ABSTRACT

The total scattering atomic pair distribution function (PDF) method was used in
the experimental work of this thesis to investigate the local structure of the
FeSb2 Iron Antimonide. We have different structural model to represent the
structure of FeSb2 compound where different structural models can be used and
compared, and the model resulting in a better fit is the best model to represent
the data. Where modeling can be done Under different length scales allowing
comparison local and average structural features. From (PDF gui) software we
can compare between the calculated PDF and the measurement PDF and this
agreement between calculated and measurement PDF can be calculated
through the residual function (Rw) and its value determines the goodness of fit,
where lower (Rw) represent better agreement.
Acknowledgments
Dedication
 TABLE OF CONTENTS
Abstract ……………………………………………………………........... i
Acknowledgments …….……………………………………………………………. ii
Dedication ....……………….……………………………………………... iii
List of Figures ....……………….………...………………………………….
List of Tables ....……………….……………………….…………………….

Chapter 1. Introduction
1.1 Semiconductor Iron Antimonide, FeSb2

1.2 FUNDAMENTALS X-RAY diffraction (Conventional Crystallographic

Methods for Average Structure Determination)

1.3 Synchrotron X-RAY diffraction study of FeSb2

1.4 FUNDAMENTALS Pair Distribution Function (PDF) Method

1.5 The Outline and Goals of this Thesis

Chapter 2. The Atomic Pair Distribution Function (PDF) Method

2.1 Introduction

2.2 Basic Description of the PDF

2.3 Parameters Influencing the PDF

2.4 Extracting Information From the PDF

2.5 Structural Modeling of the PDF

2.6 PDFgui software

2.7 Rietveld refinement

Chapter 3: Results and Discussion

3.1 PDF Analysis of the local structure of FeSb2

Chapter 4: Concluding Remarks

 Chapter 1
Introduction

1.1 Semiconductor Iron Antimonide, FeSb2

1.1.1 Chemical Synthesis of Iron Antimonide (FeSb2)

1.1.2 Thermoelectric Properties

1.2 FUNDAMENTALS X-RAY diffraction (Conventional

Crystallographic Methods for Average Structure
Determination)

1.2.1 Basics of X-ray Diffraction

XRD is pertinent to the study of materials as it provides information on the
arrangement of atoms within a material. It has been embraced by many
scientific fields and applied to a range of materials, from minerals to proteins
and more.19 The technique is fundamental to the field of crystallography, the
study of the arrangement of atoms in crystalline materials. Our sample, FeSb2,
is one such crystalline material. What qualifies as crystalline, and how XRD
works in such materials, is discussed below.

1.2.2 Crystalline Materials

Crystals are distinguished from other materials by the highly ordered way in
which their atoms are arranged. One can think of a crystal as an extensive 3-
dimensional pattern comprised of two components: nuclei centered about
specific points in the pattern, and the overlying landscape of electron density
surrounding the nuclei and shaping chemical bonds. This electronic
environment generates Coulombic forces, which in turn restrict the movement
of atoms away from their prescribed positions. With this mechanism behind
ordering, crystals are necessarily solids- the distances between molecules in
liquids and gases are too great for Coulombic forces to be able to confine
atoms in the same way. In place of forces, crystals may also be described by
the corresponding potential energy; atoms settle in regions where the potential
energy is at a minimum, as determined by the presence of neighboring charges.
The network of bonds and atoms that compose a crystal is called the crystal
lattice. The seed of the pattern- the smallest unique grouping of atoms which is
repeated to build the lattice- is called the unit cell. For the multitude of
different crystal compositions found in nature or grown in a laboratory, there
are a smaller number of common symmetries that define lattice types. The
broadest level of categorization for a crystal involves distinguishing the unit
cell as belonging to one of seven lattice systems: cubic, tetragonal,
orthorhombic, monoclinic, trigonal, hexagonal, or triclinic. The lattice systems
are distinguishable by different conditions on the unit cell lattice parameters,
such as the size of the cell along different orthonormal axes a, b, and c, as well
as angles α, β, and γ between adjacent cell faces. Atoms can be arranged
differently within the framework of these lattice types, resulting in 230 lattice
space groups with unique geometries and symmetries. It should be noted that
different methods of classifying crystal lattices exist, and the identification of
230 space groups follows the convention of the International Tables for X-ray
Crystallography. Each space group is given an identifier using Hermann-
Mauguin notation. Simple unit cells representing the cubic, tetragonal, and
orthorhombic lattice systems, including face-centered and body-centered
variations, are shown in Fig 1.1 The diagrams can be recognized as 9 of the 14
Bravais lattices, which are not discussed in this work but still important to
crystallography.
 FIG. 1.1 Examples of unit cells for cubic, tetragonal, and orthorhombic crystal systems.

When extending the field of view beyond a single unit cell to consider many
units cells at once, the repetitious arrangement of atoms in a crystal creates the
appearance of planes of atoms separated by empty spaces. Many planes exist
for each space group. A common system for identifying lattice planes is with
Miller indices h, k, and l. In simple terms, the h, k, and l represent the
fractional coordinates where a particular plane intersects the a, b, and c axes of
a unit cell, respectively. This method avoids troublesome coordinates by
working in reciprocal space. For example, if a plane never intersects with one
of the axes, the intersection point in real space would be “infinity.” However,
the Miller index value for this (non-existent) intersection would be zero, as the
reciprocal of infinity approximates as zero. Likewise, a plane which intersects
at a halfway point along a unit cell axis would have a Miller index of 2 for that
direction.
The distance between atoms in a lattice, and thus between atomic planes, is on
the angstrom to nanometer scale. X-rays have wavelengths on the order of an
angstrom, and as a result X-rays in a crystal can be diffracted by lattice planes.

