Documenti di Didattica
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in
CHEMISTRY
by
AKSHAJ PREM
(13003)
DEPARTMENT OF CHEMISTRY
INDIAN INSTITUTE OF SCIENCE EDUCATION AND
RESEARCH BHOPAL
BHOPAL – 462 066
APRIL 2018
i
i
Indian Institute of Science Education and Research,
Bhopal
DEPARTMENT OF CHEMISTRY
CERTIFICATE
This is to certify that AKSHAJ PREM, BS-MS (Dual Degree) student in the Department of
April 2018
i
ACADEMIC INTEGRITY AND
COPYRIGHT DISCLAIMER
I hereby declare that this MS-Thesis is my own work and, to the best of my
and no substantial proportions of material which have been accepted for the award of any
other degree or diploma at IISER Bhopal or any other educational institution, except where
I certify that all copyrighted material incorporated into this document is in compliance
with the Indian Copyright (Amendment) Act (2012) and that I have received written
permission from the copyright owners for my use of their work, which is beyond the scope of
that law. I agree to indemnify and saveguard IISER Bhopal from any claims that may arise
April 2018
IISER Bhopal Akshaj Prem
ii
ACKNOWLEDGEMENT
First of all I like to express my sincere gratitude to my MS project supervisor Dr.
Chemistry Laboratory (CCCL) and for the support, encouragement and enthusiasm he has
shown. I would like to thank Mr. Rohit Bhowal for guiding me throughout my project and
also other lab mates Dr. Manjeet Singh, Ms. Peuli Ghosh, Mr.Subhrajyoti Bhandari, Mr.
Rahul Shukla, Mr. Pradip Kumar Mondal, Ms. Avantika Hasija, Ms. Gulshan Rani, Mr. Devi
Prasad A S, Mr. Athul Babu T, Mr. Ajay Kharbade and Ms. Shraddha Gedam for supporting
me. I would like to acknowledge IISER Bhopal and convey my regards to Department of
Suprakash Biswas and Dr. Apurba Lal Koner for the support in photophysical measurements.
I really appreciate their support. I am thankful to all my friends at IISER Bhopal for
supporting me and being with me throughout the journey five years at IISER Bhopal.
Finally, I would like to thank my family and friends for being with me always and supporting
me.
Akshaj Prem
iii
ABSTRACT
Co-crystals are gaining the extensive interest of researchers from various fields of chemical
drop grinding method with components in 1:1 stoichiometric ratio was used for co-
crystallization. Co-crystals were isolated as single crystals by slow evaporation method and
and infrared spectroscopy have been done to characterize the co-crystals .Charge transfer
stabilizing factors in the crystal packing are π···π stacking and hydrogen bonding interactions.
iv
LIST OF SYMBOLS OR
ABBREVIATIONS
SCXRD Single Crystal X-ray Diffraction
DNB 3,5-Dinitrobenzonitrile
TMB 3,3ʹ,5,5ʹ-Tetramethylbenzidine
λ Wavelength
v
LIST OF FIGURES AND TABLES
Title Page
grinding.
crystals.
pattern.
pattern.
pattern.
pattern.
Figure 14: Packing view of co-crystal 1 via N–H···O, N–H···N and C–H···O 17
vi
Figure 16: Packing diagram of co-crystal 2 showing interactions. 19
interactions.
interactions.
interactions.
Figure 23: Packing diagram of co-crystal 4 via C–H···O and N–H···O interactions. 25
Figure 24: Packing view of the crystal structure highlighting the zigzag molecular 25
chain.
vii
TABLE OF CONTENTS
i. Certificate
iii. Acknowledgement
iv. Abstract
v. List of Symbols
1. Introduction … 1-4
a) UV-Vis Spectroscopy
b) IR Spectroscopy
4. Conclusions … 28
5. References … 29-33
viii
ix
1. INTRODUCTION
Co-crystals
Co-crystals are crystalline single phase materials composed of two or more different
crystals,1,2,3,4,5 has been a topic of debate in the literature. As co-crystals have the opportunity
to access new solid forms and therefore modified physical properties they have high
relevance in both academic research and industrial applications. Co-crystallisation has shown
compressibility8 and physical stability.9 There are many different methods in which
crystallization can be done for a single component system including cooling, solvent
the melt, crystallization from gels,11 use of supercritical fluids,12 pressurisation13 and many
more.
