlier,
is for pressurizing the liquid helium supply dewar with about 2 to 4 psi of pressure.
Gauges on helium supply dewars can be very inaccurate, so do not count on them to give
you an accurate reading. A helium pressure above the liquid forces the Helium into the
magnet dewar.

The transfer line is usually inserted into the magnet until it contacts a transfer flange in
the bottom of the magnet. The nitrogen ports on the magnet should be plugged with a
check valve during filling of the helium dewar of the magnet. This step prevents
cryopumping, a process whereby nitrogen, water, and oxygen are condensed out of the
atmosphere into the nitrogen dewar due to the magnet stacks being cooled by the helium.
Many labs loosely plug the helium vents with tissue during the fill. This cuts down on
cryopumping should the flow of the venting He drop.

The best way to determine if the magnet is full is to look for a change in the gas cloud
coming out of the magnet vents. When the magnet is full the cloud becomes very thick
with a deep white center plume with a slight blue tint. The helium vents on the magnet
should be closed promptly after the magnet is full.

Unix Primer

Most NMR spectrometers are controlled by a computer workstation. The NMR program
which gives your spectrometer the look and feel you are used to is running on this
computer. This computer is most likely running a UNIX operating system. The operating
system is equivalent to DOS on a Microsoft system or OS-5 on a Macintosh system.
Although you may be able to perform all the file transfer and manipulation commands
from your NMR program, you may find it useful to know a few UNIX commands. This
chapter is intended to give you enough information about UNIX to perform simple tasks
in the UNIX operating system.

The UNIX file system is divided into directories, which are equivalent to folders in some
operating systems. Because UNIX is a multi-user system, there must be a way to keep
your directories separate (and safe) from someone else's. To achieve this, there are
accounts with passwords and ownership of directories. For example, you have an account
which has a password. Logging on under your account gives you access to your
directories and to other directories for which you have access (permission).

The most useful, but least used command in UNIX is man. This is short for manual and
gives you on-line help on every UNIX command. The more you use it, the easier it is to
use. The animation window contains a table of a few simple UNIX commands. Entries
in italics are examples and can be any string of characters or numbers.

The Basics of NMR

Chapter 9
CARBON-13 NMR

Introduction
Decoupling
NOE
Population Inversion
1-D C-13 Spectra

Introduction

Many of the molecules studied by NMR contain carbon. Unfortunately, the carbon-12
nucleus does not have a nuclear spin, but the carbon-13 (C-13) nucleus does due to the
presence of an unpaired neutron. Carbon-13 nuclei make up approximately one percent of
the carbon nuclei on earth. Therefore, carbon-13 NMR spectroscopy will be less sensitive
(have a poorer SNR) than hydrogen NMR spectroscopy. With the appropriate
concentration, field strength, and pulse sequences, however, carbon-13 NMR
spectroscopy can be used to supplement the previously described hydrogen NMR
information. Advances in superconducting magnet design and RF sample coil efficiency
have helped make carbon-13 spectroscopy routine on most NMR spectrometers.

The sensitivity of an NMR spectrometer is a measure of the minimum number of spins

detectable by the spectrometer. Since the NMR signal increases as the population
difference between the energy levels increases, the sensitivity improves as the field
strength increases. The sensitivity of carbon-13 spectroscopy can be increased by any
technique which increases the population difference between the lower and upper energy
levels, or increases the density of spins in the sample. The population difference can be
increased by decreasing the sample temperature or by increasing the field strength.
Several techniques for increasing the carbon-13 signal have been reported in the NMR
literature.

Unfortunately, or fortunately, depending on your perspective, the presence of spin-spin

coupling between a carbon-13 nucleus and the nuclei of the hydrogen atoms bonded to
the carbon-13, splits the carbon-13 peaks and causes an even poorer signal-to-noise ratio.
This problem can be addressed by the use of a technique known as decoupling, addressed
in the next section.
Decoupling

The signal-to-noise ratio in an NMR spectrometer is related to the population difference

between the lower and upper spin state. The larger this difference the larger the signal.
We know from chapter 3 that this difference is proportional to the strength of the Bo
magnetic field.

To understand decoupling, consider the familiar hydrogen NMR spectrum of HC-

(CH2CH3)3. The HC hydrogen peaks are difficult to see in the spectrum due to the
splitting from the 6 -CH2- hydrogens. If the effect of the 6 -CH2- hydrogens could be
removed, we would lose the 1:6:15:20:15:6:1 splitting for the HC hydrogen and get one
peak. We would also lose the 1:3:1 splitting for the CH3 hydrogens and get one peak.
The process of removing the spin-spin splitting between spins is called decoupling.
Decoupling is achieved with the aid of a saturation pulse. If the affect of the HC
hydrogen is removed, we see the following spectrum. Similarly, if the affect of the -CH3
hydrogens is removed, we see this spectrum.