1.2.3 Determining Lattice Parameters Through X-Ray Diffraction

The technique of X-ray diffraction relies on the interaction of X-rays with

the electrons of atoms within a material. As part of the electromagnetic
spectrum, X-rays constitute oscillating electric and magnetic fields of a certain
frequency. Charged particles (such as electrons in a lattice) in the presence of
an oscillating electric field will be compelled to oscillate themselves.
Acceleration is part of this oscillatory motion and accelerating charged
particles release radiation. The particles oscillate in space with the same
frequency as the incident radiation, and therefore generate radiation with the
same frequency. For X-rays interacting with electrons in the context of
diffraction, the time-averaged emitted radiation will be in the form of a
spherical wave (regardless of the incident waveform), and the corresponding
atom can be modelled as a point source.
 Emitted spherical waves from each atom will interfere constructively or
destructively with each other, and the resulting interference patterns can be
detected and analyzed. Due to the large number of lattice planes, the
constructive interference is highly selective by the time it exits a sample and
interacts with a detector. Fortunately, the complex conditions on constructive
interference in a crystal lattice can be summed up simply using Bragg’s Law.
Fig 1.2 shows a diagram of X-ray diffraction from lattice planes as well as the
mathematical formulations behind Bragg’s Law. Bragg’s law models
diffraction of an X-ray from a lattice plane as ray scattering from a surface, a
much simpler process to analyze. The intensity of the diffracted radiation is
only non-zero if these scattered X-rays interfere constructively. The scattering
process is coherent if the path length difference for a ray scattered from one
lattice plane and a ray scattered from the next lattice plane is an integer
multiple of X-ray wavelength λ. As can be calculated from Fig.1.2, the path
length difference between two scattered rays is 2dsinθ. The variable d
represents the spacing between consecutive lattice planes. The variable θ
denotes the angle between the incident radiation and plane surface (as well as
the angle between reflected ray and plane surface, in accordance to the law of
reflection).

FIG. 1.2 Diagram for the formulation of Bragg’s Law. Bragg’s Law simplifies the
conditions for constructive interference of diffracted X-rays. In this diagram, X-rays are
incident from the upper left and reflected to the upper right. The detector, not shown in
this diagram, would be placed at a distance to the upper right.

When the incident X-ray wavelength is constant, there will be a unique angle θ
where constructive interference can occur for every family of planes with the
same d-spacing. The technique of X-ray diffraction relies on measuring the
angle θ of diffracted X-rays to calculate the d-spacing between lattice planes.
The relationship between lattice spacing d, lattice parameters a, b, and c, and
Miller Indices h, k, and l is known for the 7 lattice systems. Once the d-spacing
is calculated using Bragg’s Law, the corresponding plane can be identified by
its Miller Indices and the lattice parameters can be calculated using equations
such as in Table 1.1

Table 1.1 Relationship between d-spacing, lattice parameters, and Miller

indices for the seven lattice systems.
SYSTEM D-SPASING

CUBIC 1 h +k +l
2 2 2
=
d2 a2

Tetragonal 1 h 2+ k 2 l 2
= 2 + 2
d2 a c

Hexagonal 2
1 4 h +hk + k l
2 2

(and Trigonal) 2
= 2
+ 2
d 3 a c

Orthorhombic 1 h k l
2 2 2
= + +
d 2 a 2 b2 c 2

Monoclinic 1 h2 k2 l2 2 hlcosβ
2
= 2 2
+ 2
+ 2 2
+ 2
d a sin β b c sin β ac sin β

[
RICLINIC 1
2
h 2 kl k
2
2 hl
2
l 2 hk
= 2 2 + ( cosβcosγ −cosα ) + 2 2 + ( cosαcosγ −cosβ ) + 2 2 + (co
d
2
a sin α bc b sin β ac c sin γ ab

1.2.4 Powder X-ray Diffraction

Bragg diffraction has been explained so far in terms of a static orientation of

sample lattice to incident X-rays. The result is a diffracted beam that produces
a spot on a detector some distance away from the sample at some angle 2θ
from the incident beam. Diffraction from a crystal is a 3-dimensional process,
and as such the spot also exists at some azimuthal angle φ from the plane of the
primary beam. Without changing the orientation of the sample, multiple lattice
planes may be able satisfy Bragg’s law for different angles θ. Multiple spots
will be detected on the detector. However, a single orientation of sample lattice
to primary beam is not enough to satisfy the Bragg condition for all possible
planes within the lattice. Researchers can either rotate the sample, in the case
of a single crystal, or use a powder sample to sample all permitted reflections
of a space group. A powder sample can be created from grinding single crystals
or bulk material into a uniformly fine powder of micron dimension particles.
Ideally, the particles of a powder sample are randomly oriented, so that on
average all possible particle alignments are represented equally. In other
words, the orientation of lattice planes to incident beam is different from
particle to particle. Given a sufficiently large number of particles, every
combination of d- spacing, θ, and φ will be sampled. The results are diffraction
cones emitted from the sample for each angle Bragg θ and the full 360-degree
range of azimuthal φ. When a detector screen is oriented perpendicular to the
axis of the incident beam, the screen intersects the cones. The image formed
consists of a series of concentric circles known as Debye rings (see Fig.1.3 and
Fig. 1.4 (a)). An illustration of this process (for a so-called Debye-Scherrer
experimental geometry) is provided in Fig. 1.3.