1
The launch pad for systematic consideration of co-crystal design and prediction was Etter's
1990 publication14 investigating the predictability of hydrogen bonds which, based on the
evidence of known crystal structures, also set forth a list of empirical hydrogen-bonding rules
for neutral, organic compounds. In this study, Etter proposed three general rules for organic
compounds:
1. All good proton donors and acceptors are used in hydrogen bonding.
hydrogen bonds.
3. The best proton donors and acceptors remaining after intramolecular hydrogen bond
Inherent to these rules is the principle that one can determine not only which donors and
acceptors are ‘good’ (for rule 1), but also those that are the ‘best’ (for rule 3). Building on
these empirical hydrogen-bonding rules, Desiraju introduced another concept in 199515 that is
“Supramolecular synthons are structural units within supermolecules which can be formed
interactions.”
The principle put forth in this study is that a supramolecular synthon must be “robust enough
evidence that the structural unit is reproducible across multiple solid state environments. An
motif in question is then shown to be robust and reproducible then it could be referred to as a
synthon. If these supramolecular synthons are genuinely reproducible, then they could be
2
Subsequent researchers in the field of crystal engineering such as Aakeröy3,16 and
knowledge-based workflow through which the relative quality of particular donors, acceptors
and synthons can be assessed quantitatively. This can then be used to predict how robust a
A co-crystal strategy can realize the introduction of diverse neutral molecules19,20 and
study of various non covalent interactions, such as hydrogen bonds, C−H···π, π···π,
3
During the structural optimization process23, parameters such as 1) strength of the
electron- donor and -acceptor groups, 2) the coplanarity of conjugated systems, and 3)
components.26
Method called “Solvent drop grinding”27 is used for co-crystallization of selected starting
materials. Electron rich and electron deficient aromatic rings are taken as starting materials to
design Strong interactions and charge transfer phenomena .The outcome of co-crystals
was confirmed by powder X-ray diffraction analysis (PXRD), and structurally characterized
4
2. MATERIALS AND METHODS
2.1. Chemicals and materials: 4-Nitro-1,8-naphthalic anhydride was obtained from Sigma-
Aldrich Co. and 3,5-Dinitrobenzonitrile which obtained from TCI Chemicals (India) Pvt. Ltd.
3,3’,5,5’-Tetramethylbenzidine were purchased from TCI Chemicals (India) Pvt. Ltd. and
were used as donors for co-crystal synthesis. All these chemicals have been used as received
without further purification. Various HPLC grade solvents of different polarity were used for
without further purification. The crystals obtained were then characterized structurally using
SCXRD.
4-Nitro-1,8-naphthalic 1,3,5-Tris(4-aminophenyl)benzene
5
2
(DNB) (TPB)
3,5-Dinitrobenzonitrile 3,3ʹ,5,5ʹ-Tetramethylbenzidine
Co-crystal 4
(DNB) (TMB)
A method known as solvent-drop grinding (SDG) was used for co-crystal synthesis by
mechanical grinding of components using mortar and pestle. The two components of co-
crystals were taken in a 1:1 stoichiometric ratio for grinding. Methanol was used as a solvent
for grinding. Grinding was usually carried out for 75 minutes with dropwise addition of
solvent at an interval of 15 minutes each. The resulting powder was air dried and crystallized
6
using various solvents in 5ml beakers and 5ml vials and then kept for crystallization at low
temperature (4˚C).28 These crystals obtained were then characterized structurally using
SCXRD. Following these experiments, the observed stoichiometric ratio, as obtained via
SCXRD, was used to reproduce the formation of all of the as-synthesized (bulk) co-crystals
and was used for all of the further experiments. Furthermore, the PXRD patterns obtained for
all of the powdered samples along with the PXRD patterns collected on the obtained single
aminophenyl) benzene taken in 1:1 molar ratio was mechanically grounded using
mortar and pestle with drop-wise addition of methanol. The resulting mixture was
temperature (4˚C).
tetramethylbenzidine taken in 1:1 molar ratio was mechanically ground using mortar
and pestle with drop-wise addition of methanol. The resulting mixture was dissolved
(4˚C).
