X-RAY STRUCTURE AND HIRSHFELD ANALYSIS OF

3-AMINO-2-CHLOROPYRIDINE-2-NITROBENZOIC ACID

CO-CRYSTAL

PNG WEN HAN

ASSOCIATE PROFESSOR DR. QUAH CHING KHENG

PUSAT PENGAJIAN SAINS FIZIK

UNIVERSITI SAINS MALAYSIA

2017/18
 X-RAY STRUCTURE AND HIRSHFELD ANALYSIS OF
3-AMINO-2-CHLOROPYRIDINE-2-NITROBENZOIC ACID
CO-CRYSTAL

By

PNG WEN HAN

FINAL YEAR PROJECT REPORT

ZCT 390/8

Thesis submitted in fulfilment of the requirements

for the degree of
Bachelor of Science

JUNE 2018

i
 ACKNOWLEDGEMENT

I would like to express my immense gratitude to my final year project (FYP)

supervisor, Associate Professor Dr. Quah Ching Kheng, for giving me the opportunity to
conduct an elementary research on X-ray crystallography. His patience, guidance, and
advice have been a great support in completing my thesis. Besides, a special thanks to our
postgraduate student, Mr. Chia Tze Shyang, for his patient guidance in our X-ray
crystallography project, this includes coaching us on the fundamental theory of X-ray
crystallography, an efficient crystal synthesis method, as well as providing support to
prepare this thesis. I also like to thank my FYP partner, Yap Jinn Ming, in providing
academic support and some useful insight that greatly assisted the project. Last but not
least, I also appreciate my family member in giving me full support and encouragement
in doing this project. This project could not have been completed without their assistance
and guidance.

ii
 TABLE OF CONTENT

ACKNOWLEDGEMENT ............................................................................................. ii

TABLE OF CONTENT ................................................................................................iii

LIST OF FIGURES ....................................................................................................... v

LIST OF TABLES .......................................................................................................vii

LIST OF SYMBOLS AND ABBREVIATIONS ........................................................viii

ABSTRAK .................................................................................................................... ix

ABSTRACT................................................................................................................... x

CHAPTER 1 INTRODUCTION AND BACKGROUND ............................................ 1

1.1 History of X-ray .............................................................................................. 1

1.2 Introduction to X-ray Crystallography ............................................................ 2

1.2.1 Crystal Structure and Its History…………………………………………..2

1.2.2 X-ray Diffraction…………………………………………………………..4
1.3 Co-crystals....................................................................................................... 6

1.4 Objectives ........................................................................................................ 6

CHAPTER 2 LITERATURE REVIEW ........................................................................ 7

2.1 Importance of Pyridine Derivative .................................................................. 7

2.2 Advantage of Crystal over Amorphous Sample .............................................. 7

2.3 Study on Co-crystal and Salt ........................................................................... 8

2.4 Study of X-ray Crystallography ...................................................................... 9

iii
 2.5 Limiting Conditions and Systematic Absences ............................................. 10

2.6 Hydrogen Bonding Interaction ...................................................................... 12

2.7 Hirshfeld Surface Analysis and Fingerprint Plot .......................................... 13

CHAPTER 3 METHODOLOGY ................................................................................ 15

3.1 Weak Acid-Weak Base Neutralization .......................................................... 15

3.2 X-ray Crystallography Method ..................................................................... 16

3.3 Structure Determination and Structure Solution using SHELXTL............... 22

3.4 Hirshfeld Surface Analysis ............................................................................ 24

CHAPTER 4 RESULTS AND DISCUSSION ............................................................ 26

4.1 Crystal Structure of 3-Amino-2-Chloropyridine-2-Nitrobenzoic Acid

Co- Crystal ..................................................................................................... 26

4.1.1 Molecular Structure…………………………………………………..…..28

4.1.2 Crystal Packing and Supramolecular Feature……………………….....…30
4.1.3 Hirshfeld Surface Analysis…………………………………………….…32

CHAPTER 5 CONCLUSION ..................................................................................... 36

REFERENCES ............................................................................................................ 37

APPENDIX .................................................................................................................. 40

iv
 LIST OF FIGURES

Figure 1.1 The wavelengths and frequencies of X-rays and other 1

electromagnetic radiations (Gleen Stark, 2017).
Figure 1.2 Two-dimensional visualization of Bragg's law (Aboalbiss, 2009). 4
Figure 1.3 Laue pattern. 5
Figure 2.1 Chemical structure of pyridine. 7
Figure 2.2 Molecular structure of 2:1 co-crystal of 2-methylbenzoic acid 13
and N,N'-bis(pyridin-4-ylmethyl)ethanediamide (Syed et al.,
2016). Hydrogen bond is represented as a cyan line.
Figure 2.3 Two-dimensional fingerprint plot of 2:1 co-crystal of 2- 14
methylbenzoic acid and N,N'-bis(pyridin-4-ylmethyl)
ethanediamide (Syed et al., 2016). The percentage contribution
of different intermolecular interactions: (a)H ∙∙∙ H, (b) O ∙∙∙ H/ H ∙∙∙
O, (c) C ∙∙∙ H/H ∙∙∙ C, (d) N ∙∙∙ H/H ∙∙∙ N, and (e) C ∙∙∙ C.
Figure 3.1 The neutralisation reaction between 2-nitrobenzoic acid and 3- 16
amino-2-chloropyridine.
Figure 3.2 The X-ray crystallography method. 17
Figure 3.3 The flowchart of X-ray diffraction method. 18
Figure 3.4 Burker SMART APEX II DUO CCD area-detector 18
diffractometer(Abbas Farhadikoutenaei, 2016).
Figure 3.5 Crystal mounting. 19
Figure 3.6 The mounted crystal is at the center of the X-ray beam(Abbas 19
Farhadikoutenaei, 2016).
Figure 3.7 An example of .cif file. 21
Figure 3.8 XPREP program. 22
Figure 3.9 The reflection data (.hkl) file. 22
Figure 3.10 An example of instruction (.ins) file. 22

v
Figure 3.11 Crystal explorer 3.1. 24
Figure 3.12 Colors that indicate the intensity of intermolecular 25
interaction(Crystal Explorer, 2013).
Figure 3.13 An example of fingerprint plot. 25
Figure 4.1 Scheme of the title co-crystal. 26
Figure 4.2 The molecular structure of title co-crystal showing the atom- 28
labeling scheme and the displacement ellipsoids at the 30%
probability level.
Figure 4.3 (a) Two-molecule aggregate sustained by O1—H1O1···N1 31
hydrogen bond and (b) supramolecular column of title co-crystal.
Figure 4.4 Hirshfeld surfaces mapped over 𝑑𝑛𝑜𝑟𝑚 of (a) base and (b) acid 32
molecules of the 1:1 title co-crystal. The contact points (red) are
labeled to indicate the atoms participating in the intermolecular
interactions.
Figure 4.5 Hirshfeld surfaces mapped over 𝑑𝑛𝑜𝑟𝑚 show hydrogen bonds 32
between neighboring molecules with the reference (a) acid and
(b) base molecules.
Figure 4.6 The two-dimensional fingerprint plots for the (a) acid, (b) base, 33
and (c) overall 1:1 co-crystal.
Figure 4.7 The two-dimensional fingerprint plot for the title 1:1 co-crystal 34
showing contribution from different contacts: (a) H∙∙∙H, (b) O∙∙
∙H/H∙∙∙O, (c) C∙∙∙H/H∙∙∙C, (d) N∙∙∙H/H∙∙∙N, and (e) C∙∙∙C.
Figure 4.8 Hirshfeld surfaces mapped over the shape index for (a) the acid 35
and (b) the base, highlighting the regions involved in the π∙∙∙π
stacking interactions.
Figure 4.9 Hirshfeld surfaces mapped over curvedness for (a) the acid and 35
(b) the base.

vi
 LIST OF TABLES

Table 1.1 Crystal systems, Bravais lattices and their unit cell 3
parameters.
Table 2.1 Limiting conditions for unit cell type. 11
Table 2.2 Limiting conditions for 21 screw axes. 11
Table 2.3 Limiting conditions for glide planes. 12
Table 3.1 List of information provided by .cif file. 21

Table 3.2 SHELXTL commands (Girolami et al., 2000). 23

Table 4.1 The crystallographic data of the title compound. 27

Table 4.2 The C − OH and C=O bond lengths (Å) of the carboxyl 29

groups of parent acid and co-crystals.

Table 4.3 The C − N − C bond angles (°) of the pyridyl groups of 29

parent base, salts and co-crystals.