FIG. 1.3. Diffraction image for a powder sample. Powder diffraction is exemplified by
the formation of Debye rings in the diffraction image. Intensities at 2θ must satisfy
Bragg’s Law, while image intensities over the range of φ are due to the random
distribution of particles in a powder.
 The intensity of counts in the Debye rings can be integrated as a function
of the angle between diffracted X-rays and the axis of the incident beam (the
semi-vertical angle of the diffraction cones). As shown in Fig. 5, the angle
from the incident beam to where the diffracted X-ray intersects the detector
screen is twice the Bragg angle θ. This is such a common experimental
geometry that the intensity of diffracted X-rays is frequently plotted as a
function of 2θ, where it is understood that 2θ is the angle relative to the
incident beam. An example of Debye rings on an area detector is shown in Fig.
1.4 (a), with the accompanying integrated 2- dimensional intensity plot shown
in Fig. 1.4 (b).

(a) (b)

FIG 1.4 (a) Detector plate image of CeO2 diffraction pattern, and (b) Integrated diffraction
pattern of CeO2. Detector plate images are integrated over φ to produce 2-dimensional
intensity plots as a function of 2θ. CeO2 is used as a standard/calibrant in XRD studies.

Bragg’s Law can be used to determine the location of diffraction peaks

based on the lattice of the sample, but it cannot explain everything about a
diffraction pattern. Bragg’s Law treats lattice planes as flat and uniformly solid
surfaces, which would result in peaks that are delta functions of equal intensity.
As can be seen in Fig. 6, actual diffraction peaks have non- negligible width
and show different intensities for different d-spacings. In order to extract
information from peak intensities and widths, we must move beyond Bragg’s
Law and consider the elemental composition of the sample and environment of
the system.

1.2.5 Factors in Diffraction Peak Profile

Bragg’s Law considers each lattice plane to be solid, with an equal

probability of scattering incident photons. However, lattice planes in a real
crystal are not solid. The likelihood of interacting with X-ray photons depends
on the density of electrons in that plane. This is turn is determined by multiple
factors, such as the density of atoms are in the plane and
the electron distribution for each atom. The electronic density of a specific
plane determines the intensity of the corresponding diffraction peak. Other
conditions may affect peak intensity, including preferred orientation, where the
particles in a powder have become aligned along a specific direction rather
than randomly distributed, causing some lattice planes to be sampled more than
others. The final diffraction pattern obtained from experiment is a combination
of material and instrumental effects. Detector efficiency and dead time affect
the recorded intensities for each reflection. The quality of the diffraction image
is limited by the resolution of the detector, which is responsible for broadening
the peak width and is frequently modelled as a Gaussian contribution to peak
shape. Also, the incident radiation will not be perfectly monochromatic for any
XRD experiment, producing a range for each Bragg angle θ. Diffraction peaks
are further broadened by variations in the d-spacing of lattice planes across the
sample. Imperfections such as site vacancies, impurities, stack faults or
twinning all contribute to variations in d-spacing. Peak broadening can also be
the result of strain on the lattice. Another example of imperfections are crystal
surfaces. The ideal crystal extends forever, whereas a powder sample is
comprised of many finite particles with surfaces that present discontinuities in
the crystal lattice. As particles get smaller, the surface imperfections become
more prominent relative to the long-range order of the interior lattice. The
smaller the particle, the more noticeable the peak broadening becomes, as one
can see from X-ray diffraction studies of nanoparticles.

1.3 Synchrotron X-RAY diffraction study of FeSb2

1.4 FUNDAMENTALS Pair Distribution Function (PDF)

Method
1.4.1 what is PDF?
Pioneering work by scientist such as “Max Vonlaue” in the early 20th century
established that x-ray diffraction is based on atomic scale units with a perfectly
spaced arrangements when this nanometer sized unit is repeated over and over
again it becomes a grid exhibiting long range order

1.5 The Outline and Goals of this Thesis

 Chapter 2

The Atomic Pair Distribution Function

(PDF) Method

2.1 Introduction

2.1.1 Why do we Study Structures of Materials?

The crystal structure of a material is the arrangement (ordering) of atoms in a

specific periodic manner which is usually described using the concepts of
lattices and unit cells. This arrangement of atoms is studied because it is
usually related to the properties of the material. Determining the structure and
understanding the properties lead to development of materials engineering and
industrial applications in different fields. Generally, there are three main types
of materials: perfectly crystalline (ordered) solid materials, perfectly non-
crystalline (disordered) materials such as liquids and glasses, and crystalline
materials with local atomic or nanometer scale disorders. Materials of the third
type are considered complex materials, and a lot of modern and
technologically important materials fall under this type of materials.

Conventional crystallographic methods used in structure determination were de-

veloped under the assumption of perfect lattice periodicity, thus they are
limited to crystalline materials, that show perfect long-range order, where they
give informa- tion about the average crystal structures of these materials.
Complex materials are generally characterized by local disorders and/or local
deviations from the average structure and the structure of the material at the
atomic (10−10 m) or nanometer (10−9 m) scale is called the local structure. Some
complex materials may have local structures completely different from their
average periodic structure unlike the local structure of perfectly crystalline
materials which is identical to their average structure. Local deviations are
usually related to the properties of complex materials more than their average
structures, thus determining these deviations is very im- portent in their
structural characterization. Applying conventional crystallographic methods to
locally disordered crystalline materials may lead to inaccurate deter- mention
of their structures. To completely understand the properties of complex
materials, local structure determination methods are needed to probe their local
structural scale in addition to their average structure determination.

2.1.2 Conventional Crystallographic Methods for Average

Structure Determination

Conventional crystallography is based on the famous Bragg’s law:

2 dsinθ=nλ (2.1)

which describes the diffraction process (mostly of x-ray or neutron beams)

from parallel lattice planes (planes of atoms) separated by the distance d. The
diffraction angle is 2θ which is the angle between the incident and diffracted
beams. Construc- tive interference of diffracted beams occurs only when the
path length difference between the beams equals an integer number (n) of
wavelengths (λ).