A saturation pulse is a relatively low power B1 field left on long enough for all
magnetization to disappear. A saturation pulse applied along X' rotates magnetization
clockwise about X' several times. As the magnetization is rotating, T2 processes cause the
magnetization to dephase. At the end of the pulse there is no net Z, X, or Y
magnetization. It is easier to see this behavior with the use of plots of MZ, MX', and MY' as
a function of time. Since the B1 pulse is long, its frequency content is small. It therefore
can be set to coincide with the location of the -CH2- quartet and saturate the -CH2- spin
system. By saturating the -CH2- spins, the -CH2- peaks and the splittings disappear,
causing the height of the now unsplit HC- and -CH3 peaks to be enhanced.

Now that the concept of decoupling has been introduced, consider the carbon-13
spectrum from CH3I. The NMR spectrum from the carbon-13 nucleus will yield one
absorption peak in the spectrum. Adding the nuclear spin from one hydrogen will split
the carbon-13 peak into two peaks. Adding one more hydrogen will split each of the
two carbon-13 peaks into two, giving a 1:2:1 ratio. The final hydrogen will split each of
the previous peaks, giving a 1:3:3:1 ratio. If the hydrogen spin system is saturated, the
four lines collapse into a single line having an intensity which is eight times greater than
the outer peak in the 1:3:3:1 quartet since 1+3+3+1=8 . In reality, we see a single line
with a relative intensity of 24. Where did the extra factor of three come from?

NOE

The answer to the question raised in the previous paragraph is the nuclear Overhauser
effect (NOE). To understand the NOE, consider a set of coupled hydrogen and carbon-13
nuclei. Assume that the red-green nuclei are carbon-13 and the blue-pink nuclei are
hydrogen.
T1CC is T1 relaxation due to interactions between carbon-13 nuclei. T1HH is T1 relaxation
due to interactions between hydrogen nuclei. T1CH is T1 relaxation due to interactions
between carbon-13 and hydrogen nuclei.

MZ(C) is the magnetization due to carbon-13 nuclei. Mo(C) is the equilibrium

magnetization of carbon-13. MZ(H) is the magnetization due to hydrogen nuclei. Mo(H) is
the equilibrium magnetization of hydrogen.

The equations governing the change in the Z magnetization with time are:

If we saturate the hydrogen spins, MZ(H) = 0.

Letting the system equilibrate, d MZ(C) /dt = 0 .

Rearranging the previous equation, we obtain an equation for MZ(C) .

.
Note that MZ(C) has increased by Mo(H) T1CC / T1CH which is approximately 2 Mo(C),
giving a total increase of a factor of 3 relative to the total area of the undecoupled peaks.
This explains the extra factor of three (for a total intensity increase of 24) for the carbon-
13 peak when hydrogen decoupling is used in the carbon-13 spectrum of CH3I.

The following spin-echo sequence has been modified to decouple the hydrogen spins
from the carbon-13 spins. The signal is recorded as the second half of the echo.

Population Inversion

Another method of improving the NMR signal in systems with spin-spin coupling is
population inversion. To understand the concept of a population inversion, recall from
Chapter 3 that Boltzmann statistics tell us that there are more spins in the lower spin state
than the upper one of a two spin state system. Population inversion is the interchange of
the populations of these two spin states so that there are more spins in the upper state then
the lower one.

To understand how a population inversion improves the signal-to-noise ratio in a

spectrum, consider the CHI3 molecule. CHI3 will have four energy levels (L1, L2, L3, and
L4) due to C-H spin-spin coupling. There are two carbon-13 absorption frequencies f1
and f2 and two hydrogen absorption frequencies f3 and f4. The population distribution
between the four levels is such that the lowest state has the greatest population and the
highest the lowest population. The two intermediate states will have populations between
the outer two as indicated by the thickness of the levels in the accompanying diagram.
The four lines in the spectrum will have intensities related to the population difference
between the two levels spanned by the frequency. The two carbon-13 absorption lines (f1
and f2) will have a lower intensity than the hydrogen lines (f3 and f4) due to the smaller
population difference between the two states joined by f1 and f2.