Table 4.4 Hydrogen-bond geometry of title compound. 30

Table 4.5 Physical parameter of π···π interactions in the title co- 31

crystal.
Table 4.6 Major percentage contribution of the different 33

intermolecular interactions to the Hirshfeld surfaces for

the acid, base and 1:1 co-crystal.

vii
 LIST OF SYMBOLS AND ABBREVIATIONS

a, b, c, 𝛼, 𝛽, 𝛾 Unit-cell parameters
𝑝𝐾𝑎 Negative base-10 logarithm of the acid dissociation constant (Ka)
.hkl File extension for reflection data file
.ins File extension for instruction file
.res File extension for result file
.raw File extension for raw data file
.p4p File extension for parameter file
.lst File extension for list file
𝑑𝑒 Distance from the surface to the nearest nucleus external to the
surface
𝑑𝑖 Distance from the surface to the nearest nucleus internal to the
surface
𝑑𝑛𝑜𝑟𝑚 Normalized contact distance
μ Absorption coefficient calculated from the atomic content of the
cell, the density and the radiation wavelength
Z The number of the formula units in the unit cell
Tmin, Tmax Minimum and maximum transmission factors applied to the
diffraction pattern
Δρmax, Δρmin The largest and smallest values of the final difference electron
density
CCD Charge-coupled Device
XRD X-ray Diffraction
SADABS Siemens Area-Detector Absorption
SAINT SAX Area-detector Integration
SMART Siemens Molecular Analysis Research Tools
FP Fingerprint plot

viii
 ABSTRAK

Ko-kirstal dalam kajian ini C7 H5 N O4 .C5 H5 Cl N2 mengandungi molekul asid 2-

nitrobenzoik dan molekul 3-amino-2-kloropiridin. Ko-kirstal ini disintesis melalui
neutralisasi alkali lemah dan asid lemah diikuti dengan kaedah penyejatan secara perlahan.
Struktur molekul dan padatan hablur dicirikan dengan mengguna keadah kristalografi
sinar-X hablur tunggal. Ko-kristal dalam kajian ini terhablur dalam sistem monoklinik
dan kumpulan ruang P2/n yang sentrosimetri. Parameter unit sel hablur adalah a =

8.661(2) Å, b = 8.322(2) Å, c = 18.740(5) Å, 𝛼 = 90°, 𝛽 = 101.278(5) °, 𝛾 = 90°.

Molekul 3-amino-2-khloropiridin diikat dengan molekul asid 2-nitrobenzoik melalui
ikatan intermolekular hidrogen O(karboksil)-H···N(pyridil). Agregat dari dua molekul
ini membentuk lajur supramolekular melalui ikatan hidrogen N(amida)-H···O(karboksil),
N(amida)-H···O(nitro), dan C(piridil)-H···O (nitro). Struktur hablur ini dikukuhkan
dengan interaksi 𝜋 ··· 𝜋 antara dua gelang benzena dan antara dua gelang piridil.
Interaksi intermolekul dikaji melalui analisis permukaan Hirshfeld. Analisis ini memberi
peratusan sumbangan kontak intermolekular dalam ko-kristal ini.

ix
 ABSTRACT

The title 1:1 co-crystal C7H5NO4·C5H5ClN2 comprises a 2-nitrobenzoic acid

molecule and a 3-amino-2-chloropyridine molecule. It was synthesized through a weak
acid-weak base neutralization followed by slow evaporation method. The molecular
structure and the crystal packing were determined using single crystal X-ray diffraction
(XRD) technique. The title co-crystal is crystallized in the centrosymmetric monoclinic

space group P2/n with unit cell parameters of a = 8.661 (2) Å, b = 8.322 (2) Å, c = 18.740
(5) Å , 𝛼 = 90 ° , 𝛽 = 101.278 (5) ° and 𝛾 = 90 ° . The 3-amino-2-chloropyridine
molecule is connected to 2-nitrobenzoic acid molecule through an intermolecular
O(carboxyl)—H···N(pyridyl) hydrogen bond into a two-molecule aggregate. The two-
molecule aggregates are then formed into a supramolecular column via intermolecular
N(amide)—H···O(carboxyl), N(amide)—H···O(nitro) and C(pyridyl)—H···O(nitro)
hydrogen bonds. The crystal structure is consolidated by weak intermolecular 𝜋 ··· 𝜋
interactions between two benzene rings and between two pyridine rings. The
intermolecular interactions were also studied by using Hirshfeld surface analysis, which
provides the percentage contributions of the intermolecular contacts of the title co-crystal.

x
 CHAPTER 1

1 INTRODUCTION AND BACKGROUND

1.1 History of X-ray

X-ray also refers to Röntgen radiation and it was named after its discoverer Wilhelm
Röntgen in 1896. The term X-ray was popularized because it signifies a radiation
unknown to the physicist during 18th century. X-ray belongs to a category of
electromagnetic radiation which has a short wavelength ranging from 0.01 to 10
nanometers. Its wavelength is longer than gamma ray, but shorter than UV ray. The
wavelengths and frequencies of X-rays and other electromagnetic radiations are shown in
Figure 1.1.

Figure 1.1 The wavelengths and frequencies of X-rays and other electromagnetic
radiations(Gleen Stark, 2017).

X-ray was discovered when Röntgen was experimenting on Crookes’ or Lenard tube.
The tube was shielded by close-fitting black paper and was placed in a dark room. As a
result, emission of rays was observed to be illuminated a barium platinocyanide covered

1
screen at two meters away. Röntgen proposed an invisible ray originating from the Lenard
tube, which is capable to penetrate the black paper and most of the substances. Then, X-
ray was first known for its penetration power. The mentioned experiment also proved the
X-ray to be insensitive to the retina of our eyes. By placing the discharge-tube on sensitive
plates oppose to one another, Röntgen had first photographed a few shadow pictures,
which is currently known as X-ray film.

1.2 Introduction to X-ray Crystallography

Crystals are long known for their regularity and symmetry. However, scientists only
begun to investigate their properties at the atomic level at 17th century. The discovery of
X-ray was then integrated into the research to interpret the atomic and molecular structure
of a crystal in a more precise manner. This field is later known as X-ray crystallography.
When a crystalline material is targeted with the X-ray beam, the beam will be diffracted
in various directions. By measuring the direction and intensities of these beams, a
crystallographer can reconstruct the three-dimensional visualization of the electron
density of a studied crystal. Knowing the electron densities, we can obtain the mean
position of the atoms as well as their chemical bonds and other crystal information.

1.2.1 Crystal Structure and Its History

Nicolas Steno, a Danish scientist is a pioneer in the investigation in crystal

symmetry. He showed that angles between the faces are the same in every exemplary of
a particular type of crystal (Molčanov & Stilinović, 2014). Later in 1784, René Just Haüy
found crystal structure has an ordered pattern which can be categorized into blocks of
same shape and size. In 1839, William Hallowes Miller proposes that each face of a
crystal has a label of three small integers, the Miller indices. Haüy’s idea such that a

2
crystal is a three-dimensional array of atoms or molecules was then be proven along the
development of X-ray crystallography. Nowadays, the three-dimensional crystals can be
categorized into 7 crystal systems, 14 Bravais lattices, 32 crystal classes and 230 space
groups. Table 1.1 shows the crystal systems, Bravais lattices and their unit-cell parameters.

Table 1.1 Crystal systems, Bravais lattices and their unit cell parameters.

Crystal system Bravais lattice Unit-cell parameters

Triclinic P 𝑎≠𝑏≠𝑐,
𝛼≠𝛽≠𝛾

Monoclinic P, C (or A or I) 𝑎≠𝑏≠𝑐,

𝛼 = 𝛾 = 90°, 𝛽 > 90°

Orthorhombic P, C, (or A or B), I, F 𝑎≠𝑏≠𝑐,

𝛼 = 𝛽 = 𝛾 = 90°

Tetragonal P, I 𝑎=𝑏≠𝑐,
𝛼 = 𝛽 = 𝛾 = 90°

Trigonal P 𝑎=𝑏≠𝑐,
𝛼 = 𝛽 = 90°, 𝛾 = 120°
(Hexagonal axes)

R 𝑎=𝑏=𝑐,
𝛼 = 𝛽 = 𝛾 ≠ 90°
(Rhombohedral axes)
Hexagonal P 𝑎=𝑏≠𝑐,
𝛼 = 𝛽 = 90°, 𝛾 = 120°

Cubic P, I, F 𝑎=𝑏=𝑐,
𝛼 = 𝛾 = 𝛽 = 90°

3
1.2.2 X-ray Diffraction

Crystal is constructed by regular arrays of atoms, while an X-ray is a form of

electromagnetic radiation. When X-ray strikes on an electron, a secondary spherical wave
is produced from the electron. This phenomenon is known as elastic scattering and the
electron is known as the scatterer. As scattering occurs on an array of the atom, the
spherical wave from each electron will interfere with each other in two ways, known as
destructive interference and constructive interference. No resultant wave is produced by
the destructive interference as the waves of equal magnitude cancel each other, whereas
constructive interference produces a resultant wave in a defined direction which can be
determined by Bragg’s law.

2 𝑑 𝑠𝑖𝑛𝜃 = 𝑛λ 1.1

where 𝑑 is the spacing between the diffracting planes, 𝜃 is the incident angle, 𝑛
indicates the order of reflection, and λ is the wavelength of the X-ray. The spots
observed on the diffraction pattern is known as the reflections. The two-dimensional
visualization of Bragg’s law is shown in Figure 1.2.

Figure 1.2 Two-dimensional visualization of Bragg's law (Aboalbiss, 2009).

4
 X-ray was chosen for crystallography technique, as it possesses an extremely short
wavelength ranged from 1 to 100 angstroms. The wavelength has the same order of
magnitude as the spacing 𝑑 between planes of a crystal. To produce significant
diffraction, the spacing between the scatters and the wavelength of the impinging wave
should be comparable. The X-ray crystallography technique requires the spacing between
scatters to be about the scale of covalent bonds. Therefore, visible light cannot provide a
sufficient resolution to determine the atomic position, as it typically has a wavelength of
5500 angstroms.