The x-ray or neutron diffraction experiments are performed on single crystals

or (mostly) on powder samples. The intensity (I) of the diffracted beams is
measured as a function of 2θ and well-defined peaks with sharp intensities
would result at positions where the Bragg’s law is satisfied obtaining what is
known as the diffraction pattern I(2θ). All the structural information about the
sample is contained in the diffraction pattern (mainly in peak positions, peak
intensities, and peak widths)

which is usually analyzed using computer programs and Rietveld refinement

methods (Dinnebier and Billinge, 2008). The structural information are

extracted with the help of crystal lattice and unit cell concepts. Peak positions

contain information about the unit cell lattice parameters (a, b, c, α, β, γ) and

the symmetry space group. Atomic positions (x, y, z) and atomic displacement

parameters (U) within the unit cell are contained in the peak intensity. The

peak width and shape are determined mainly by instrument parameters, crystal

size and lattice defects (or inhomogeneities).

Only the Bragg scattering (which is the coherent scattering) is of importance in

conventional crystallographic analysis. Background scatterings are subtracted

from the diffraction patterns, and these include incoherent scattering such as

Compton scattering, scattering from the surrounding environment such as the

air, sample holder, etc., and diffuse scattering which is a result of local

deviations. Discarding the diffuse scattering amounts for loss of important

information about the local structure. No clear and sharp Bragg peaks exist for

non-crystalline samples or for local disorders. This is why the long-range lattice

periodicity is of great importance, as a pre-assumption, in Bragg based

conventional crystallographic methods. The long-range periodic structure is

the average crystal structure.

It is important to note that the diffraction measurements for the determination of

average crystal structures using conventional crystallography are usually done in

reciprocal space (or momentum space) where the diffracted intensity is measured

as a function of the momentum transfer Q (or the diffraction vector)

which is defined as the difference between the incident and scattered

wavevectors, kinit and kfinal, respectively, and whose magnitude is given by:

4 π sinθ 2 πn
Q= =
λ d

where λ is the wavelength of the incident beam. This is equivalent to the

Bragg’s equation; it is another representation of the Bragg’s law (Dinnebier
and Billinge, 2008). The Q range is controlled by the value of λ. For average
structure determination, laboratory x-ray sources are enough such as the Cu
radiation which has a wavelength of 1.54 Å. The maximum Q value in this
case is about 8 Å-1 (Dinnebier, et al., 2008). This is not usually the case for local
structure determination as will be discussed shortly. Theoretical and experimental
details about the diffraction process, data analysis, and average crystal structure
determination can be found elsewhere (Cullity, 1978; Dinnebier, et al., 2008).

2.1.3 Local Structure Determination Methods

One of the most powerful methods for investigating and determining the local
structural features of materials, and which has proven its capability on a wide
range of complex materials, is the atomic pair distribution function (PDF)
method. The PDF method will be used in the work presented in this thesis to
investigate the local structure and the differences from the average structure on
a sample of the Iron Antimonide FeSb2. Brief description of this method will be
given in this and the next sections.

One of the most general properties of the PDF method is that no assumption
of perfect lattice periodicity is necessary, which means that it can be applied

to crystalline materials (in which case it gives identical and complementary

results to conventional methods), non-crystalline materials (in which case there
are no clear and sharp Bragg peaks meaning that conventional methods cannot be
applied), materials where the local-range shows deviations from their average
long-range crystal structure, and materials that crystallize to a limited range
(such as nanocrystalline materials) (Egami and Billinge, 2003; Billinge and
Kanatzidis, 2004; Proffen, et al., 2003). As mentioned earlier, information about
the local structure and deviations are contained in the diffuse scattering in the
diffraction pattern. The PDF method has its strength in taking into account the
diffuse scattering as well as the Bragg scattering coming from the long-range
ordered structure, i.e., it is a total scattering method. The diffuse scattering
appears in between and underneath the Bragg peaks. In order to be able to use
the PDF method and extract the atomic scale local structural information
from the sample, we need high penetrating beams. For this reason, beams with
shorter wavelengths, i.e., with high enough energy, must be used. This means
that we need a larger Q-range compared to conventional methods according to

equation (2.2). Usually, high maximum Q values of about 30-50 ˚A

are needed in PDF analysis (Dinnebier, et al., 2008). The effect of low and

finite Q-ranges on the PDF will be discussed later. The direction of the vector

Q does not really matter for scatterings from isotropic samples (such as liquids,
glasses, and crystalline powder samples) and the scattering will in general

depend only on the magnitude of Q (Egami and Billinge, 2003; Dinnebier, et al.,

2008). The experiment on Nd0.5Sr0.5MnO3 were performed on a powder sample

and the discussion and the equations of the PDF described in the next

sections are under the assumption of isotropic scattering. The development of

synchrotron x-ray and pulsed spallation neutron sources made it possible to

reach higher Q values and to carry the PDF measurements with good quality

and high accuracy. Modern computer programs also made it easier to analyze

the diffraction experimental data. This is why the PDF method is promising

and fastly spreading and becoming widely used for local structural analysis of

a very wide range of complex materials. A brief historical re- view of the

successful applications of the PDF method to different types of materials,

starting from liquids and amorphous materials since 1930 to recent developments

on locally disordered crystalline materials and nano-crystalline materials, is

presented by (Billinge, 2004; Egami and Billinge, 2003).