If the populations of L3 and L1 are inverted or interchanged with a frequency selective

180 degree pulse at f3, the signal at f2 will be enhanced because of the greater population
difference between the states joined by f2. It should be noted that the signal at f1 will be
inverted because the upper state of the two joined by f1 has a greater population than the
lower one. An example of a population inverting pulse sequence designed to enhance the
carbon-13 spectral lines is depicted in the animation window. The 180 degree pulse at f3
has a narrow band of frequencies centered on f3 that selectively rotates only the
magnetization at f3 by 180 degrees.

1-D C-13 Spectra

The following table of compounds contains links to their corresponding one-dimensional

carbon-13 NMR spectra. The spectra were recorded on a 300 MHz NMR spectrometer
with a delay time between successive scans of two seconds. This relatively short delay
time may cause differences in the peak heights due to variations in T1 values. Other
differences may be caused by variations in the nuclear Overhauser effect. In spectra
recorded with deuterated chloroform (CDCl3) as the lock solvent, the three peaks at = 75
are due to splitting of the CDCl3 carbon-13 peak by the nuclear spin = 1 deuterium
nucleus.
Molecule Formula Solvent Spectrum
cyclohexane C6H12 CDCl3
benzene C6H6 CDCl3
toluene C6H5CH3 CDCl3
ethyl benzene C6H5CH2CH3 CDCl3
acetone CH3(C=O)CH3 CDCl3
methyl ethyl ketone CH3(C=O)CH2CH3 CDCl3
ethanol CH3CH2OH CDCl3
ethanol CH3CH2OH D2O
1-propanol CH3CH2CH2OH CDCl3
2-propanol (CH3)2CHOH CDCl3
t-butnol (CH3)3COH CDCl3
2-butanol CH3CH2CH(OH)CH3 CDCl3
pyridine C5H5N CDCl3

The Basics of NMR

Chapter 10
2-D TECHNIQUES

Introduction
J-resolved
COSY
Examples

Introduction

In Chapter 6 we saw the mechanics of the spin echo sequence. Recall that a 90 degree
pulse rotates magnetization from a single type of spin into the XY plane. The
magnetization dephases, and then a 180 degree pulse is applied which refocusses the
magnetization.

When a molecule with J coupling (spin-spin coupling) is subjected to a spin-echo

sequence, something unique but predictable occurs. Look at what happens to the
molecule A2-C-C-B where A and B are spin-1/2 nuclei experiencing resonance. The
NMR spectrum from a 90-FID sequence looks like this.

With a spin-echo sequence this same molecule gives a rather peculiar spectrum once the
echo is Fourier transformed. Here is a series of spectra recorded at different TE times.
The amplitude of the peaks have been standardized to be all positive when TE=0 ms.

To understand what is happening, consider the magnetization vectors from the A nuclei.
There are two absorptions lines in the spectrum from the A nuclei, one at +J/2 and one
at -J/2. At equilibrium, the magnetization vectors from the +J/2 and -J/2 lines in the
spectrum are both along +Z.

A 90 degree pulse rotates both magnetization vectors into the XY plane. Assuming a
rotating frame of reference at o = , the vectors precess according to their Larmor
frequency and dephase due to T2*. When the 180 degree pulse is applied, it rotates the
magnetization vectors by 180 degrees about the X' axis. In addition the +J/2 and -J/2
magnetization vectors change places because the 180 degree pulse also flips the spin state
of the B nucleus which is causing the splitting of the A spectral lines.

The two groups of vectors will refocus as they evolve at their own Larmor frequency. In
this example the precession in the XY plane has been stopped when the vectors have
refocussed. You will notice that the two groups of vecotrs do not refocus on the -Y axis.
The phase of the two vectors on refocussing varies as a function of TE. This phase varies
as a function of TE at a rate equal to the size of the spin-spin coupling frequency.
Therefore, measuring this rate of change of phase will give us the size of the spin-spin
coupling constant. This is the basis of one type of two-dimensional (2-D) NMR
spectroscopy.

J-resolved

In a 2-D J-resolved NMR experiment, time domain data is recorded as a function of TE

and time. These two time dimensions will referred to as t1 and t2. For the A2-C-C-B
molecule, the complete time domain signals look like this.

This data is Fourier transformed first in the t2 direction to give an f2 dimension, and then
in the t1 direction to give an f1 dimension.

Displaying the data as shaded contours, we have the following two-dimensional data set.
Rotating the data by 45 degrees makes the presentation clearer. The f1 dimension gives
us J coupling information while the f2 dimension gives chemical shift information. This
type of experiment is called homonuclear J-Resolved 2-D NMR. There is also
heteronuclear J-resolved 2-D NMR which uses a spin echo sequence and techniques
similar to those described in Chapter 9.

