P sain ph-d presentation(12.06.2019)

"Crystal Engineering
by
Arene-polyfluorarene π-π stacking"
by
Prithwish Sain
(PhD Student)
18 October 2019
Supervisors: A.Prof. Graham Saunders (Chief Supervisor)
A.Prof. Joseph Lane (Co-Supervisor)

18 October 2019© THE UNIVERSITY OF WAIKATO • TE WHARE WANANGA O WAIKATO 2
Outline
• Introduction
• Background
• Research Questions
• Research Methods
• Work to Date
• Resources Required
• Thesis Outline
• Timeline
• Acknowledgements

Objectives
• To discover and examine new arene-
polyfluoroarene co-crystals with desired or latent
physicochemical properties, by exploiting π-π
stacking.
• To use the most economically viable and green
method for the production of co-crystals.
• To generate data for future uses.

The hierarchy of matter
Present research domain

Crystal engineering
•aims to control molecular solid-state structures with
desired physical properties, based on the
comprehension of intermolecular interactions.
•plans have mainly depended on hydrogen bonding,
coordination bonds, and other intermolecular forces
such as π-π stacking, halogen bonding and
hydrophobic interactions.
•wide-ranging applications in pharmaceuticals,
cosmetics, agrochemical, photoelectronics, and non-
linear optics.

The energy associated with
intermolecular interactions
Nature of interaction Strength(kJ mole-1) Examples
Covalent Bond 200–400 -O-H, -C-H, -N-H, H-Cl, etc.
Ion-Ion 100-350 Na+Cl-
Ion-Dipole 50-200 Na+Cl- in H2O
Hydrogen Bond 4-120 H2O- H2O interactions
Dipole-Dipole 5-50 Iδ+-Clδ- … Clδ-- Iδ+
Cation-π 5–80 Na+-Ph or metal ion-π-interactions
Anion- π intearction ~20-50 anion–π interactions in the active
site of urate oxidase
π- π Stacking <50 Ph ···Ph, PhF-Ph etc.
van der Waals <5 CH3···CH3, CH3···Ph
Heteroatom/Halogen 1-2 N ··· Cl, I···I, Br ··· Br
Hydrophobic effects Entropy

π-π interaction
•π-interactions (arene interactions) are
typically non-covalent interactions involving π-
delocalized electron systems.
•according to the electrostatic theory of
interaction, an electron rich system interacts
with an electron deficient system such as metal
ion, neutral molecule, anion, or another π-
system.

Preferential structural π–π arrangements
Ref: S. Tsuzuki, T. Uchimaru and M. Mikami, The Journal of Physical Chemistry A, 2006, 110, 2027-2033.
Probable π-π stacking geometric configurations in terms of skeletal formulae and corresponding quadrupoles

Substituent effects on the nature and
geometry of π-π interactions
dimer method R (Å) ∆Eint (kJ mol-1)
benzene-benzene MP2/aug-cc-pVTZ 3.70 -13.64
benzene-phenol MP2/aug-cc-pVTZ 3.60 -15.69
benzene-toluene MP2/aug-cc-pVTZ 3.65 -16.48
benzene-fluorobenzene MP2/aug-cc-pVTZ 3.70 -15.94
benzene-benzonitrile MP2/aug-cc-pVTZ
3.60 -20.33
Ref: M. O. Sinnokrot and C. D. Sherrill, The Journal of Physical Chemistry A, 2003, 107, 8377-8379.

Co-crystals
•single phase crystalline materials
prepared by mixing two or more
components in a stoichiometric ratio.
•in crystal engineering research, it
allow scientists to use various
intermolecular interactions (π-π) for
engineering new materials.
•structure & properties are different
to the starting materials.

Phase diagram of a binary mixture
(detection of co-crystal from m.p measurements)
Ref: G. P. Stahly, Crystal Growth & Design, 2009, 9, 4212-4229.

Powder X-ray diffraction (PXRD) patterns
of a co-crystal and its constituents
Experimental PXRD patterns (λ = 1.5405 Å) of (a) naphthalene, (b) octafluoronapthalene, (c) the
product of grinding a stoichiometric mixture of naphthalene and octafluoronapthalene, and (d) that
of calculated from the structure determined by single crystal X-ray diffraction (NPOFNP )
(Ref: G. C. Saunders and T. T. Wehr-Candler, Journal of Fluorine Chemistry, 2013, 153, 162-164.)

Research Questions
• how can π-π stacking be exploited to
produce arene-polyfluorarene co-crystalline
solids?
• how can π-π stacking be used to control the
crystal structure ?
• how can computational techniques be applied to
understand the intermolecular interactions
in the crystalline state?
• how can π-π stacking be capitalized to
produce a series of multi-component co-
crystals using crystal engineering principles?