2.2 Basic Description of the PDF

2.2.1 Pair distribution function g(r)

In the literature, the PDF G(r) is usually defined as “a measure of the

probability of finding an atom at a distance r from another atom” (Billinge,

2002). In other words, it represents a distribution or a histogram of inter-

 atomic distances, or bond lengths, in the material (Proffen, et al., 2003;

Bordet, 2015) and the definition is written as (Egami and Billinge, 2003;

Billinge and Kanatzidis, 2004; Petkov, 2012):

G ( r )=4 πr ρ o [ g ( r )−1 ] =4 πr [ ρ ( r )−ρ o ] (2.3)

r is the inter-atomic distance which is the separating distance between two

atoms

in a pair, g(r) is the pair distribution function, ρ(r) is the pair density function,
ρ◦

is the average number density of atoms, and G(r) is called the reduced pair
distribution function. ρ(r), g(r), and G(r) in general contain the same structural
information and are all abbreviated as PDF; they are related to each other
according to equation (2.3) with some differences in their basic properties and
behaviors and in general G(r) is the mostly used function (Egami and Billinge,
2003; Dinnebier, et al., 2008). ρ(r) is given by (Egami and Billinge, 2003):

1
2∑ ∑
ρ ( r ) = ρo g ( r ) = δ (r−r νμ )(2.4)
4 πN r υ μ

where N is the total number of atoms in the sample and rνµ is the separation
between the νth atom and the µth atom. ρ(r) describes the distribution of inter-
atomic distances through the Dirac delta function δ. The sum is over all the
atoms in the sample.

2.2.2 The Measured PDF

 The PDF can be obtained experimentally through high energy synchrotron
x-ray or neutron diffraction experiments to allow for enough large Q-range as
mentioned earlier. It is known that diffraction experiments can be performed
either on single crystals (when available) or on powder (polycrystalline)

samples (which has proven its great accuracy in determining crystal

structures). The PDF method has advantages in non-crystalline and crystalline
powder (isotropic) samples since it can be averaged over all directions and
taken as a one-dimensional function i.e., all the atomic pairs separated by the
same distance r appear as a single PDF peak independent of their different
orientations. It thus has less advantages in single crystals since the directional
information are important and, in this case, the PDF must be obtained in three
dimensions which is not as easy as the one-dimensional PDF (Egami and
Billinge, 2003; Petkov, 2012; Proffen, et al., 2003).
The scattered intensity I(Q) is measured and then it is corrected (by
elimination of incoherent scattering, surrounding environment scatterings, etc.)
and normalized to obtain the total scattering structure function S(Q) which
contains both the Bragg and diffuse scatterings in reciprocal space. From the
definition of the PDF and the fact that the diffuse scattering come from the
atomic-scale disorders in the sample, we can describe the diffuse scattering as
containing information about two-body interactions or correlations.
The coherent (corrected) intensity is given by (Dinnebier, et al., 2008;
Egami
and Billinge, 2003):
sinQ Rνμ
I ( Q ) =∑ b ν b μ (2.5)
νμ Q R νμ

where Rµν is the magnitude of the difference between the positions of the νth
atom and the µth atom and b is the atomic scattering length.
 The Normalized Structure function is given by (Dinnebier, et al., 2008;
Egami and Billinge, 2003):

I ( Q ) + ⟨ b ⟩ − ⟨ b2 ⟩
2
S ( Q )= 2
(2.6)
N ⟨b ⟩

where (b) is the average scattering length of the sample.

S(Q) is then Fourier transformed from reciprocal space to real space to obtain
the PDF G(r) (Egami and Billinge, 2003):
∞ ∞
2 2
G ( r )= ∫ Q [ S ( Q )−1 ] sin ( Qr ) dQ= ∫ F (Q ) sin ( Qr ) dQ( 2.7)
π 0 π 0

F(Q) = Q[S(Q) - 1] is the reduced total scattering structure function. The PDF
is thus based on Fourier transformation of the diffraction data into real space
which

has more advantages in analyzing the diffuse scattering than in reciprocal space
generally because the diffuse scattering appears underneath the Bragg peaks
with relatively low intensity making it difficult to analyze in reciprocal space.
G(r) is the function that is directly related to the Fourier transformation
according to equation (2.7) and this is why it is the mostly used in the
description of the PDF (Egami and Billinge, 2003; Dinnebier, et al., 2008). The
correction, normalization, and Fourier transformation to obtain G(r) are done
using computer programs such as PDFgetX2 and PDFgetX3 for x-rays (Qiu, et
al., 2004(a); Juhas, et al., 2013) and PDFgetN for neutrons (Peterson, et al.,
2000). Detailed descriptions of the PDF experiments and data correction and
normalization are given by (Egami and Billinge, 2003).

2.2.3 The Calculated PDF:

The PDF can be calculated from a structural model of the atomic arrangements
using the equation (Egami and Billinge, 2003):

1 bν bμ 1
G ( r )= ∑ ∑
r ν μ ⟨ b⟩ 2
δ ( r−r νμ ) −4 πr ρo= R ( r )−4 πr ρo (2.8)
r

b is the atomic scattering length, which in the case of x-rays is equal to the
atomic

form factor f(Q) and ⟨ b ⟩ is the average scattering length of the sample. The sum
b ν bμ
is over all the atoms in the sample. R ( r )=∑ ∑ 2
δ ( r −r νμ ) is called the radial
ν μ ⟨b ⟩
distribution function (RDF) and it is related to g(r), ρ (r), and G(r) through
(Egami and Billinge, 2003):

R ( r )=4 π r 2 ρ o g ( r )=4 π r 2 ρ ( r ) =r [ G ( r )+ 4 π ρo ] (2.9)

The RDF gives the number of atoms at a distance r from another atom. It can
be described as follows: if we have an arrangement of atoms, a random atom
can

be chosen as a reference atom (or the atom at the origin) and a spherical shell is
drawn centered at this origin. This shell is expanded to find every other atom in
the sample. Whenever an atom is found situated on the shell at a certain
separation r from the origin, an R(r) peak is assigned at this distance. This is
repeated by making each atom in the sample as the origin and finding its
separation from the other atoms. This description is shown schematically (in
two dimensions) in figure (2.1). The intensity of each peak depends on the
number of atoms which were found on the shell at the distance r and on the
scattering length of each atom in the pair. This is a schematic description of
how to calculate a PDF from the atomic arrangements of a structure. It can be
summarized by the statement given by (Billinge and Kanatzidis, 2004): “The
function G(r) gives information about the number of atoms in a spherical shell
of unit thickness at a distance r from a reference atom. It peaks at characteristic
distances separating pairs of atoms”.