COSY
The application of two 90 degree pulses to a spin system will give a signal which varies
with time t1 where t1 is the time between the two pulses. The Fourier transform of both
the t1 and t2 dimensions gives us chemical shift information. The 2-D hydrogen correlated
chemical shift spectrum of ethanol will look like this. There is a wealth of information
found in a COSY spectrum. A normal (chemical shift) 1-D NMR spectrum can be found
along the top and left sides of the 2-D spectrum. Cross peaks exist in the 2-D COSY
spectrum where there is spin-spin coupling between hydrogens. There are cross peaks
between OH and CH2 hydrogens , and also between CH3 and CH2 hydrogens
hydrogens. There are no cross peaks between the CH3 and OH hydrogens because there is
no coupling between the CH3 and OH hydrogens.

Heteronuclear correlated 2-D NMR is also possible and useful.

Examples

The following table presents some of the hundreds of possible 2-D NMR experiments
and the data represented by the two dimensions. The interested reader is directed to the
NMR literture for more information.
2-D Experiment (Acronym) Information
f1 f2
Homonuclear J resolved J
Heteronuclear J resolved JAX X

Homoculclear correlated spectroscopy (COSY) A A

Heteronuclear correlated spectroscopy (HETCOR) A X

Nuclear Overhauser Effect (2D-NOE) H, JHH H, JHH

2D-INADEQUATE A + X X

The following table of molecules contains links to their corresponding two-dimensional

NMR spectra. The spectra were recorded on a 300 MHz NMR spectrometer with CDCl3
as the lock solvent.

Molecule Formula Type Spectrum

methyl ethyl ketone CH3(C=O)CH2CH3 COSY
ethanol CH3CH2OH COSY
1-propanol CH3CH2CH2OH COSY
2-propanol (CH3)2CHOH COSY
2-butanol CH3CH2CH(OH)CH3 COSY
ethyl benzene C6H5CH2CH3 COSY
pyridine C5H5N COSY
 The Basics of NMR
Chapter 11
ADVANCED SPECTROSCOPIC TECHNIQUES

Introduction
Diffusion
Spin Relaxation Time
Solid State
Microscopy
Solvent Suppression
Field Cycling NMR

Introduction

Nuclear magnetic resonance spectroscopy is one of the richest spectroscopies available.

In previous chapters you have seen how it can be used to elucidate chemical structure. In
this chapter you will see some of the other more advanced applications of NMR. Two of
these techniques, solid state NMR and gradient enhanced spectroscopy, will assist us
further in the determination of molecular structure. Two additional techniques will assist
us in studying molecular dynamics, or the rotational and translational motions of
molecules. The last technique, NMR microscopy, will enable us to determine the spatial
distribution of nuclear spins in a sample.

Diffusion

Diffusion is the motion of particles due to Brownian motion. The diffusion coefficient, D,
is a measure of the diffusion. The pulsed-gradient spin-echo sequence permits us to
measure the diffusion coefficient. The sequence is in theory capable of measuring both
the rotational and translational diffusion coefficients, but is used primarily for studying
translational diffusion.

To understand how the pulsed-gradient spin-echo sequence allows us to measure

diffusion, consider the timing diagram for the sequence. This sequence is very similar to
the spin echo sequence introduced in Chapter 6, except that two gradient pulses have
been applied. These two gradient pulses are identical in amplitude, G, and width, . The
two gradient pulses are separated by a time and are placed symmetrically about the 180
degree pulse.

The function of the gradient pulses is to dephase magnetization from spins which have
diffused to a new location in the period . These pulses have no effect on stationary
spins. For example, a stationary spin exposed to the first gradient pulse, applied along the
Z axis, will acquire a phase in radians given by

=2 z Gz dt .
The spin will acquire an equal but opposite phase from the second pulse since the pulses
are on different sides of the 180 degree RF pulse. Thus, their effects cancel each other
out.

Consider the following illustration of the effect of the gradient pulses on the phase of
stationary and moving spins. The illustration presents the phase of a diffusing spin
relative to that of a reference spin and a stationary spin. The reference spin is one which
experiences no gradient pulses. The stationary spin is not diffusing during the time
illustrated by the sequence. The diffusing spin moves along Z during the sequence. The
blue line in the timing diagram represents the time of the 180 degree pulse in the spin
echo sequence. When you put the illustration into motion, the stationary spin comes back
into phase with the reference one, indicating a positive contribution to the echo. The
diffusing spin does not come back into phase with the reference spin so it diminishes the
echo height.