In 1921, there is a conversation arose between Paul Peter Ewald and Max von Laue
whether a crystal can be used as a diffraction grating for X-ray. Ewald’s resonator model
cannot be validated using visible light since the wavelength is larger than the spacing
between the resonator. Laue suggests that an X-ray is a viable option as electromagnetic
radiation with smaller wavelength is required to observe the small spacing of resonator.
Then, Laue designed an X-ray diffraction experiment which involves shining a beam of
X-ray through a copper sulfate and its diffraction pattern was recorded on the
photographic plate. The plate shows a pattern of reflections (Laue pattern) arranged as
intersecting circles around the central beam spot. Figure 1.3 is an example of Laue pattern
(Friedrich et al., 1912; Laue, 1901).

Figure 1.3 Laue pattern.

Laue was then awarded the Nobel prize in physics in 1914 for his contribution on
developing a law that connects the scattering angles, the size and the direction of the unit-
cell spacing (Eckert, 2012).

5
1.3 Co-crystals

Co-crystal is a multi-component molecular crystal (Bond, 2007). It consists of two

or more components that form a unique crystalline structure having unique properties
(Stahly, 2007). Co-crystal has been widely applied in pharmaceutical industry. In drug
making, co-crystal coformers have potential to provides drugs with enhanced properties
like stability, solubility, and bioavailability (Almarsson & Zaworotko, 2004). Ionic salt
has a complete transfer of hydrogen atom from acid to base, while co-crystal has
incomplete transfer of hydrogen atom from acid to base. Despite the complete or
incomplete transfer of hydrogen atom, both compounds still hold a hydrogen bond
between the protonation and deprotonation sites.

1.4 Objectives

The objectives of this project are:

1. To prepare and crystallize a co-crystal of carboxylic acid/pyridine complex.

2. To determine the X-ray structure of prepared co-crystal by single crystal X-ray
diffraction technique.
3. To study the intermolecular interactions of prepared co-crystal.

6
 CHAPTER 2

2 LITERATURE REVIEW

2.1 Importance of Pyridine Derivative

Pyridine is a type of heterocyclic compound; thus, pyridine and its derivative are
significant in the context of heterocyclic chemistry. Pyridine and its derivative are often
tended to form a hydrogen bond with a more electronegative atom (Jeffrey, 1997). In
crystal growth, pyridine is used as a versatile solvent in organic synthesis and a functional
building block in organic chemistry. A large group of compound containing the pyridine
is applied as polymers, antioxidant, insecticide, food flavoring, adhesive, disinfectant,
agrochemicals and herbicide (Green et al., 1995). The pyridine moiety also can be found
in natural products such as pyridoxine (vitamin B6) and nicotinic acid (vitamin B3). The
chemical structure of pyridine is shown in Figure 2.1.

Figure 2.1 Chemical structure of pyridine.

2.2 Advantage of Crystal over Amorphous Sample

A crystal exhibits more regularity and has less random-oriented molecules as

compared to liquid, powder or amorphous samples. A crystalline sample has periodicity
due to its composition of repeated unit cells in three independent directions. Account for
the periodicity, X-ray diffractions of a crystal produce stronger signals because crystal
tends to concentrate the weak scattering of individual unit cells into much powerful
coherent reflection than the signal noise. However, the single crystals of asymmetric and
complicated molecules are hard to obtain experimentally.

7
2.3 Study on Co-crystal and Salt

The difference between salt and co-crystal is the proton transfer, which incomplete
proton transfer resulting in co-crystal. The transfer of proton from one molecule can be
estimated by the difference in 𝑝𝐾𝑎 value between acid and basic function groups (“rule
of three”) as shown in equation 2.1,

∆𝑝𝐾𝑎 = 𝑝𝐾𝑎 𝑏𝑎𝑠𝑒 − 𝑝𝐾𝑎 𝑎𝑐𝑖𝑑 ≥ 3 (2.1)

The difference of ∆𝑝𝐾𝑎 less than zero exclusively result in a co-crystal formation,
while differences greater than three forms a molecular salt (Ward et al., 2003).In the range
0 < ∆𝑝𝐾𝑎 < 3, the crystallization may result in salt, co-crystal or disordered solid form
with incomplete proton transfer (Mohamed et al., 2009). Among 109 compounds
synthesized from pyridine groups and carboxylic acid groups, no co-crystal but 38 salts
were formed for those with ∆𝑝𝐾𝑎 > 3, while 22 co-crystals but no salt were formed for
those with ∆𝑝𝐾𝑎 < 0 (Andreas Lemmerer et al., 2014). The unpredictability was
observed at intermediate range 0 < ∆𝑝𝐾𝑎 < 3, where 15 co-crystals and 34 salts were
formed(Andreas Lemmerer et al., 2014). However, ∆𝑝𝐾𝑎 is still a good predictor of the
synthesis outcomes (Lemmerer et al., 2015).

One of the applications of co-crystal is in drug study. Compared to salts, the targeted
supramolecular synthesis and the structural prediction of co-crystals are easier (Aakeröy
et al., 2007). This indicates a co-crystal has potential to produce drug in diverse solid
form for development into effective and viable drug product(Aakeröy et al., 2007).

8
2.4 Study of X-ray Crystallography

X-ray crystallography has wide applications in the fields of material science,

pharmaceutical science, chemical science and biochemistry. In minerology, X-ray
diffraction (XRD) method has been used to identify the arrangement of atoms in minerals
and metals. In biology, the structure of a crystalline matter of biological molecule such as
protein, nucleic acid and enzyme can be investigated further for its chemical and
biological properties. In the field of chemistry, X-ray crystallography is useful to study
chemical bonds and non-covalent interactions. Preliminary studies revealed the typical
radii of atoms and confirmed many chemical bonding derived from theoretical models.
The tetrahedral bonding of carbon in diamond is one of the theoretical models confirmed
by X-ray diffraction (Bragg & Bragg, 1913). Besides, X-ray crystallography also helps
greatly in the development of supramolecular chemistry. In the pharmaceutical industry,
the ability of solid material to exist in more than one form of crystal structure or
polymorphism may affect the crystal’s size and regularity, and thus affect the quality of
the single crystal. The technique to purify chemicals (recrystallization) is used to reduce
these irregularities in small molecule crystals. Additionally, X-ray diffraction method is
also used for the identification of antibiotic drugs because the drug's crystal exhibits a
unique XRD pattern.

The importance of X-ray crystallography in structure determination is notable

because, 99% over 800,000 of the structure in the Cambridge Structural Database (as of
in year 2016) were determined by X-ray diffraction.

The analysis on molecular geometry at atomic resolution has been impossible before
X-ray crystallography was introduced. With the graphic visualization and the advanced
computation integrated into X-ray crystallography research, we can visualize a three-
dimensional molecular structure and study the molecular geometry such as bond angle,
bond length and torsion angle with the help of software like Mercury. Bond length is the

9
distance between two nuclei of two bonded atoms. Bond angle is defined as the angle
between three atoms. The angle between two planes containing two sets of three-atom
which having two in common is a torsion angle. From the molecular geometry, several
useful physical parameters of a crystal can be obtained and analyzed further for their
properties in interdisciplinary research.

2.5 Limiting Conditions and Systematic Absences

The translational symmetry and unit cell type can be determined using limiting
conditions and systematic absences. Limiting conditions are valid for the hkl coordinates
where constructive interference occurs. For instance, the limiting condition hkl : h + l =
2n (n = integer ) holds true if sum of h and l are even integers for all observed reflections
(hkl). On the contrary, the systematic absences occur at index with h + l ≠ 2n or h + l =
2n + 1.
The limiting conditions of unit cell types are listed in Table 2.1. If all three limiting
conditions of A, B and C are fulfilled, the resultant unit cell type can be deduced as face
centered. If none of the mentioned limiting conditions are met, then the result is a
primitive cell. The limiting conditions of 21 screw axes and the limiting conditions of
glide planes are listed in Table 2.2 and Table 2.3 respectively.

10
 Table 2.1 Limiting conditions for unit cell type.

Unit-cell type Limiting conditions Translational associated with unit-

cell type

P None None

A hkl : k + l = 2n b/2+c/2

B hkl : h + l = 2n a/2+c/2

C hkl : h + k = 2n a/2+b/2

I hkl : h + k + l = 2n a/2+b/2+c/2

F hkl : h + k = 2n a/2+b/2
hkl : k + l = 2n b/2+c/2
hkl : h + l = 2n a/2+c/2

Table 2.2 Limiting conditions for 21 screw axes.