Figure 2.1: A schematic representation of the RDF; peaks of R(r) appears whenever several atoms
are situated on a spherical shell of unit thickness at a specific distance r from the origin (from
Billinge, 2007).

The calculated PDF can be fitted and compared with the measured PDF
through a process called modeling to extract the local structural information of
the sample. The parameters of the model are refined in order to obtain a best
agreement be- tween the calculated and the measured PDFs. The PDF
modeling and the refinable parameters will be described later in this chapter.

2.3 Parameters Influencing the PDF

According to discussions by (Proffen, et al., 2003; Bordet, 2015; Petkov,

2012; Toby and Egami, 1992; Qiu, et al., 2004(b); Proffen, 2006), the most
influencing parameters on the quality of the data and the obtained PDF can be
generally divided into: experimental parameters and sample parameters. The
former includes the Q-range, the instrumental resolution, counting statistics,
and the radiation beam used (x-rays or neutrons) and the latter include the
particle size, the degree of disorder (or structural coherence) and the atomic
thermal motion. To obtain high quality data and PDFs, some requirements and
conditions are imposed on the experimental parameters such as large enough
Q-range, as mentioned earlier, good instrumental resolution, and good counting
statistics. Neglecting these requirements will intro- duce errors in the PDFs and
decrease their quality. A summary of the effects and consequences of these
parameters is presented below.

2.3.3 Experimental Influencing Parameters

2.3.1.1 The Finite Q-range and Low Qmax value:

The ideal Q-range according to equation (2.7) is from 0 to 1 which can't be

reached in real experiments. In other words, the Q-range reachable by
experiments is finite (Qmin < Q < Qmax). If the finite value of Qmax was low (by
using x-ray laboratory sources for example), it would then have some
consequences on the obtained PDF. The effect of low Qmax is shown in figure
(2.2) where the resolution in real space G(r) is decreased meaning that
important and detailed local structural information might be lost. Sharp and
well-defined resolved peaks are clear for Qmax = 35Å−1 while they appear as one
broad peaks

for lower values of Qmax. This is why it is necessary to reach enough Q max
values experimentally. An example of a structural information that might be
lost when Qmax is low is the different but close bond lengths Zn - Se and Zn -
Te in the compound ZnSe0.5Te0.5 which was studied using neutron diffraction
(Qiu, et al., 2004); the bond lengths differ by 0.14 Å and the peaks start to
resolve, revealing this difference and the exact bond length for the two pairs, at
larger values of Qmax (> 40Å). The resolution in r is usually written as (Egami
and Billinge, 2003; Petkov, 2012):

2π
δr= (2.10)
Qmax

Another effect of the finite Q-range is the appearance of termination ripples

which can be described as the small broad peaks that appear between the
positions.

Figure 2.2: The effect of the value of Qmax on the PDF G(r) (from Bordet,
2015).of the real and sharp atomic pair peaks in the PDF (Egami and Billinge,
2003; Toby and Egami, 1992).

2.3.1.2 The Instrumental resolution:

The instrumental resolution is the resolution in the steps of Q (∆Q) in
reciprocal space (or the Bragg diffraction angle 2θ) which is generally
determined by the scattered beam detector used in the experimental setup. Low
instrumental resolution causes exponential damping of the PDF peak intensities
at larger values of r compared to low r values. Better resolution allows for
more structural information to be extracted since peaks will be present at large
values of r. This is shown in figure (2.3) where the PDFs were obtained using
two different instrumental resolution on a sample of nickel.

Figure 2.3: The effect of the resolution of the instrument on the PDF of nickel;
(up) better instrumental resolution, (down) less instrumental resolution where
the damping at larger values of r is clear (from Proffen, 2006).

2.3.1.3 The Type of the Radiation Beam Used and Counting Statistics
In general, using neutron beams may have advantages more than using x-rays.

For example, in the case of neutrons, there is no Q-dependent atomic form

factor killing the intensity at high Q unlike x-rays. Neutrons are also more
sensitive to materials with low atomic number Z in contrast to x-rays and in
addition neutrons are preferable for studying materials with magnetic
properties. The experimental data (I(2θ)) of Nd0.5Sr0.5MnO3 were obtained from
synchrotron x-ray diffraction measurements and some effects of using x-rays
are discussed here. In the case of x-ray beams, the decrease of the atomic form
factor f(Q) with increasing Q will affect the structure factor S(Q) according to
equation (2.6) since the normalization is done by dividing by ⟨ b ⟩ 2 which in the
case of x-rays is equal to the atomic form factor as mentioned earlier. The
effect of this appears as noisy amplified data at large values of Q in F(Q) which
in turn will result in noisy and low-quality PDFs as shown in figure (2.4) for
the CdTe nano-particles. Increasing the counting statistics of the detector at
high values of Q may reduce the noise effects since they are inversely
proportional to the counting (S(Q)/N) (Egami and Billinge, 2003). A decrease
in the signal and noise in the PDF are also present in the case of neutrons, but
the decrease comes mainly from the atomic displacements, as will be discussed
below, and not from a Q-dependent atomic form factor.
 Figure 2.4: An example showing the effect of low counting at high Q for an x-ray
diffraction experiment on CdTe nanoparticles; (a) The noise produced in F(Q)
by lower counting statistics at high Q (red) compared to larger counting (black),
(b) The noise in the respective obtained PDF (from Petkov, 2012)

Another consequence caused by using x-rays is the fact that the atomic form
factor f(Q) depends on the atomic number (Z) of the element; atoms with low
Z (such as oxygen) have low f(Q), and this is reflected in the PDF as small
peaks for the atomic pairs that contain low Z atoms. This is shown in figure
(2.5) for the x-ray PDF of LaMnO 3 compared to neutrons for which their
scattering length is large for low Z atoms resulting in more intense peaks; this
is clear in the first peak representing the Mn - O pair.