benzene taken in 1:1 molar ratio was mechanically ground using mortar and pestle
taken in 1:1 molar ratio was mechanically ground using mortar and pestle with drop-
7
TAPB+NNA
TMB+NNA
TAPB+DNB
TMB+DNB
8
2.3. Characterization Studies
Single crystals of co-crystal 1, co-crystal 2, co-crystal 3 and co-crystal 4 suitable for X-Ray
single crystal analysis were obtained by slow evaporation method at low temperature, by
using solvent dichloromethane. Single Crystal X-ray Diffraction data were collected on
Bruker AXS Kappa APEXII diffractometer using MoKα radiation (λ= 0.71073 Å) and
APEX2 software.29 Data integration and reduction were carried out with SAINT.30 Both
Both the crystal structures were solved by direct methods using SIR 2014.32 The crystal
structure refinement was done in the program package WinGX33 and all non-hydrogen atoms
were refined anisotropically by full matrix least squares calculations based on F2 with
SHELXL–2016.34All of the hydrogen atoms have been located from the difference Fourier
map. Details of crystal data, data collection and refinement details are provided in the
following Table. The PLATON35 and MERCURY36 programs were used for structure
9
Z´, Z 2, 8 2, 8 3, 8 2, 8
a( Å ) 15.0020(5) 10.9617(5) 28.799(6) 31.2029(11)
b( Å ) 7.5587(2) 15.6825(8) 7.2045(13) 6.8944(3)
c( Å ) 25.1734(8) 13.4532(7) 28.780(5) 19.5728(8)
α ) 90 90 90 90
β ) 101.094(2) 99.498(2) 119.657(5) 99.506(2)
γ ) 90 90 90 90
Volume (Å-3) 2801.21(15) 2281.0(2) 5189.1(17) 4152.8(3)
Density (g cm-3) 1.408 1.408 1.430 1.387
F 000), μ mm-1) 1236, 0.096 1016, 0.098 2320, 0.100 1824, 0.098
θ min, max) 1.938, 25.087 1.884, 27.877 3.561, 28.926 2.110, 30.344
hmin,max, kmin,max, (-17,17), (-9,9), (-14,13), (-18,20), (-22,37), (-9,9), (-44,44), (-9,9),
lmin,max (-29,30) (-17,17) (-38,32) (-27,27)
Treatment of Located Located Located Located
Hydrogen
No. unique 4933, 3424 5437, 2409 6436, 2819 6174, 4369
ref/obs. Ref.
No of Parameter 489 400 439 358
R_all, R_obs 0.0903, 0.0605 0.1966, 0.0838 0.2112,0.0970 0.0866, 0.0564
wR2_all, 0.1723, 0.1540 0.2289, 0.1755 0.2635,0.2031 0.1582, 0.1400
wR2_obs
Δρmin,max(eÅ-3) -0.367, 0.606 -0.390, 0.285 -0.414 , 0.331 -0.354, 0.445
G.o.F 1.054 0.978 0.985 1.030
Perkin-Elmer DSC 6000 Instrument under nitrogen gas atmosphere was used for the DSC
experiment. Precisely weighed sample of each co-crystal were placed in non-hermetic sealed
aluminum pans and then allowed to scan with respect to an aluminum pan containing
vacuum.
10
All of the samples were scanned at a rate of 5˚C/min in different ranges of temperature under
powder of each sample was placed on a silica sample holder and measured by a continuous
scan between 5 to 55º in 2θ with a step size of 0.013103º. Simulated powder X-ray
diffraction patterns of all co-crystals were obtained by Mercury 3.6 software package [10].
11
Figure 6:Experimental PXRD pattern of co-crystal 1 with simulated PXRD pattern.
12
Figure 8:Experimental PXRD pattern of co-crystal 3 with simulated PXRD pattern.
13
2.3.4. Spectroscopic Studies
14
(b) Infrared Spectroscopy (IR)
The dry powder was mixed and pelletized with KBr for recording IR. The IR spectra
were obtained on PerkinElmer Spectrum BX FT-IR spectrometer operated via Spectrum
v5.3.1 software.
15
3. RESULTS AND DISCUSSION
All co-crystals were synthesized using potential electron rich and electron acceptor molecules
as components. Solvent drop grinding (SDG) method in which each of the constituents were
taken in a 1:1 ratio and crystallized using various solvents of different polarity to obtain novel
co-crystals. Four co-crystals were synthesized and characterized by single crystal X-ray
diffraction studies.
Co-crystal 1
TAPB : NNA crystallizes in the monoclinic crystal system with the centrosymmetric space
group P21/c. The asymmetric unit consists of one of TAPB and one NNA molecule and the
16
Figure 13: Packing diagram of co-crystal 1 showing interactions.