Screw axis Orientation Limiting Translation

condition component

21 Parallel to a-axis h00 : h = 2n a/2

21 Parallel to b-axis 0k0 : k = 2n b/2

21 Parallel to c-axis 00l : l = 2n c/2

11
 Table 2.3 Limiting conditions for glide planes.

Glide Plane Orientation Limiting Translation

condition component

a Perpendicular to b-axis h0l : h = 2n a/2

a Perpendicular to c-axis hk0 : h = 2n a/2

b Perpendicular to a-axis 0kl : k = 2n b/2

b Perpendicular to c-axis hk0 : k = 2n b/2

c Perpendicular to a-axis 0kl : l = 2n c/2

c Perpendicular to b-axis h0l : l = 2n c/2

n Perpendicular to a-axis 0kl : k + l = 2n b/2 + c/2

n Perpendicular to b-axis h0l : h + l = 2n a/2 + c/2

n Perpendicular to c-axis hk0 : h + k = 2n a/2 + b/2

2.6 Hydrogen Bonding Interaction

Molecules in the crystal are held together through weak interaction forces. In 1993,
our understanding of factors that control on the crystallographic form of a crystal is
rudimentary because chemist is more familiar with intramolecular bonding and rarely
focus on designing molecule in crystalline form. After that, more researches in crystal
engineering show that hydrogen bond is the factor that control the crystalline form
(Aakeröy & Seddon, 1993). Therefore, hydrogen bond also affects some important
physical phenomena such as optical properties, thermal stability, crystallographic form,
color, solubility and conductivity (Aakeröy & Seddon, 1993). Hydrogen bond is the
strongest among the weak interaction forces between two non-covalently bonded
molecules. The study of hydrogen bonding is essential to understand the fundamental

12
science and practical application in the chemical and pharmaceutical industries.
Investigations in recent years have recognized different kinds of hydrogen bonds and their
structural features.
Hydrogen bond is important to the crystal packing and supramolecular chemistry. In
the field of crystal engineering, carboxylic acids are one of the most common functional
groups which suitable for the preparation of multicomponent crystal. This is because these
carboxylic acids produce more stable supramolecular heterosynthons with compounds
containing nitrogen sustained by hydrogen bonds (Figure 2.2).

Figure 2.2 Molecular structure of 2:1 co-crystal of 2-methylbenzoic acid and N,N'-
bis(pyridin-4-ylmethyl)ethanediamide(Syed et al., 2016). Hydrogen bond is represented
as a cyan line.

2.7 Hirshfeld Surface Analysis and Fingerprint Plot

Hirshfeld surface analysis is an approach to investigate the molecular interactions in

a crystal with the help of CrystalExplorer software(Wolff et al., 2012). This software
package involves high-level programming and graphic, quantum chemistry and crystal
engineering, in contrast to those analyses which focused entirely on the discussion of
crystal packing, and intermolecular angles and distances, via ball and stick model
(Spackman & Jayatilaka, 2009). CrystalExplorer encodes information about all
intermolecular interactions as a Hirshfeld surface, but interactive graphics are required to
extract these information (Spackman & McKinnon, 2002). Fingerprint plot overcomes
this problem by summarizing the nature and type of intermolecular interactions in a two-

13
dimensional mapping. The fingerprint plot represents a function of the closest distances
from the point to nuclei inside and outside the Hirshfeld surface (Spackman & McKinnon,
2002). Therefore, all intermolecular interactions in a crystal can be easily identified and
classified together with the percentage contribution of each intermolecular interaction
from the fingerprint plot as shown in Figure 2.3.

Figure 2.3 Two-dimensional fingerprint plot of 2:1 co-crystal of 2-methylbenzoic acid

and N,N'-bis(pyridin-4-ylmethyl)ethanediamide (Syed et al., 2016). The percentage
contribution of different intermolecular interactions: (a)H∙∙∙H, (b) O∙∙∙H/ H∙∙∙O, (c) C ∙∙∙
H/H ∙∙∙ C, (d) N ∙∙∙ H/H ∙∙∙ N, and (e) C ∙∙∙ C.

14
 CHAPTER 3

3 METHODOLOGY

3.1 Weak Acid-Weak Base Neutralization

The synthesis of co-crystal involves the neutralization of a weak acid and a weak base.
The reaction begins with mixing weak acidic solution with weak basic solution. The
mixture was then gently heated until the solutes were completely dissolved. The mixture
was then left at the room temperature with proper cover for slow evaporation. The slow
evaporation process normally took about a week to be completed and to yield a co-crystal.
Carboxylic acid and pyridine are the most common weak acid and weak base for the
preparation of co-crystal (Weyna et al., 2009). We selected 3-amino-2-chloropyridine as
the weak base and mixed with different weak acids to form different co-crystals. The
weak acids used for reactions are listed as followed,

1. 2-Nitrobenzoic acid 12. o-Anisic acid

2. 3-Nitrobenzoic acid 13. m-Anisic acid
3. 4-Nitrobenzoic acid 14. p-Anisic acid
4. Succinic acid 15. o-Toluic acid
5. 2-Pyridine-carboxylic acid 16. m-Toluic acid
6. Phthalic acid 17. p-Toluic acid
7. Terephthalic acid 18. 2,4-Dichlorobenzoic acid
8. Isophthalic acid 19. 4-Chlorobenzoic acid
9. Anthranilic acid 20. 2-Chlorobenzoic acid
10. 3-Aminobenzoic acid 21. 3-Chlorobenzoic acid
11. 4-Aminobenzoic acid 22. 2-Hydroxybenzoic acid

15
The title compound, 3-amino-2-chloropyridine-2-nitrobenzoic acid co-crystal, was
obtained through the procedures mentioned using 2-nitrobenzoic acid, 3-amino-2-
chloropyridine and methanol as the weak acid, the weak base and the solvent, respectively
(Figure 3.1). The difference of 𝑝𝐾𝑎 value of the title compound was obtained using ACD
chemistry software for synthesis outcome prediction.

𝐶𝐻3 𝑂𝐻

Figure 3.1 The neutralisation reaction between 2-nitrobenzoic acid and 3-amino-2-
chloropyridine.

3.2 X-ray Crystallography Method

The physics of X-ray crystallography is emphasized on the diffraction of X-ray by a

crystalline material. This scientific method is the only analytical technique that can
provide the molecular structure of a given compound in the solid crystalline state with
uncompromising certainty (Ooi, 2010). A summary on the X-ray diffraction method is
shown in Figure 3.2.

16
 Figure 3.2 The X-ray crystallography method.

Taking the analogy of light being reflected by microscopic lenses, the crystal sample
behaves the same way when the X-ray is focused on it. Fulfillment of Bragg's condition
enables the constructively interfered rays to be reflected and collected as the diffraction
pattern. By analyzing the diffraction pattern, we can obtain crystal information such as
the arrangement of atoms, bond lengths, bond angles and torsion angles. The X-ray
diffraction analysis is a systematic procedure which involves steps as shown in Figure
3.3. Bruker SMART APEX II DUO CCD area-detector diffractometer (Figure 3.4) was
used for X-ray crystallography analysis in this project.

17
 Figure 3.3 The flowchart of X-ray diffraction method.

Figure 3.4 Burker SMART APEX II DUO CCD area-detector diffractometer(Abbas

Farhadikoutenaei, 2016).

18
The descriptions of steps in X-ray diffraction method are as followed,
a) Crystal Evaluation
The crystal of the title compound was preliminary evaluated under a light
microscope to examine its quality. The good quality crystal was chose and mounted
onto the diffractometer (Ooi, 2010).
b) Crystal Mounting
The selected crystal was mounted on top of a fiber glass needle attached to the copper
tube, then it was placed on the goniometer head. A suitable crystal generally has a
dimension of 0.5𝑚𝑚 × 0.5𝑚𝑚 × 0.5𝑚𝑚 which is comparable to the minimum
diameter of the X-ray beam. Figure 3.5 shows the crystal glued on the top of the fiber
glass (Ooi, 2010).

Figure 3.5 Crystal mounting.

c) Crystal Alignment
The head of the goniometer was aligned to make sure the mounted crystal was at the
center of the X-ray beam (Figure 3.6) (Ooi, 2010).

Cold nitrogen
CCD

Goniometer
head

Figure 3.6 The mounted crystal was at the center of the X-ray beam(Abbas
Farhadikoutenaei, 2016).

19
d) Crystal Evaluation 2
Further evaluation was done on the crystal through the rotation photo. This enables
us to determine the crystallinity of the sample and to estimate the quality of the
crystal based on the diffraction spots recorded on the rotation photo (Ooi, 2010).

e) Determination of the Unit Cell

This stage provided information to confirm a crystal in single crystalline state and
its unit cell (Ooi, 2010).

f) Data Collection Strategy

A systematic plan was suggested based on the crystal quality and the unit cell to give
best quality data under optimum time (Ooi, 2010).

g) Data Collection
The duration of data collection depends on the crystal system in which a higher
symmetry crystal requires lesser time. The data collection duration normally ranges
from 45 minutes to several weeks (Ooi, 2010).

h) Data Reduction
The reflections on the frame were converted into a set of integrated intensities. All
data were scaled by data reduction during this process (Ooi, 2010).

i) Structure Determination and Refinement

The space group of the sample can be identified computationally using XPREP
software in the SHELXTL program package based on the data collected. The
information regarding the space group and its unit cell is written into an instruction
(.ins) file.

20
j) Structure analysis, Elucidation and Preparing Publication Materials
SHELXTL and PLATON package were used for structure analysis, elucidation
and preparing publication material. An interactive molecular graphics and
publication quality diagrams can be obtained through the “XP” command in
SHELXTL program. “XP” obtained data from .res file and write the .ins file for next
series of refinement. The last refinement process generates a Crystallographic
Information File (.cif )file (referred to Figure 3.7), which is used as crystal data for
publication and molecular visualization (Ooi, 2010). Table 3.1 shows the list of
information provided by (.cif )file.

Figure 3.7 An example of .cif file.