Figure 2.5: An example of the PDFs of LaMnO3 showing the differences when x-rays and neutrons
are used; the difference coming from the fact that neutrons are more sensitive to low Z atoms
unlike x-rays (from Bordet, 2015).

2.3.2 Sample Influencing Parameters:

2.3.2.1 Structural Coherence and Particle Size:
Crystalline samples show large number of Bragg and PDF peaks to a large r
range. This is not the case for non-crystalline disordered materials and
nanoparticles. Thus, the PDF is affected by the structural coherence of the
sample; structural coherence describes the degree of the disorder in the sample.
For non-crystalline materials, disordered materials, and nanoparticles, the
intensity of the PDF peaks shows exponential damping, where they disappear
at a certain value of r, similar to the damping due to low instrumental
resolution but in a faster way than that expected by the instrumental resolution.
This is why large values for Qmax are not generally necessary for these types of
materials unlike crystalline materials. The degree of the fall off the PDF
intensity could thus be a measure for the type of the material and its degree of
distortions. In the case of Nanoparticles, it provides a measure of its size at the
value where the PDF shows no peaks as in figure (2.4 (b)).

2.3.2.2 Atomic Displacements

Atomic displacements are generally results of the thermal motion of the atoms
in the pair around the equilibrium. The motions of two atoms may be of two
types: correlated (in-phase) or un-correlated (out-of-phase) (Jeong, et al.,
1999). The degree of thermal motion, which is measured by the atomic
displacement parameter (U), and the type of the motion produce effects in the
PDF, mainly in the peak width. Larger thermal motion (due to higher
temperature) and uncorrelated motion both lead to an increase in the PDF peak
width and a decrease in its intensity, while less thermal motion and correlated
motion produce narrow sharp and intense peaks. The difference between the
correlated and un-correlated atomic motions is schematically shown in figure
(2.6).
Figure 2.6: (a) The un-correlated atomic motion and (b) the correlated atomic
motion (from Jeong, et al., 1999).
At low values of atomic pair separation r, the atoms tend to move in a correlated
manner due to the low density of atomic pairs and this causes the first PDF peaks
of the first neighboring atoms to be sharper (less width) compared to peaks at
larger r coming from far neighbors; the increased atomic separation affects the
correlated motion where it becomes more un-correlated since the density of atomic
pairs in- creases with r. In other words, the PDF peak width depends on r; it
increases with increasing r.

2.4 Extracting Information From the PDF

Structural information about the studied sample are contained in the measured
PDF. Using the PDF method allows for extracting information at different length
scales: short, medium, and long ranges, making it appropriate for both local and
average structure determination. Two types of information can be extracted from
the PDF: direct and indirect information, these are described below.

2.4.1 Direct Information

The measured PDF is obtained after correction and normalization of the diffraction
data as discussed earlier; the measured PDF is thus an absolute function where
some structural information is extracted directly and easily from it. This is why this
information are described as direct information and they are contained in the PDF
peak positions, intensities, and shapes (Egami and Billinge, 2003; Dinnebier, et al.,
2008).
2.4.1.1 Peak Position

Peaks of the PDF appear at distances (r) separating pairs of atoms. Thus, the peak
position yields directly the atomic pair separation or the bond length. Peaks at low
r correspond to atomic pairs of shorter bond lengths and peaks at higher r to atomic
pairs of longer bond lengths. The lowest r value is the distance between an atom
and its first nearest neighboring atoms. No real peak exists for r values lower than
the first neighbor distance. The PDF peaks extend to the largest inter-atomic
distance in the whole sample. Non-crystalline materials have very small number of
broad PDF peaks, due to the very short-range order and the long-range disordered
structure, where they appear at low r values only. On the other hand, crystalline
materials have large number of sharp and well-defined peaks extending to large
values of r because of their long-range order.

2.4.1.2 Peak Intensity

The PDF Peak intensity, or more precisely the PDF peak integrated intensity, is
directly related to the number of the atoms at a distance r from another certain
atom; this number is called the coordination number. The integrated intensity is
proportional to the coordination number at r; larger integrated intensity
corresponds to a larger coordination number. This can be directly obtained by
b ν bμ
integrating R ( r )=∑ ∑ 2
δ (r−r νμ) (Egami and Billinge, 2003) which describes the
ν μ ⟨b ⟩
coordination number as the number of atoms situated at a spherical shell centered
at an origin atom as described earlier:
r2

N C =∫ R ( r ) dr (2.11)
r1
where NC is the coordination number, and r 1 and r2 are the integration limits
defining the peak with the coordination number NC.

2.4.1.3 Peak Width

As mentioned earlier, atomic displacements contribute to the increase of the width

of the PDF peak. The ideal PDF consists of well-defined delta functions, but in real
samples, this is not the case due to the atomic displacements which result in a
probability distribution of the inter-atomic distance. The type of this distribution (a
Gaussian distribution for example) is determined directly by examining the PDF
peak shape and width. This is where the probabilistic description of the PDF comes
from.