The relationship between the signal (S) obtained in the presence of a gradient amplitude
Gi in the i direction and the diffusion coefficient in the same direction is given by the
following equation where So is the signal at zero gradient.

S/So = exp[-(Gi )2 Di ( - /3)]

The diffusion coefficient is typically calculated from a plot of ln(S/So) versus (G )2 (

- /3). Diffusion in the x, y, or z direction may be measured by applying the gradient
respectively in the x, y, or z direction.

Spin Relaxation Time

The spin-lattice and spin-spin relaxation times, T1 and T2 respectively, of the components
of a solution are valuable tools for studying molecular dynamics. You saw in Chapter 3
that T1-1 is proportional to the number of molecular motions at the Larmor frequency,
while T2-1 is proportional to the number of molecular motions at frequencies less than or
equal to the Larmor frequency. When we are dealing with solutions these motions are
predominantly rotational motions.

There are many pulse sequences which may be used to measure T1 and T2. The inversion
recovery, 90-FID, and spin-echo sequences may be used to measure T1. Each technique
has its own advantages and disadvantages. The spin-echo sequence may be used to
measure T2.

T1 Measurement
Recall the timing diagram for an inversion recovery sequence first presented in Chapter
6.
The signal as a function of TI when the sequence is not repeated is

S = k ( 1 - 2eTI/T1 ) .

If the curve is well defined (i.e. if there is a high density of data points recorded at
different TI times), the T1 value can be determined from the zero crossing of the curve
which is T1 ln2.

Alternatively the relaxation curve as a function of TI may be fit using the equation

S = So (1 - 2e-TI/T1).

This approach is favored when there are fewer data points as a function of TI.

T1 may also be determined from a 90-FID or spin-echo sequence which is repeated at

various repetition times (TR). For example, if the 90-FID sequence is repeated many
times at TR1 and then many times at TR2, TR3, etc, the plot of signal as a function of TR
will be an exponential growth of the form

S = k ( 1 - eTR/T1 ) .

This data may be fit to obtain T1.

The difficulty with fitting this data and the inversion recovery data is a lack of knowledge
of the value of the equilibrium magnetization or signal So. Other techniques have been
proposed which do not require knowledge of the equilibrium magnetization or signal .

T2 Measurement
Measurement of the spin-spin relaxation time requires the use of a spin-echo pulse
sequence. The echo amplitude, S, as a function of echo time, TE, is exponentially
decaying. Plotting ln(S/So) versus TE yields a straight line, the slope of which is -1/T2.
A linear least squares algorithm is often used to find the slope and hence T2 value. This
approach can result in lead to large errors in the calculated T2 values when the data has
noise. The later points in the decay curve have poorer signal-to-noise ratio than the earlier
points, but are given equal weight by the linear least squares algorithm. The solution to
this problem is to use a non-linear least squares procedure.

Solid State

We saw in Chapter 4 that the magnitude of the chemical shift is related to the extent to
which the electron can shield the nucleus from the applied magnetic field. In a spherically
symmetric molecule, the chemical shift is independent of molecular orientation. In an
asymmetric molecule, the chemical shift is dependent on the orientation. The magnetic
field experienced by the nucleus varies as a function of the orientation of the molecule in
the magnetic field. The NMR spectrum from a random distribution of fixed
orientations, such as in a solid, would look like this. The larger signal at lower field
strength is due to the fact that there are more perpendicular orientations. In a nonviscous
liquid, the fields at the various orientations average out due to the tumbling of the
molecule.

The anisotropic chemical shift is one reason why the NMR spectra of solid samples
display broad spectral lines. Another reason for broad spectral lines is dipolar broadening.
A dipolar interaction is one between two spin 1/2 nuclei. The magnitude of the
interaction varies with angle and distance r. As a function of , the magnetic field B
experienced by the red nucleus is

(3cos2 - 1).

A group of dipoles with a random distribution of orientations, as in a solid, gives this

spectrum. The higher signal at mid-field strength is due to the larger presence of
orientations perpendicular to the direction of the Bo field. This signal is made up of
components from the red and blue nuclei in the dipole. In a nonviscous liquid, the
interaction averages out due to the presence of rapid tumbling of the molecule.

When the angle in the above equation is 54.7o, 125.3o, 234.7o, or 305.3o, the dipole
interaction vanishes. The angle 54.7o is called the magic angle, m.