Table 3.1 List of information provided by .cif file.

Type of information Details

Crystal Structure
Atom detail
Molecular detail
Description of crystal
Space group of title compound
Dimensions and angles of unit cell
Volume and density of unit cell
Positions of atoms
Displacement parameters of atoms
Occupancy of atoms
Bond lengths and bond angles
Torsion angles
Connectivity tables

21
3.3 Structure Determination and Structure Solution using SHELXTL

First, the “XPREP” command was used for space group determination, unit cell
transformations, reciprocal space plots, and absorption corrections. XPREP (Figure 3.8)
reads the raw data file (.raw file) and the parameter file (.p4p file) outputted by the
diffractometer control program and produced new .hkl file (Figure 3.9) and .ins file
(Figure 3.10) for structure solution process. The structure determination was followed by
structure solution using XS and the structure refinement using XL (Girolami et al., 2000).

Figure 3.8 XPREP program.

Figure 3.9 The reflection data (.hkl) file.

Figure 3.10 An example of instruction (.ins) file.

22
 In the XS program, a list of atomic coordinates was written to the .res file and save
as .ins file for next series of structure refinement. Meanwhile, a detailed listing of the
program’s activities was written to the .lst file (Girolami et al., 2000). At the end of XS
program, the consistency between the resulting electron density and the experiment data
is indicated by a RE value, which a value less than 0.3 is acceptable.

Structure refinement is done for every minor change to the model. During the
structure solution, atoms with abnormally large thermal parameter were removed from
the atom list followed by a refinement process. Next, all non-hydrogen atom is refined
anisotropically. Some common SHELXTL commands are listed in Table 3.2. The
nitrogen-bound hydrogen atoms were located from difference Fourier maps and refined
freely while the carbon-bound hydrogen atoms were positioned geometrically and refined
using a riding model, Uiso(H) = 1.2 × Ueq(C). The unit cell parameters in the .res file were
checked to be consistent with the values provided in the .lst file.

Table 3.2 SHELXTL commands (Girolami et al., 2000).

Command Function
ACTA Tells XL to prepare output table for .cif file

CONF Tells XL to generate tables of torsional angles

ANIS Turns all the hydrogen atoms anisotropic
FMAP Determines parameters for Fourier calculations
L.S. Determines the number of least squared refinement performed
AFIX Add constraint to targeted atom.

At the end of the refinement process, the weighting scheme was changed to new value
suggested by XL program. It is done by overwrite the WGHT values at the top of .res file
with values at the bottom of .res file repeatedly until the WGHT values at top matches
the one at the bottom.

23
3.4 Hirshfeld Surface Analysis

Hirshfeld surface analysis is useful in determining the intermolecular interactions in

a crystal by using Crystal Explorer(Wolff et al., 2012) (Figure 3.11).

Figure 3.11 Crystal explorer 3.1.

The two main parameters involved in the Hirshfeld surface analysis are 𝑑𝑖 and 𝑑𝑒 ,
where 𝑑𝑒 is the distance from the surface to the nearest nucleus external to the surface,
while 𝑑𝑖 is distance from the surface to the nearest nucleus internal to the surface.
𝑑𝑛𝑜𝑟𝑚 is a normalized contact distance and it can be obtained by calculating the sum of
the normalized values of 𝑑𝑖 and 𝑑𝑒 (Equation 3.1). The normalization of 𝑑𝑖 and 𝑑𝑒 is
done with reference to van der Waals radius of the involved atom.

𝑑𝑖 − 𝑟𝑖𝑣𝑑𝑊 𝑑𝑒 − 𝑟𝑒𝑣𝑑𝑊 (3.1)

𝑑𝑛𝑜𝑟𝑚 = +
𝑟𝑖𝑣𝑑𝑊 𝑟𝑒𝑣𝑑𝑊

Taking the van der Waals contact as the reference, the color gradient (Figure 3.12)
ranged from white to blue represents the intermolecular contact that equal or larger than
the van der Waals, while the color gradient from white to red represents intermolecular
contact equal or smaller than the van der Waals contact.

24
 Fingerprint plot (Figure 3.13) is a visual summary of the frequency of 𝑑𝑒 and 𝑑𝑖
across the surface of the molecule. Each point on the fingerprint represents a unique
pair of 𝑑𝑒 and 𝑑𝑖 (Spackman & McKinnon, 2002). The color of each point is defined
by the contribution to the overall intermolecular interaction, which the colors goes from
uncolored, blue green and red, indicating the smallest contribution to the largest
contribution.

Figure 3.12 Colors that indicate the intensity of intermolecular interaction(Crystal

Explorer, 2013).

Figure 3.13 An example of fingerprint plot.

25
 CHAPTER 4

4 RESULTS AND DISCUSSION

4.1 Crystal Structure of 3-Amino-2-Chloropyridine-2-Nitrobenzoic Acid Co-

Crystal

The 1:1 co-crystal of 3-amino-2-chloropyridine-2-nitrobenzoic acid was acquired

through the neutralization reaction of a weak base and a weak acid followed by slow
evaporation method. The scheme of the title co-crystal is shown in Figure 4.1. The
molecular structure and crystal packing were characterized using single crystal X-ray
diffraction (XRD) technique. The title co-crystal is crystallized in the monoclinic P2/n

space group with unit cell parameters of a = 8.661 (2) Å, b = 8.322 (2) Å, c = 18.740 (5) Å,
𝛼 = 90 ° , 𝛽 = 101.278 (5) ° and 𝛾 = 90 ° . The crystallographic data of the title
compound is shown in Table 4.1.

Figure 4.1 Scheme of the title co-crystal.

26
 Table 4.1 The crystallographic data of the title compound.

Crystal data

Chemical formula C7H5NO4·C5H5ClN2

Mr 295.68
Crystal system, space group Monoclinic, P2/n
Temperature (K) 296
a, b, c (Å) 8.661 (2), 8.322 (2), 18.740 (5)
β (°) 101.278 (5)
3
V (Å ) 1324.7 (6)
Z 4
Radiation type Mo Kα
−1
µ (mm ) 0.31
Crystal size (mm) 0.39 × 0.18 × 0.12
Data collection
Diffractometer Bruker SMART APEX II DUO CCD area-
detector
Absorption correction Multi-scan (SADABS; Bruker, 2009)
Tmin, Tmax 0.700, 0.746
No. of measured, independent and 19594, 3078, 2123
observed [I > 2σ(I)] reflections
Rint 0.035
(sin θ/λ)max (Å−1) 0.654
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.063, 0.195, 1.07
No. of reflections 3078
No. of parameters 193
No. of restraints 3
H-atom treatment H atoms treated by a mixture of independent
and constrained refinement
Δρmax, Δρmin (e Å−3) 0.49, −0.45
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS2013 (Sheldrick, 2008) ,
SHELXL2014 (Sheldrick, 2015), SHELXTL(Sheldrick, 2008), Mercury (Macrae et al., 2008), PLATON
(Spek, 2009), publCIF (Westrip, 2010).

27
4.1.1 Molecular Structure

The molecular structure of title co-crystal is shown in Figure 4.2. The carboxyl group
is twisted out of the plane of benzene ring as indicated by the O1-C12-C6-C7 torsion
angle of -131.4 (3)°. The nitro group is also twisted away from the attached benzene ring
with the O3-N3-C7-C8 torsion angle of -145.9 (4)°. The large deviations of carboxyl and
nitro groups from attached benzene ring are probably due to the steric repulsion between
these two adjacent groups.

Figure 4.2 The molecular structure of title co-crystal showing the atom-labeling scheme
and the displacement ellipsoids at the 30% probability level.

The location of acidic H atom, H1O1, is nearer to the atom O1 instead of the atom
N1 indicated the characteristic of title compound as a co-crystal. The C-N-C bond angle
of pyridyl group and the two C-O bond lengths of carboxyl group were compared between
the title compound and reported 3-amino-2-chloropyridine and 2-nitrobenzoic acid
molecules.
Table 4.2 shows the list of two C-O bond lengths of carboxyl groups of title compound
and four reported compounds consisting of 2-nitrobenzoic acid (parent acid) molecule
from the Cambridge Structural Database (CSD) (Groom & Allen, 2014). Table 4.3 shows
the list of C − N − C bond angles of pyridyl groups of title compound and four reported
compounds consisting of 3-amino-2-chloropyridine (parent base) molecule from the
Cambridge Structural Database (CSD) (Groom & Allen, 2014) . The asymmetric carboxyl
group (C − OH bond length ≫ C = O bond length) of title compound is similar to those of

28
parent acid and reported co-crystals in Table 4.2, and also the C − N − C bond angle of
pyridyl group of title compound is smaller than 120° and similar to those of parent base
and reported co-crystal (JUHKUU) in Table 4.3, indicating the characteristic of title
compound as a co-crystal. The C − N − C bond angles of pyridyl groups of reported salts
(BUBWIF and UBEKAP) are widened with angles larger than 120° due to the effect of
protonation. Additionally, the ∆𝑝𝐾𝑎 value of the title compound is -0.63. This is
consistent with the “rule of three” which states a negative ∆𝑝𝐾𝑎 value results in a co-
crystal.

Table 4.2 The C − OH and C=O bond lengths (Å) of the carboxyl groups of parent acid
and co-crystals.