Research Materials

Continued..

Research Methods
(preparation)
•solvent-based: solvent evaporation,
crystallization from solution or active co-crystallization
and anti-solvent addition, slurring.
•solid-based: co-grinding or mechanical mixing,
solvent-assisted grinding, sonication, melting.

Research Methods
(Characterization)
Four main methods are available for studying the
intermolecular interactions in molecular co-crystals:
•X-Ray Diffraction (PXRD and Single crystal
XRD).
•Spectroscopic methods (FT-IR, Raman)-
Optional
•Thermogravimetric analysis (TGA) and
Differential Scanning Calorimetry (DSC).
•Computational technique (e.g. wB97xD).

Work to date
S.N Compound’s Name
(chemical formula)
m.p (C) of
constituents
m.p (C) of Co-
crystals
Feasibility of
Co-crystal
formation
1. Decafluorobiphenyl (C12F10) 68-70 C12F10 - C10H8
49.8 - 50
Yes
Napthalene (C10H8) 78.2
liquid
No
Pentamethylbenzene (C11H16) 49-51
3. Decafluorobiphenyl (C12F10 ) 68-70 C12F10 - C10H14
38.6-39.6
May be
1,2,4,5-Tetramethylbenzene(C10H14) 78
4. Octafluoronapthalene(C10F8) 87-88 C10F8 - C10H8
133-133.3
Yes
Napthalene (C10H8), 78.2
5. Octafluoronapthalene (C10F8) 87-88 C10F8 - C12H18
183.2-183.7
Yes
Hexamethylbenzene (C12H18) 165
133.6-133.9
Yes
Pentamethylbenzene(C11H16) 49-51
86.4-86.7
Yes
1,2,4,5-Tetramethylbenzene(C10H14) 78
84.1-84.4
Yes
Phenanthrene (C14H10) 98-100

9. Pentafluoroaniline (C6H2F5N) 33-35 C6H2F5N - C12H18
79-163
May be
liquid
No
Pentamethylbenzene (C11H16) 49-51
Liquid
No
1,2,4,5-
Tetramethylbenzene(C10H14)
78
59.4-59.6
Yes
64.00(1), 126.8(2),
160.0(3)
May be
42.4(1), 43.8(2)
Yes
15. Tetrafluorophthalonitrile(C8F4N2) 81-86 C8F4N2 - C10H8
134.3, 136.8,
138.2
Yes
16. Tetrafluorophthalonitrile(C8F4N2) 81-86 C8F4N2 - C14H10
135.5-135.8
Yes
Continued…

PXRD patterns of a co-crystals of S.No. 6,7, and 8
2θo
2θo
2θo
Figure-A PS-2: PXRD patterns of Figure-B PS-3: PXRD patterns of Figure-C PS-1: PXRD patterns of
(a) perfluoronapthalene,
(b) pentamethylbenzene,
(c) 1:1 co-crystal of
perfluoronapthalene-
pentamethylbenzene.
(d) tetramethylbenzene,
(e)perfluoronapthalene,
(f) 1:1 co-crystal of
perfluoronapthalene-
tetramethylbenzene.
(g) perfluorobiphenyl,
(h) phenanthrene,
(i) 1:1 co-crystal of
perfluorobiphenyl-
phenanthrene.

T= 283-303 K T= 250 K T= 200 K
T= 150 K T= 100 K
Effect of temperature on co-crystal structure
( Low temperature study )
1:1 co-crystal of perfluoronaphthalene-naphthalene (C10F8-C10H8),
monoclinic, P 21/c, mw. 400.28, m.p. 133.0-133.3 oC