If all the molecules could be positioned at m, the spectrum would narrow to the fast
tumbling limit.

Since this is not possible, the next best thing is to cause the average orientation of the
molecules to be m.

Even this is not exactly possible, but the closest approximation is to rapidly spin the
entire sample at an angle m relative to Bo. In solid state NMR, samples are placed in a
special sample tube and the tube is placed inside a rotor. The rotor, and hence the sample,
are oriented at an angle m with respect to the Bo magnetic field. The sample is then
spun at a rate of thousands of revolutions per second.

The spinning rate must be comparable to the solid state line width. The centrifigal force
created by spinning the sample tube at a rate of several thousands of revolutions per
second is enough to destroy a typical glass NMR sample tube. Specially engineered
sample tubes and rotors are needed.

Microscopy

NMR microscopy is the application of magnetic resonance imaging (MRI) principles to

the study of small objects. Objects which are studied are typically less than 5 mm in
diameter. NMR microscopy requires special hardware not found on conventional NMR
spectrometers. This includes gradient coils to produce a gradient in the magnetic field
along the X, Y, and Z axes; gradient coil drivers; RF pulse shaping software; and image
processing software. Resultant images can have 20 to 50 m resolution. The reader
interested in more information on NMR microscopy is encouraged to read the author's
hypertext book on MRI entitled The Basics of MRI located at
http://www.cis.rit.edu/htbooks/mri/.

Solvent Suppression

Occasionally, it becomes necessary to eliminate the signal from one constituent of a

sample. An example is an unwanted water signal which overwhelms the signal from the
desired constituent. If T1 of the two components differ, this may be accomplished by
using an inversion recovery sequence, presented in Chapter 6. To eliminate the water
signal, choose the TI to be the time when the water signal passes through zero.
TI = T1 ln2

In this example, a TI = 1 s would eliminate the water signal.

Another method of eliminating a solvent absorption signal is to saturate it. In this

procedure, a saturation pulse similar to that employed in C-13 NMR (See Chapter 9) is
used to decouple hydrogen coupling. The frequency of the saturation pulse is set to the
solvent resonance. The width of the saturation pulse is very long, so its bandwidth is very
small causing it to affect only the solvent resonance.

Field Cycling NMR

Field cycling NMR spectroscopy is used to obtain spin-lattice relaxation rates, R1, where
R1 = 1/T1 ,

as a function of magnetic field or Larmor frequency. Therefore, field cycling NMR finds
applications in the study of molecular dynamics. The animation window contains an
example of results from a field cycling NMR spectrometer. The plot represents the R1
value of the hydrogen nuclei in various concentration aqueous solutions of Mn+2 at 25o as
a function of the proton Larmor frequency.

Many different techniques have been used to obtain R1 as a function of magnetic field.
Some techniques move the sample rapidly between different magnetic field strengths.
One of the more popular techniques keeps the sample at a fixed location and rapidly
varies the magnetic field the sample experiences. This technique is referred to as rapid
field cycling NMR spectroscopy.

The principle behind a rapid field cycling NMR spectrometer is to polarize the spins in
the sample using a high magnetic field, Bp. The magnetic field is rapidly changed to the
value at which relaxation occurs, Br. Br is the value at which R1 is to be determined. After
a period of time, τ , the magnetic field is switched to a value, Bd, at which detection of a
signal occurs. Bd is fixed so that the operating frequency of the detection circuitry does
not need to be changed. The signal, an FID, is created by the application of a 90o RF
pulse. The timing diagram for this sequence can be found in the animation window.
The FT of the FID represents the amount of magnetization present in the sample after
relaxing for a period τ in Br. A plot of this magnetization as a function of τ is an
exponentially decaying function, starting from the equilibrium magnetization at Bp and
going to the value at Br. When a single type of spin is present, the relaxation is
monoexponential with rate constant R1 at Br.

When Br is very large compared to Bd, Bp is often set to zero and the plot of this
magnetization as a function of τ is an exponentially growing function.