Compound C − OH C=O CSD Reference

Refcode
Parent acid 1.3154 (2) 1.2301 (2) NBZOAO (Zhurov & Pinkerton,
05 2015)
4,4'-Bipyridine bis(2- 1.291 (3) 1.206 (3) GAWJEU (Dai et al., 2005)
nitrobenzoic acid) co-
crystal
2-Nitrobenzoic acid 2- 1.302 (3) 1.204 (4) ORIKOR (Hariprasad et al., 2016)
ethoxybenzamide co-
crystal
Isoquinoline 1-oxide 1.298 (3) 1.205 (3) TAWNEL (Moreno-Fuquen et al.,
2-nitrobenzoic acid 2005)
co-crystal
Title co-crystal 1.269 (4) 1.169 (5) - This work

Table 4.3 The C − N − C bond angles (°) of the pyridyl groups of parent base, salts
and co-crystals.

Compound C−N−C CSD Refcode Reference

Parent base 117.0 (2) YELSEO (Saha et al., 2006)
3-Amino-2-chloropyridinium 123.4 (3) BUBWIF (Koleva et al., 2009)
hydrogen squarate salt
3-amino-2-chloropyridinium 123.4 (2) UBEKAP (Stilinović & Kaitner,
picrate salt 2011)
2-chloro-4-nitrobenzoic acid 2- 118.0 (1) JUHKUU (Lemmerer et al.,
chloropyridin-3-amine co-crystal 2015)
Title co-crystal 118.5 (2) - This work

29
4.1.2 Crystal Packing and Supramolecular Feature

The crystal packing of the title co-crystal is dominated by hydrogen bonds. The
hydrogen-bond geometry of the title co-crystal is given in Table 4.4. Figure 4.3(a) shows
that 2-nitrobenzoic acid molecule is connected to 3-amino-2-chloropyridine molecule by
intermolecular O1—H1O1···N1 hydrogen bond, forming a two-molecule aggregate. The
two-molecule aggregates are then connected into a supramolecular column (Figure 4.3(b))
along a-axis via intermolecular N2—H1N2···O3, N2—H2N2···O2 and C4—H4A···O4
hydrogen bonds. The crystal structure is consolidated by weak intermolecular 𝜋 ··· 𝜋
interactions between two benzene rings and between two pyridine rings with
centroid···centroid distances of 3.828 (2) and 3.5495 (18) Å, respectively (Table 4.5).

Table 4.4 Hydrogen-bond geometry of title compound.

D—H···A D—H (Å) H···A (Å) D···A (Å) D—H···A (º)

N2—H2N2···O2i 0.86 (3) 2.13 (3) 2.920 (4) 152 (2)

N2—H1N2···O3ii 0.87 (3) 2.54 (3) 3.316 (6) 150 (3)

O1—H1O1···N1 0.83 (3) 1.82 (4) 2.642 (4) 170 (4)

C4—H4A···O4iii 0.93 2.55 3.404 (4) 153

Symmetry codes: (i) x−1, y, z; (ii) −x+1, −y, −z+1; (iii) −x+2, −y, −z+1.

30
 a)

b)

Figure 4.3 (a) Two-molecule aggregate sustained by O1—H1O1···N1 hydrogen bond

and (b) supramolecular column of title co-crystal.

Table 4.5 Physical parameter of π···π interactions in the title co-crystal.

Ring 1 Ring 2 Centroid··· Dihedral Symmetry code

centroid distance angle (°)
(Å)
C6-C11 C6-C11 3.828 (2) 4.35 (15) −x+3/2, y, −z+1/2
N1, C1-C5 N1, C1-C5 3.5495 (18) 0.00 (13) −x+1, −y, −z+1

31
4.1.3 Hirshfeld Surface Analysis

The Hirshfeld surfaces mapped over 𝑑𝑛𝑜𝑟𝑚 of acid and base molecules (Figure 4.4),
show two notable bright red spots labelled as 2 and 3, representing the acceptor and the
donor, respectively, of strong intermolecular O(carboxyl)—H ∙∙∙ N(pyridyl) hydrogen
bond. Another four faint red spots labelled as 1 and 4 to 8 indicate three other hydrogen
bonds. The sites 1 & 4, 5 & 7 and 6 & 8 represent the N(amide)—H⋯O(carboxyl),
N(amide)—H ⋯ O(nitro) and C(pyridyl)—H ⋯ O(nitro) hydrogen bonds. The
neighbouring molecules in close contacts to the Hirshfeld surfaces are shown in Figure
4.5.

a) 1 b)

4
7
2 6
7

3
8
5
8
Figure 4.4 Hirshfeld surfaces mapped over dnorm of (a) base and (b) acid molecules of
the 1:1 title co-crystal. The contact points (red) are labeled to indicate the atoms
participating in the intermolecular interactions.

a) b)

Figure 4.5 Hirshfeld surfaces mapped over dnorm show hydrogen bonds between
neighboring molecules with the reference (a) acid and (b) base molecules.

32
 The two-dimensional fingerprint (FP) plots of the acid, base, and co-crystal are shown
in Figure 4.6. The prominent long spikes at 𝑑𝑒 + 𝑑𝑖 ~ 1.6 Å of the FP plots of acid and
base molecules (Figures 4.6(a) & 4.6(b)) are the result of short O(carboxyl)—H ∙∙
∙N(pyridyl) interaction. The FP plot of co-crystal (Figure 4.6(c)) shows a pair of sharp
spikes at 𝑑𝑒 + 𝑑𝑖 ~ 2.0 Å mainly contributed by N(amide)—H⋯O(carboxyl) interaction.

Table 4.6 shows the percentage contribution of the different intermolecular

interactions to the Hirshfeld surfaces for the acid, base and the title co-crystal.

a) b) c)

Figure 4.6 The two-dimensional fingerprint plots for the (a) acid, (b) base, and (c)
overall 1:1 co-crystal.

Table 4.6 Major percentage contribution of the different intermolecular interactions to

the Hirshfeld surfaces for the acid, base and 1:1 co-crystal.

Contact Acid Base Co-crystal

H⋯H 21.2 26.6 25.2

O⋯H/ H⋯O 38.7 22.5 31.4
C⋯H/ H⋯C 11.9 8.3 11.1
N⋯H/ H⋯N 5.8 9.6 3.3
C⋯C 4.8 5.7 5.6

33
 The delineated FP plots of H∙∙∙H, O∙∙∙H/H∙∙∙O, C∙∙∙H/H∙∙∙C, N∙∙∙H/H∙∙∙N, and C∙∙∙C
interactions are shown in Figure 4.7. The H∙∙∙H contacts (Figure 4.7(a)) has asymmetrical
points scattered over the plot without a single peak and contribute 25.2% to the overall
interactions of co-crystal. The O∙∙∙H/H∙∙∙O contact (Figure 4.7(b)) contribute 31.4% to the
overall interactions of co-crystal. A symmetrical wing is observed in the FP plot of C∙∙
∙H/H∙∙∙C contact (Figure 4.7(c)), contributing to 11.1% of overall Hirshfeld surface. In FP
plot for N∙∙∙H/H∙∙∙N contact (Figure 4.7(d)), a pair of sharp spikes at both sides and
scattered points in the middle contribute insignificantly to Hirshfeld surface with a
contribution of 3.3% from overall interactions. The FP plot of C∙∙∙C (Figure 4.7(e))
contact shows a pattern of distorted triangle with a blunt tip, contributing 5.6% of overall
interactions.

a) b) c)

d) e)
Figure 4.7 The two-dimensional fingerprint plot for the title 1:1 co-crystal showing
contribution from different contacts: (a) H∙∙∙H, (b) O∙∙∙H/H∙∙∙O, (c) C∙∙∙H/H∙∙∙C, (d)
N∙∙∙H/H∙∙∙N, and (e) C∙∙∙C.

34
 The presence of 𝜋 ∙∙∙ 𝜋 stacking interaction can be displayed in shape-indexed surface
and curvedness by using Crystal Explorer 3.1. In Figure 4.8, the appearances of red and
orange regions identified with arrows indicate 𝜋 ∙∙∙ 𝜋 stacking interactions. This weak
interaction can also be indicated by flat regions on the Hirshfeld surface mapped with
curvedness (Figure 4.9).

a) b)
Figure 4.8 Hirshfeld surfaces mapped over the shape index for (a) the acid and (b) the
base, highlighting the regions involved in the π∙∙∙π stacking interactions.

a) b)

Figure 4.9 Hirshfeld surfaces mapped over curvedness for (a) the acid and (b) the base.

35
 CHAPTER 5

CONCLUSION

The 1:1 co-crystal of 3-amino-2-chloropyridine-2-nitrobenzoic acid was prepared

and was grown by solution growth technique at room temperature.

The molecular structure and crystal packing of the title co-crystal were characterized
using single crystal X-ray diffraction (XRD) technique. The title co-crystal is crystallized
in the centrosymmetric monoclinic space group P2/n. A notable twist is observed between
the carboxyl and nitro groups and the attached benzene ring of the acid molecule. Two-
molecule aggregate containing the acid and base molecules was sustained by
intermolecular O(carboxyl)—H···N(pyridyl) hydrogen bond. The supramolecular
column is then formed along a-axis via intermolecular N(amide)—H···O(carboxyl),
N(amide)—H···O(nitro) and C(pyridyl)—H···O(nitro) hydrogen bonds. The crystal
structure is consolidated by weak intermolecular 𝜋 ··· 𝜋 interactions between two
benzene rings and between two pyridine rings.