NNA is an electron deficient (acceptor) and TAPB is an electron rich (donor) molecule and
Figure 14: Packing view of co-crystal 1 via N–H···N, N–H···O and C–H···O interactions
along the b axis.
17
TAPB is a propeller shaped molecule with dihedral angles of 14˚, 34˚ and 38˚ between the
central and peripheral aryl rings. The two adjacent donor molecules in the crystal lattice are
connected via N–H···N interactions while the donor and acceptor molecules are connected
via strong N–H···O and weak C(sp2)–H···O interactions when the crystal packing is viewed
18
Co-crystal 2
TMB : NNA crystallizes in the monoclinic crystal system with centrosymmetric space group
P21/c. The asymmetric unit consists of one TMB and one NNA molecule and there are a total
19
In this co-crystal TMB is electron rich molecule (donor) while NNA is electron deficient
molecule (acceptor) and the principal driving force for packing the two molecules in the
Figure 17: Packing diagram of co-crystal 2 showing N–H···O and C–H···O interactions.
also present in the crystal lattice. The donor and acceptor molecules in adjacent stacking
columns are connected via strong and directional N–H···O interactions when viewed down
the ab plane while weak C(sp3)–H···O interactions connects the donor and acceptor
molecules from adjacent stacked columns as well as between molecules of the same column
20
Table 4: Interaction table of co-crystal 2
Co-crystal 2
C10(π)···C27(π) x,1/2-y,-1/2+z 3.329
Co-crystal 3
21
TAPB:DNB crystallizes in the monoclinic crystal system with centrosymmetric space group
C2/c. There is one TAPB, one DNB and one water molecule in the asymmetric unit and there
In this co-crystal TAPB is an electron rich molecule (donor) while DNB is an electron
deficient molecule (acceptor). The principal driving force for packing the two molecules in
the crystal lattice is π···π stacking interactions between the donor and acceptor molecules.
Figure 20: Packing diagram of co-crystal 3 showing C–H···O and N–H···O interactions.
22
TAPB is a propeller shaped molecule with dihedral angles of 5˚, 14˚ and 24˚ between the
central and peripheral aryl rings. Apart from the π···π stacking interactions, there are exists
additional non-covalent contacts between the two components and guest water molecules
present in the crystal lattice. The two adjacent donor molecules are connected through the
guest water molecule via strong N–H···O interactions, while the neighbouring donor and
acceptor molecules are connected via strong N–H···O and weak C(sp2)–H···O interactions
23
N2–H2A···O5 1/2-x,1/2+y,1/2-z 3.048 2.245 152
N1–H1A···O5 1-x,1-y,1-z 2.959 2.597 103
N3–H3B···O5 1/2-x,1.5-y,1-z 3.111 2.299 153
Co-crystal 4
TMB:DNB crystallizes in the monoclinic crystal system with centrosymmetric space group
C2/c. There is one TMB and one DNB molecule in the asymmetric unit and there are a total
interactions.
24
Here DNB is electron deficient (acceptor) due to the presence of two nitro groups and one
cyano group and TMB is electron rich (donor) due to the presence of amine and methyl
groups. The two molecular components are stacked over each other through π···π stacking
and N···π interactions which are perpendicular to the molecular planes of both the molecules
Figure 23: Packing diagram of co-crystal 4 via C–H···O and N–H···O interactions down the
ac plane.
The adjacent donor and acceptor molecules of this co-crystal are connected to each other via
strong N–H···O and weak C(sp2/sp3)–H···O interactions in the crystal lattice. Here the donor
and acceptor molecules together are layered over alternate molecules along the b axis in a
zigzag like pattern forming an infinite molecular chain. TMB and DNB molecules along the
chain are connected to each other via strong N–H···O and weaker C(sp2)–H···O interactions
while the adjacent molecular chains are held together via weak C(sp3)–H···O interactions.
Figure 24: Packing view of the crystal structure highlighting the zigzag molecular chain
25
Figure 25: Packing motifs of co-crystal 4 via C–H···N interactions involving the amino
There also exists the presence of weak C(sp2)–H···N(sp3) interactions between the amine
group of the donor and the aromatic proton of the acceptor molecules while there are weak
C(sp2)–H···N(sp) between the cyano group and aromatic proton of acceptor molecules.
26
N3···C1(π) x,y,z 3.089
Furthermore, the PXRD patterns obtained for all of the powdered samples along with the
PXRD patterns collected on the obtained single crystals are in complete agreement with
each other. Homogeneity and phase purity of samples can be established by PXRD patterns.