Glossary
Artifact
A feature which appears in an NMR spectrum of a molecule which should not be
present based on the chemical structure and pulse sequence used. [Chapter 7]
Chemical Screening
The screening of an applied magnetic field experienced by a nucleus due to the
electron cloud around an atom or molecule. [Chapter 4]
Chemical Shift
A variation in the resonance frequency of a nuclear spin due to the chemical
environment around the nucleus. Chemical shift is reported in ppm. [Chapter 4]
Coil
One or more loops of a conductor used to create a magnetic field. In NMR, the
term generally refers to the radiofrequency coil. [Chapter 7]
Convolution
A mathematical operation between two functions. [Chapter 2]
Complex Data
Numerical data with a real and an imaginary component. [Chapter 2]
Continuous Wave (CW)
A form of spectroscopy in which a constant amplitude electromagnetic wave is
applied. [Chapter 3]
Coordinate Transformation
A change in the axes used to represent some spatial quantity. [Chapter 2]
Cryopumping
The condensation of air onto a surface cooled by a cryogenic liquid . [Chapter 8]
Dephasing Gradient
A magnetic field gradient used to dephase transverse magnetization. [Chapter 11]
Digital Filtering
A feature found on may newer spectrometers which eliminates wraparound
artifacts by filtering out the higher frequency components in the time domain
spectrum. [Chapter 7]
Doubly balanced mixer
An electrical device, often referred to as a product detector, which is used in
NMR to convert signals from the laboratory frame of reference to the rotating
frame of reference. [Chapter 7]
Echo
A form of magnetic resonance signal from the refocusing of transverse
magnetization. [Chapter 6]
Echo Time ( TE )
The time between the 90 degree pulse and the maximum in the echo in a spin-
echo sequence. [Chapter 6]
Exchange, Chemical
The interchange of chemically equivalent components on a molecule. [Chapter 3]
Exchange, Spin
The interchange of spin state between two nuclei. [Chapter 3]
Figure-8 Coil
A magnetic field gradient coil shaped like the number eight. [Chapter 7]
Free induction decay ( FID )
A form of magnetic resonance signal from the decay of transverse magnetization.
[Chapter 4]
Fourier transform ( FT )
A mathematical technique capable of converting a time domain signal to a
frequency domain signal and vice versa. [Chapter 5]
Gradient ( G )
A variation in some quantity with respect to another. In the context of NMR, a
magnetic field gradient is a variation in the magnetic field with respect to
distance. [Chapter 7]
Gyromagnetic Ratio
The ratio of the resonance frequency to the magnetic field strength for a given
nucleus. [Chapter 3]
Imaginary Component
The component of a signal perpendicular to the real signal. [Chapter 5]
Imaging Sequence
A specific set of RF pulses and magnetic field gradients used to produce an
image. [Chapter 11]
Inversion Recovery Sequence
A pulse sequence producing signals which represent the longitudinal
magnetization present after the application of a 180o inversion RF pulse. [Chapter
6
Inversion Time (TI)
The time between the inversion pulse and the sampling pulse(s) in an inversion
recovery sequence. [Chapter 6]
K-Space
That image space represented by the time and phase raw data. The Fourier
transform of k-space is the magnetic resonance image. [Chapter 5]
Larmor frequency
The resonance frequency of a spin in a magnetic field. The rate of precession of a
spin packet in a magnetic field. The frequency which will cause a transition
between the two spin energy levels of a nucleus. [Chapter 3]
Longitudinal Magnetization
The Z component of magnetization. [Chapter 3]
Lorentzian Lineshape
A function obtained from the Fourier transform of an exponential function.
[Chapter 5]
Magnitude
The length of a magnetization vector. In NMR, the square root of the sum of the
squares of the Mx and My components, i.e. the magnitude of the transverse
magnetization. [Chapter 2]
Magnetic Resonance Imaging (MRI)
An imaging technique based on the principles of NMR. [Chapter 11]
Negative Frequency Artifact
The appearance of smaller in amplitude peaks in one half of the spectrum which
are the mirror image of ones in the opposite half. [Chapter 8]
Net Magnetization Vector
A vector representing the sum of the magnetization from a spin system. [Chapter
3]
Nuclear Magnetic Resonance (NMR)
A spectroscopic technique used by scientists to elucidate chemical structure and
molecular dynamics. [Chapter 1]
Pixel
Picture element. [Chapter 1]
Precess
A rotational motion of a vector about the axis of a coordinate system where the
polar angle is fixed and the azmuthal angle changes steadily. [Chapter 3]
Proportionality Constant
A constant used to convert one set of units to another. [Chapter 8]
Pulse Sequence
A series of RF pulses and/or magnetic field gradients applied to a spin system to
produce a signal whose behavior gives information about some property of the
spin system. [Chapter 4]
Quadrature Detection
Detection of Mx and My simultaneously as a function of time. [Chapter 9]
Radio Frequency
A frequency band in the electromagnetic spectrum with frequencies in the millons
of cycles per second. [Chapter 3]
Raw data
The Mx and My data as a function of time and/or other parameters in an NMR
pulse sequence. This is also called k-space data. [Chapter 10]
Real
The component of a signal perpendicular to the imaginary signal. [Chapter 2]
Repetition Time
The time between repetitions of the basic sequence in a pulse sequence. [Chapter
6]
Resonance
An exchange of energy between two systems at a specific frequency. [Chapter 3]
RF Coil
An inductor-capacitor resonant circuit used to set up B1 magnetic fields in the
sample and to detect the signal from the sample. [Chapter 7]
RF Pulse
A short burst of RF energy which has a specific shape.
Rotation Matrix
A matrix used to describe the rotation of a vector. [Chapter 3]
Sample Probe
That portion of the NMR spectrometer containing the RF coils and into which the
sample is placed. [Chapter 7]
Saddle Coil
A coil geometry which has two loops of a conductor wrapped around opposite
sides of a cylinder. [RF: Chapter 7]
Spin
A fundamental property of matter responsible for NMR and MRI. [Chapter 3]
Spin Density
The concentration of spins. [Chapter 6]
Spin-Echo
An NMR sequence whose signal is an echo resulting from the refocusing of
magnetization after the application of 90o and 180o RF pulses. [Chapter 6]
Spin-Lattice Relaxation
The return of the longitudinal magnitization to its equilibrium value along the +Z
axis. [Chapter 3]
Spin-Lattice Relaxation Time ( T1 )
The time to reduce the difference between the longitudinal magnitization and its
equilibrium value by a factor of e. [Chapter 3]
Spin Packet
A group of spins experiencing the same magnetic field. [Chapter 3]
Spin-Spin Relaxation
The return of the transverse magnitization to its equilibrium value (zero). [Chapter
3]
Spin-Spin Relaxation Time
The time to reduce the transverse magnetization by a factor of e. [Chapter 3]
Sinc Pulse
An RF pulse shaped like Sin(x)/x. [Chapter 5]
Superconduct
To have no resistance. A perfect superconductor can carry an electrical current
without losses. [Chapter 7]
T2*
Pronounced T-2-star. The spin-spin relaxation time composed of contributions
from molecular interactions and inhomogeneities in the magnetic field. [Chapter
3]
Timing Diagram
A multiaxis plot of some aspects of a pulse sequence as a function of time.
[Chapter 6]
Transverse magnetization
The XY component of the net magnetization. [Chapter 3]