2.4.2 Indirect Information

Most of the structural information about the sample cannot be obtained directly.
These include quantitative determination of the different parameters and the
differences between the local and average structures of the sample which are
usually related to the important properties of the sample. These kinds of
information are obtained through modeling of the PDF and thus are called indirect
information. The modeling of the PDF to obtain this information is discussed in the
next section.

2.5 Structural Modeling of the PDF

2.1.1 What is Modeling?

Modeling is calculating the PDF using a structural model of the atomic

arrangements, as described earlier through equation (2.8), and comparing (fitting) it
to the experimentally obtained PDF. The structural model is defined through the
space group symmetry, lattice parameters, atomic positions, atomic displacement
parameters, and the atomic site occupancy in the unit cell of the sample. The
different parameters influencing the PDF must be considered in modeling. The
parameters that can be varied to obtain a better agreement between the calculated
model and the data are called refinement parameters and they are of two general
types (Billinge, 2002): sample dependent parameters and experimental dependent
parameters. Different structural models can be used and compared, and the model
resulting in a better fit is the best model to represent the data. The modeling can
also be done under different conditions (such as varying temperature) and at different
length scales allowing for comparison of local and average structural features. The
agreement between the calculated PDF and the measured PDF can be calculated
through the equation (Egami and Billinge, 2003):

√
N

∑ ω ( r i ) [G obs ( r i ) −Gcalc ( r i ) ]2
i=1
Rω = N
(2.12)
∑ ω( r i)G 2
obs (r i)
i=1

Rw is called the residual function and its value determines the goodness-of-fit;
lower Rw represents better agreement. Gobs and Gcalc are the observed and calculated
PDFs, respectively. w(ri) is the weighting factor. Usually, a value of around 10 %
of Rw represents a good fit for crystalline samples.

Modeling is done using computer programs such as the PDFgui program (Farrow,
et al., 2007) which will be used in this thesis work. The refinement parameters
according to the program PDFgui are discussed below. All the equations used to
account for the different effects are used by the program. Initial values of the
sample dependent and experimental dependent parameters are provided by the user
and are then varied until the best fit is reached.

2.5.2 Refinement Parameters

2.5.2.1 Sample Dependent Parameters:

These include the structural information about the sample which are generally
obtained from conventional crystallographic analysis: the lattice parameters, the
atomic positions, atomic occupancy of each site, and the space group symmetry.
They also include information about the atomic thermal motion and correlated or
un-correlated motion of the atoms. Structural parameters can be refined, and space
group symmetry constraints can be imposed in order not to break the symmetry of
the structure. Since the thermal motion and the un-correlated motion of the atoms
contribute to the PDF peak width as described earlier, they must be taken into
account for the PDF peak width of the calculated PDF. This is done through
multiplying by a Gaussian distribution function determined mainly from the atomic
displacement parameters (uij) which can be varied in the PDFgui program. The
correlated atomic motion at low r must also be considered. The parameter δ in
PDFgui sharpens the PDF peak at low r. The parameters affecting the PDF peak
width are considered through the equation:

'

√
σ ij=σ ij 1−
δ1 δ2 2 2
− 2 +Q broad r ij ¿
r ij r ij

This equation is used by PDFgui. σij is the corrected width σ 'ij is the width due to the
thermal and uncorrelated motion, δ1 and δ2 are the peak sharpening parameters; in
PDFgui the δ1 parameter is used in the high temperature case and δ2 in the low
temperature case, and Qbroad is an experimental dependent parameter contributing to
the peak width and is described below. Accounting for the correlated atomic
motion in PDF is discussed in a study by (Jeong, et al., 1999) on samples of Ni and
InAs. Another sample dependent parameter contained in the PDFgui program is the
phase scale factor. This parameter is used to account for different crystallo- graphic
phases in the sample. Refining this parameter allows for the quantitative
determination of the fraction of each phase in the sample in question.

2.5.2.2 Experimental Dependent Parameters

The finite maximum value of Q used in the Fourier transformation of F(Q) to

obtain G(r) must be provided and it cannot be refined. The effect of finite Q max is
considered in calculating G(r) by a function called the since function which is
given by (Egami and Billinge, 2003; Billinge, 2002):

[ ]
∞ '
1 ' sin Q max (r −r ) sin Qmax (r +r ' ) '
'
G ( r )= ∫
π 0
G (r )
r−r '
−
r +r '
dr (2.14)

sin Qmax r
is called the termination function, and G (r) is the PDF without the effect
r
of finite Qmax. This is to take account for the termination ripples that appear due to
the finite Q-range as mentioned earlier.

PDFgui allows for refinements over different length scales defined through a
minimum and a maximum value of r. This is called the refinement range and the
model is calculated through this range only, and the resulting refined values are
valid for this range.

The experimental dependent parameters which can be refined in PDFgui include

the Qdamp, the Qbroad, and the data scale factor. The Q damp parameter is used to
account for the exponential dampening of the PDF G(r) at high r values due to the
effect of the instrumental resolution. The following equation is used by PDFgui:
2
−(r Qdamp )
2
B ( r )=e (2.15)

B(r) is called a Gaussian dampening function.

The Qbroad parameter takes account for the broadening of the PDF peaks at high r
that generally comes from the noise at high Q values. In general, the two
parameters Qdamp and Qbroad have greater effect at higher values of r and since they
account for experimental effects, they can be obtained through modeling the PDF
of a standard sample, such as nickel, and the resulting refined values can then be
used for the sample in question without further refinement.

The data scale factor is refined to account for any errors coming from the
correction and normalization of the diffraction data. By default, the value of the
data scale factor is unity and refined values close to unity indicate, in general, good
correction and normalization of the data (Billinge, 2002).