Thermal stabilities of the bulk materials have been investigated by DSC. These are based on
principle of change in heat (either in terms of endothermic or exothermic process) with the
TAPB 165
Co-crystal 1 173.00
27
NNA 226-229
TMB 168-171
Co-crystal 2 148.93
DNB 126-130
TABP 165
Co-crystal 3 191.43
DNB 126-130
TMB 168-171
Co-crystal 4 188.71
The thermal stability of the co-crystals were assessed by differential scanning calorimetry
(DSC) and then compared with the starting materials. It was observed that although the
thermal stability of co-crystal 1 is slightly greater than TAPB but it is considerably much
lesser than NNA, while co-crystal 2 is thermally much less stable than either of the starting
materials. But co-crystal 3 and co-crystal 4 shows sharp endothermic peaks at higher
temperature than both the starting materials indicating greater thermal stability than both the
components.
In the UV-Visible specta there is a significant red shift observed in co-crystals as compared
to the starting materials. The absorption maxima of co-crystals occur in a range of 500-
700nm except for co-crystal 2. In the case of co-crystal 1 an absorption peak is observed at
657 nm, which is significantly red shifted from the absorption peaks of both the starting
materials (408 nm-TAPB, 396-NNA). Whereas in co-crystal 2, the absorption peak (460nm),
is slightly shifted in comparison to the starting materials, which shows absorption maxima at
412 nm (TMB) and 396nm (NNA) respectively. Co-crystal 3 has an absorption peak at 535
nm which shows a major shift as compared to its starting materials (407 nm-TAPB, 382 nm-
DNB). Co-crystal 4 has a very large shift in the absorption maxima as compared to both the
28
starting materials. Co-crystal 4 shows absorption peak at 638nm and starting materials have
absorption maxima at 412 nm (TMB) and 382nm (DNB). This suggests the existence of
charge transfer, the mechanism for this process forms the future course of study.
In infrared spectroscopy characteristic peaks of C=O and N-O of NNA was observed at 1750
cm-1 and 1530 cm-1 respectively and for TAPB a characteristic peak of N-H was observed at
3347 cm-1. In the case of the co-crystal 1, a red shifted peak for N-O (1516 cm-1) was found
as compared to the starting material (NNA). For co-crystal 2, it showed a red shifted peak for
N-H at 3358 cm-1 as compared to TMB which has a characteristic peak at 3379 cm-1. DNB
which is one of the staring materials of co-crystal 3, shows characteristic peaks of C≡N and
N-O at 2249 cm-1 and 1555 cm-1 respectively. As compared with the stretching frequencies of
DNB, co-crystal 3 shows a red shift for C≡N (2240 cm-1). In the case of co-crystal 4, it shows
red shifts for C≡N (2234 cm-1) and N-O (1542 cm-1). These shifts can be due to the presence
29
4. CONCLUSIONS
In summary we have developed several mixed Charge Transfer solid state materials each
based on two components system and displays mechanochromism upon mechanical grinding
recognition between donor and acceptor molecules results in adjusting the stacking modes of
the donor molecules upon introduction of the acceptor. Because of the unique mixed stacking
of D··A··D··A··D in the crystalline state, the charge transfer state has been achieved;
therefore such a packing arrangement is beneficial for the development of efficient solid state
materials for next-generation luminescent materials. The future work will be focussed on
present in the reported co-crystals. Beside this, we will also check these co-crystals for
Author Contributions
Akshaj Prem performed the co-crystal synthesis, IR measurements and crystal structure
refinement by himself. Mr. Rohit Bhowal (PhD Research scholar, CCCL) did the single
crystal data collection, and gave initial guidance to Akshaj Prem about crystallization
procedures. Akshaj Prem carried out solid state UV-visible spectra measurements under the
guidance of Suprakash Biswas (PhD Research Scholar, Dr. Apurba Lal Koner Lab). Mr.
Manoj Kumar Tripathi (operator, CIF, IISER Bhopal) recorded the PXRD measurements.
Mr. Manoj Kumar Rout (operator, CIF, IISER Bhopal) recorded the DSC data. All the
ORTEPs, packing diagrams and graphs were drawn by Akshaj Prem using Mercury 3.10 and
Origin 8 softwares respectively. Akshaj Prem wrote the report with inputs from Dr. Deepak
Chopra.
30
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