List of Symbols
Symbol Definition
Å Angstrom (10 meters)
-10

Bo Static magnetic field

B1 The radio frequency magnetic field
C Contrast
C Electrical eapacitance
COSY 2-D correlated spectroscopy
CW Continuous wave
D Deuterium
D Diffusion coefficient
Chemical shift
Magnetic field gradient pulse width
Magnetic field gradient pulse separation
Chemical shift
E Energy
f Frequency
FID Free induction decay
FT Fourier transform
Gi Magnetic field gradient in the i direction
Gyromagnetic ratio
h Planck's constant
H Hydrogen
IFT Inverse Fourier transform
IM Imaginary part of a complex number
J Joule
J Spin-spin coupling constant
k Boltzmann constant
k kilo (103)
k Proportionality constant
K Kelvin temperature
L Electrical Inductance
m milli (10-3)
M mega (106)
micro (10-6)
Mo Equilibrium magnetization
MX X component of magnetization
MX' X' component of magnetization
MY Y component of magnetization
MY' Y' component of magnetization
MZ Z component of magnetization
MXY Transverse component of magnetization
MRI Magnetic resonance imaging
Resonance frequency in Hertz
N Number of averages
N+ Spin population in low energy state
N- Spin population in high energy state
NMR Nuclear magnetic resonance
Resonance frequency in radians per second
Ohm, impedance
3.14159...
Phase angle
ppm Parts per million
R1 Spin-lattice relaxation rate
RE Real part of a complex number
RF Radio frequency
s Second
Chemical shielding constant
SAR Specific absorption rate
Sinc Sin(x)/x
SNR Signal-to-noise ratio
T Temperature
T Tesla
T1 Spin-lattice relaxation time
T2 Spin-spin relaxation time
T2* T2 star
T2inhomo Inhomogeneous T2
Rotation angle
TE Echo Time
TI Inversion Time
TR Repetition Time
X X axis in laboratory coordinate system
X' Rotating frame X axis
Y Y axis in laboratory coordinate system
Y' Rotating frame Y axis
Z Z axis in laboratory coordinate system
1-D One-dimensional
2-D Two-dimensional