Using the Hirshfeld surface analysis, the percentage of contribution of each contact
can be obtained from the fingerprint plot. X-ray crystallography is the most promising
technique to study the molecular structure of a chemical compound, which is crucially
important for crystal engineering, pharmaceutical and drug industries.

36
 REFERENCES

Aakeröy, C. B., Fasulo, M. E. & Desper, J. (2007). Mol. Pharm. 4, 317–322.

Aakeröy, C. B. & Seddon, K. R. (1993). Chem. Soc. Rev. 22, 397–407.

Abbas Farhadikoutenaei (2016). (USM Doctoral dissertation), 48.

Aboalbiss (2009). File:Bragg’s Law.PNG - Wikimedia Commons

https://commons.wikimedia.org/wiki/File:Bragg%27s_Law.PNG (accessed
03/05/2018).
Almarsson, Ö. & Zaworotko, M. J. (2004). Chem. Commun. 0, 1889.

Andreas Lemmerer, C., Lemmerer, A., Govindraju, S., Johnston, M., Motloung, X. &
Savig, K. L. (2014). 17, 3543–3718.

Bond, A. D. (2007). CrystEngComm. 9, 833.

Bragg, W. H. & Bragg, W. L. (1913). Nature. 91, 557–557.

Bruker, S. (2009). Bruker AXS Inc., Madison, Wisconsin, USA.

Crystal Explorer (2013). File:Dnorm colours.png - CrystalExplorer Wiki .

http://crystalexplorer.scb.uwa.edu.au/wiki/index.php/File:Dnorm_colours.png
(accessed 02/05/2018)

Dai, Y.-M., Huang, J.-F. & Shen, H.-Y. (2005). Acta Crystallogr. Sect. E Struct. Reports
Online. 61, o3919–o3920.

Eckert, M. (2012). Ann. Phys. 524, 83–85.

Friedrich, W., Knipping, P. & Laue, M. (1912). Kgl. Bayer Akad. Wiss. 303,.

Girolami, G. S., Brumaghim, J. L., Priepot, J. G. & Goveia, J. P. (2000). 1–37.

37
Gleen Stark (2017). X-ray | radiation beam | Britannica.com (accessed 26/04/2018).

Green, G. R., Evans, J. M., Vong, A. K., Katritzky, A. R., Rees, C. W. & Scriven, E. F.
(1995). Pyran Their Benzo Deriv. Synth. 5, 469.

Groom, C. R. & Allen, F. H. (2014). Angew. Chemie Int. Ed. 53, 662–671.

Hariprasad, V. M., Nechipadappu, S. K. & Trivedi, D. R. (2016). Cryst. Growth Des. 16,
4473–4481.

Jeffrey, G. A. (1997). An introduction to hydrogen bonding Oxford University Press.

Koleva, B. B., Kolev, T., Seidel, R. W., Spiteller, M., Mayer-Figge, H. & Sheldrick, W. S.
(2009). J. Phys. Chem. A. 113, 3088–3095.

Laue, M. v (1901). Physics (College. Park. Md). 1921, 347–355.

Lemmerer, A., Govindraju, S., Johnston, M., Motloung, X. & Savig, K. L. (2015).
CrystEngComm. 17, 3591–3595.

Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E.,
Rodriguez-Monge, L., Taylor, R., Streek, J. vd & Wood, P. A. (2008). J. Appl.
Crystallogr. 41, 466–470.

Mohamed, S., Tocher, D. A., Vickers, M., Karamertzanis, P. G. & Price, S. L. (2009).
Cryst. Growth Des. 9, 2881–2889.

Molčanov, K. & Stilinović, V. (2014). Angew. Chemie Int. Ed. 53, 638–652.

Moreno-Fuquen, R., Montaño, A. M. & Atencio, R. (2005). Acta Crystallogr. Sect. E

Struct. Reports Online. 61, o3061–o3062.

Ooi, L. (2010). Principles of x-ray crystallography Oxford University Press.

38
Rahman, M. L., Kulkarni, A. D., Mohd. Yusoff, M., Kwong, H. C. & Quah, C. K. (2016).
Acta Crystallogr. Sect. E Crystallogr. Commun. 72, 283–286.

Saha, B. K., Nangia, A. & Nicoud, J.-F. (2006). Cryst. Growth Des. 6, 1278–1281.

Sheldrick, G. M. (2008). Acta Crystallogr. Sect. A Found. Crystallogr. 64, 112–122.

Sheldrick, G. M. (2015). Acta Crystallogr. Sect. C Struct. Chem. 71, 3–8.

Spackman, M. A. & McKinnon, J. J. (2002). CrystEngComm. 4, 378–392.

Stahly, G. P. (2007). Cryst. Growth Des. 7, 1007–1026.

Stilinović, V. & Kaitner, B. (2011). Cryst. Growth Des. 11, 4110–4119.

Syed, S., Jotani, M. M., Halim, S. N. A. & Tiekink, E. R. T. (2016). Acta Crystallogr. Sect.
E Crystallogr. Commun. 72, 391–398.

Ward, S. C., Hursthouse, M. B., Woods, D. C. & Lewis, S. M. (2003).

Westrip, S. P. (2010). J. Appl. Crystallogr. 43, 920–925.

Weyna, D. R., Shattock, T., Vishweshwar, P. & Zaworotko, M. J. (2009). Cryst. Growth
Des. 9, 1106–1123.

Wolff, S. K., Grimwood, D. J., McKinnon, J. J., Turner, M. J., Jayatilaka, D. & Spackman,
M. A. (2012).

Zhurov, V. V. & Pinkerton, A. A. (2015). J. Phys. Chem. A. 119, 13092–13100.

39
 APPENDIX

supporting information

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT

(Bruker, 2009); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used

to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: SHELXTL (Sheldrick, 2008),

Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek,

2009), publCIF (Westrip, 2010).

3-Amino-2-chloropyridine-2-nitrobenzoic acid

Crystal data

C7H5NO4·C5H5ClN2 F(000) = 608

Mr = 295.68 Dx = 1.483 Mg m-3

Monoclinic, P2/n Mo Kα radiation, λ = 0.71073 Å

a = 8.661 (2) Å Cell parameters from 4121 reflections

b = 8.322 (2) Å θ = 2.4–23.3°

c = 18.740 (5) Å μ = 0.31 mm-1

β = 101.278 (5)° T = 296 K

V = 1324.7 (6) Å3 Block, yellow

Z=4 0.39 × 0.18 × 0.12 mm

Data collection

Bruker APEX Duo CCD area detector 3078 independent reflections

diffractometer

Radiation source: fine-focus sealed tube 2123 reflections with I > 2σ(I)

Graphite monochromator Rint = 0.035

φ and ω scans θmax = 27.7°, θmin = 2.2°

Absorption correction: multi-scan h = -11→11

(SADABS; Bruker, 2009)

Tmin = 0.700, Tmax = 0.746 k = -10→10

40
 19594 measured reflections l = -24→24

Refinement

Refinement on F2 3 restraints

Least-squares matrix: full Hydrogen site location: mixed

R[F2 > 2σ(F2)] = 0.063 H atoms treated by a mixture of independent and

constrained refinement

wR(F2) = 0.195 w = 1/[σ2(Fo2) + (0.0961P)2 + 0.5226P]

where P = (Fo2 + 2Fc2)/3

S = 1.07 (D/σ)max < 0.001

3078 reflections Dρmax = 0.49 e Å-3

193 parameters Dρmin = -0.45 e Å-3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated
using the full covariance matrix. The cell esds are taken into account individually in the
estimation of esds in distances, angles and torsion angles; correlations between esds in cell
parameters are only used when they are defined by crystal symmetry. An approximate
(isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) for

(mo_g2no2_0m)

x y z Uiso*/Ueq

Cl1 0.31422 (9) 0.33589 (10) 0.43123 (4) 0.0737 (3)

O1 0.7039 (3) 0.4085 (3) 0.41393 (13) 0.0901 (7)

O2 0.9117 (3) 0.2686 (6) 0.4522 (2) 0.171 (2)

O3 0.8512 (5) 0.0992 (4) 0.3226 (3) 0.200 (2)

O4 1.0600 (3) 0.0812 (3) 0.28222 (16) 0.1010 (8)

N1 0.5806 (3) 0.2629 (3) 0.51490 (12) 0.0633 (6)

N2 0.1962 (3) 0.1211 (3) 0.53583 (16) 0.0745 (7)

N3 0.9615 (4) 0.1584 (3) 0.30304 (17) 0.0833 (8)

C1 0.4284 (3) 0.2394 (3) 0.50524 (13) 0.0547 (6)

C2 0.3541 (3) 0.1422 (3) 0.54858 (14) 0.0560 (6)

41
 C3 0.4535 (4) 0.0688 (3) 0.60635 (16) 0.0675 (7)

H3A 0.4118 0.0029 0.6379 0.081*

C4 0.6128 (4) 0.0929 (4) 0.61727 (16) 0.0718 (8)

H4A 0.6792 0.0437 0.6561 0.086*

C5 0.6736 (3) 0.1898 (4) 0.57062 (15) 0.0699 (8)

H5A 0.7819 0.2050 0.5779 0.084*

C6 0.9027 (3) 0.4261 (3) 0.34743 (14) 0.0571 (6)

C7 0.9680 (3) 0.3340 (3) 0.29970 (14) 0.0559 (6)

C8 1.0337 (3) 0.3979 (4) 0.24540 (15) 0.0673 (7)

H8A 1.0758 0.3317 0.2141 0.081*

C9 1.0362 (4) 0.5606 (4) 0.23815 (18) 0.0806 (9)

H9A 1.0814 0.6066 0.2019 0.097*

C10 0.9729 (4) 0.6562 (4) 0.2838 (2) 0.0825 (9)

H10A 0.9744 0.7673 0.2783 0.099*

C11 0.9058 (4) 0.5894 (4) 0.33884 (17) 0.0724 (8)

H11A 0.8630 0.6560 0.3698 0.087*

C12 0.8401 (3) 0.3575 (4) 0.40999 (17) 0.0699 (8)

H2N2 0.136 (3) 0.177 (3) 0.5029 (14) 0.082 (11)*

H1N2 0.156 (4) 0.048 (3) 0.5596 (16) 0.086 (10)*

H1O1 0.674 (5) 0.355 (4) 0.4459 (17) 0.113 (14)*

Atomic displacement parameters (Å2) for (mo_g2no2_0m)

U11 U22 U33 U12 U13 U23

Cl1 0.0734 (5) 0.0828 (5) 0.0669 (5) 0.0024 (3) 0.0186 (3) 0.0162 (3)

O1 0.0676 (13) 0.130 (2) 0.0800 (14) 0.0133 (13) 0.0333 (11) 0.0276 (14)

O2 0.0880 (18) 0.276 (5) 0.169 (3) 0.075 (2) 0.072 (2) 0.149 (3)

O3 0.214 (4) 0.0765 (19) 0.363 (7) -0.021 (2) 0.187 (5) 0.012 (3)

O4 0.1139 (19) 0.0779 (15) 0.115 (2) 0.0264 (14) 0.0323 (16) -0.0094 (14)

N1 0.0605 (13) 0.0730 (14) 0.0598 (12) -0.0049 (11) 0.0202 (10) -0.0078 (11)

N2 0.0633 (15) 0.0757 (16) 0.0899 (18) -0.0008 (12) 0.0282 (13) 0.0201 (14)

N3 0.0917 (19) 0.0644 (16) 0.103 (2) -0.0023 (14) 0.0416 (17) 0.0002 (14)

C1 0.0622 (14) 0.0535 (13) 0.0518 (12) -0.0002 (11) 0.0198 (10) -0.0044 (10)

C2 0.0623 (14) 0.0530 (13) 0.0571 (13) 0.0013 (11) 0.0224 (11) -0.0032 (11)

42
 C3 0.0796 (18) 0.0651 (16) 0.0619 (15) 0.0032 (14) 0.0244 (13) 0.0050 (13)

C4 0.0771 (19) 0.0772 (19) 0.0593 (16) 0.0121 (15) 0.0086 (13) -0.0019 (14)

C5 0.0584 (15) 0.086 (2) 0.0652 (17) -0.0021 (14) 0.0129 (13) -0.0144 (14)

C6 0.0522 (13) 0.0643 (16) 0.0571 (13) -0.0002 (11) 0.0165 (11) 0.0023 (11)

C7 0.0497 (13) 0.0597 (15) 0.0593 (14) -0.0023 (10) 0.0134 (11) 0.0015 (11)

C8 0.0619 (15) 0.0811 (19) 0.0624 (15) -0.0010 (14) 0.0209 (13) 0.0038 (14)

C9 0.079 (2) 0.090 (2) 0.0774 (19) -0.0113 (17) 0.0272 (16) 0.0198 (17)

C10 0.092 (2) 0.0571 (17) 0.098 (2) -0.0101 (15) 0.0179 (19) 0.0143 (16)

C11 0.0758 (18) 0.0645 (18) 0.0781 (19) 0.0035 (14) 0.0178 (15) -0.0045 (14)

C12 0.0563 (15) 0.089 (2) 0.0680 (16) 0.0094 (14) 0.0219 (13) 0.0139 (15)

Geometric parameters (Å, º) for (mo_g2no2_0m)

Cl1—C1 1.735 (3) C3—H3A 0.9300

O1—C12 1.269 (3) C4—C5 1.368 (4)

O1—H1O1 0.827 (10) C4—H4A 0.9300

O2—C12 1.169 (4) C5—H5A 0.9300

O3—N3 1.194 (4) C6—C11 1.370 (4)

O4—N3 1.193 (3) C6—C7 1.380 (4)

N1—C1 1.310 (3) C6—C12 1.498 (4)

N1—C5 1.334 (4) C7—C8 1.367 (4)

N2—C2 1.353 (4) C8—C9 1.361 (4)

N2—H2N2 0.862 (10) C8—H8A 0.9300

N2—H1N2 0.867 (10) C9—C10 1.360 (5)

N3—C7 1.464 (4) C9—H9A 0.9300

C1—C2 1.390 (3) C10—C11 1.394 (5)

C2—C3 1.386 (4) C10—H10A 0.9300

C3—C4 1.369 (4) C11—H11A 0.9300

C12—O1—H1O1 107 (3) C4—C5—H5A 119.3

C1—N1—C5 118.5 (2) C11—C6—C7 117.1 (2)

C2—N2—H2N2 120 (2) C11—C6—C12 119.2 (3)

C2—N2—H1N2 119 (2) C7—C6—C12 123.6 (3)

H2N2—N2—H1N2 120 (3) C8—C7—C6 123.3 (3)

43
O4—N3—O3 123.0 (3) C8—C7—N3 116.5 (3)

O4—N3—C7 119.2 (3) C6—C7—N3 120.1 (2)

O3—N3—C7 117.7 (3) C9—C8—C7 118.6 (3)

N1—C1—C2 125.1 (2) C9—C8—H8A 120.7

N1—C1—Cl1 116.24 (19) C7—C8—H8A 120.7

C2—C1—Cl1 118.7 (2) C10—C9—C8 120.2 (3)

N2—C2—C3 122.2 (2) C10—C9—H9A 119.9

N2—C2—C1 122.7 (3) C8—C9—H9A 119.9

C3—C2—C1 115.1 (2) C9—C10—C11 120.6 (3)

C4—C3—C2 120.4 (3) C9—C10—H10A 119.7

C4—C3—H3A 119.8 C11—C10—H10A 119.7

C2—C3—H3A 119.8 C6—C11—C10 120.2 (3)

C5—C4—C3 119.5 (3) C6—C11—H11A 119.9

C5—C4—H4A 120.2 C10—C11—H11A 119.9

C3—C4—H4A 120.2 O2—C12—O1 123.2 (3)

N1—C5—C4 121.4 (3) O2—C12—C6 123.1 (3)

N1—C5—H5A 119.3 O1—C12—C6 113.7 (3)

C5—N1—C1—C2 -0.4 (4) O4—N3—C7—C8 29.7 (4)

C5—N1—C1—Cl1 -179.26 (19) O3—N3—C7—C8 -145.9 (4)

N1—C1—C2—N2 -179.5 (3) O4—N3—C7—C6 -153.5 (3)

Cl1—C1—C2—N2 -0.7 (3) O3—N3—C7—C6 30.9 (5)

N1—C1—C2—C3 0.9 (4) C6—C7—C8—C9 0.5 (4)

Cl1—C1—C2—C3 179.70 (19) N3—C7—C8—C9 177.2 (3)

N2—C2—C3—C4 179.8 (3) C7—C8—C9—C10 -0.7 (5)

C1—C2—C3—C4 -0.6 (4) C8—C9—C10—C11 0.5 (5)

C2—C3—C4—C5 -0.1 (4) C7—C6—C11—C10 -0.1 (4)

C1—N1—C5—C4 -0.4 (4) C12—C6—C11—C10 175.9 (3)

C3—C4—C5—N1 0.6 (4) C9—C10—C11—C6 -0.1 (5)

C11—C6—C7—C8 -0.1 (4) C11—C6—C12—O2 -125.2 (5)

C12—C6—C7—C8 -175.9 (3) C7—C6—C12—O2 50.5 (5)

C11—C6—C7—N3 -176.7 (3) C11—C6—C12—O1 53.0 (4)

44
 C12—C6—C7—N3 7.6 (4) C7—C6—C12—O1 -131.4 (3)

Hydrogen-bond geometry (Å, º) for (mo_g2no2_0m)

D—H···A D—H H···A D···A D—H···A

N2—H2N2···Cl1 0.86 (3) 2.60 (3) 2.978 (3) 108 (2)

N2—H2N2···O2i 0.86 (3) 2.13 (3) 2.920 (4) 152 (2)

N2—H1N2···O3ii 0.87 (3) 2.54 (3) 3.316 (6) 150 (3)

O1—H1O1···N1 0.83 (3) 1.82 (4) 2.642 (4) 170 (4)

C4—H4A···O4iii 0.93 2.55 3.404 (4) 153

Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y, -z+1; (iii) -x+2, -y, -z+1.

Document origin: publCIF [Westrip, S. P. (2010). J. Apply. Cryst., 43, 920-925].

45