Experimental single crystal XRD data for
1:1 perfluoronaphthalene-naphthalene at various temperatures
CSD entry:
NPOFNP
Crystal249 Crystal250 Crystal251 Crystal252
Cell length ‘a’ Å 7.457 7.4226 7.3825 7.3492 7.3124
Cell length ‘b’ Å 8.503 8.4850 8.4651 8.4440 8.4324
Cell length ‘c’ Å 12.710 12.6258 12.5621 12.5125 12.4637
Cell angle ‘beta’ 99.48 99.102 98.888 98.694 98.529
Cell Volume 794.895 785.16 775.63 767.56 760.03
Cell formula Unit ‘Z’ 2 2 2 2 2
temperature (K) 283-303 250 200 150 100
Crystal density diffrn. 1.671 1.6929 1.7137 1.7318 1.7489
R-Factor (%) 6.5 6.39 4.62 4.37 4.45
% of cell length reduced with
reference to initial value (at
283-303 K )
a nil 0.21 0.45 0.69 0.83
b nil 0.47 1.00 1.50 1.94
c nil 0.66 1.16 1.56 1.93
Distance
between arenes
stacked in a
column (Å)
ArF-ArF planes 6.844 6.810 6.771 6.743 6.704
Ar-Ar planes 7.004 6.979 6.947 6.916 6.885
ArF-Ar planes 0.00 0.00 0.00 0.00 0.00
ArFcent.-ArFcent. 7.457 7.432 7.383 7.349 7.312
ArFcent.-ArFplane. 6.847 6.813 6.771 6.743 6.704
Arcent.-Arcent. 7.457 7.423 7.383 7.349 7.312
Arcent.-Arplane. 7.004 6.979 6.947 6.916 6.885
ArFcent-Arcent 3.729 3.711 3.691 3.675 3.656
ArFcent- Arplane 3.502 3.490 3.473 3.458 3.442
ArFPlane-Arcent 3.423 3.384 3.385 3.372 3.352
Angle (arenes in
a column)
ArF-ArF planes 0.00 0.00 0.00 0.00 0.00
Ar-Ar planes 0.00 0.00 0.00 0.00 0.00
ArF-Ar planes 3.69 3.89 4.13 4.08 4.30

2θo Shift with temperature
(Calculated PXRD patterns of 1:1 co-crystal of octafluoronapthalene-naphthalene at 5 different)
temperatures
2θo

Thesis outline
Chapter 1 Introduction and overview of the thesis
Chapter 2 Review of relevant literature on the Crystal
Engineering
Chapter 3 Various types of interactions
Chapter 4 Co-crystal
Chapter 5 Methods and Experimental technique
Chapter 6 XRD analysis of co-crystal
Chapter 7 FT-IR and Raman Spectroscopic analysis for newly
built π-π stacked arene-perfluoroarene co-crystals.
Chapter 8 Computational work
Chapter 9 General discussion, conclusion and future research
10 References
11 Appendices

Resource requirements
• Multiple Laboratories.
• General Laboratory equipment.
• Chemicals.
• Laboratory space.
• PXRD and XRD.
• FTIR and Raman Spectroscopy.
• DSC (differential scanning calorimetry).

Activity 1st Year(2019)
(2 months steps)
2nd Year(2020)
(2 months steps)
3rd Year(2021)
(2 months steps)
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
1 Understanding and developing
the research problem,
2
2 Various co-crystal preparation,
characterisation, full proposal and
presentation.
4 6
3 Co-Crystal preparation and
analysis
8 10 12
4
Characterisations
14 16
5 Developing theory and calculation
of various interaction energy
18 20
6 Rechecking the co-relating
among experimental results and
theoretical calculation.
22 24
7 Writing Thesis 26 28 30
8 Completing final draft of thesis
and submission.
32 34
9 Thesis Defence 36
PhD

Acknowledgements
• Saunders, A.Professor Graham (Chief Supervisor),
• Lane, A.Professor Joseph (Co-supervisor),
• Little, Mr. John (Lab Team Leader),
• Stockdill, Mrs Jenny (Technician),
• Turner, Mrs Helen (Technical Officer).
• PhD colleagues (Tom, Humair, Mohammad, Atiga, Sravan …)

The University of Waikato
Private Bag 3105
Hamilton, New Zealand
0800 WAIKATO
www.waikato.ac.nz
Thankyou

For example the melting point of a succinic acid (m.p. 135.3 oC) – urea (m.p. 188.9 oC) co-crystal is 149.9oC which is
different to the melting points of both components.
The pharmaceutical industry uses co-crystals for improving different properties, such as water solubility, dissolution rate,
melting point, chemical stability, and bioavailability of a drug without changing the chemical composition of the active
pharmaceutical ingredients (API). Other industries such as electronic, photographic, propellant, chemical processing,
paper, and textile industries (co-crystal of urea and sugar as a textile finishing agent) are also using co-crystals to process
their desired products for human use

Intermolecular interactions

Benzene Dimer
Coupled cluster single-double and perturbative triple (CCSD(T)):
4.68 kJ mole-1 for parallel face-face (sandwich),
8.45 kJ mole-1 for parallel displaced (offset)
9.08 kJ mole-1 for perpendicular T-shaped (edge to face)

C6H6• • • • C6F6 C6H6• • • • C6Cl6 C6H6• • • • C6Br6
-26.36 kJ mole-1
-36.82 kJ mole-1
-33.89 kJ mole-1
C6H6• • • • C6I6 C6H6• • • • C6(CN)6
Not available -46.024 kJ mole-1
The effect of polarized substituents on stabilization
energies of π-π stacked structure.

Coupled cluster single-double and perturbative triple (CCSD(T)):
Quantum chemistry composite methods
computational chemistry
Gaussian-1 (G1) introduced by John Pople, Gaussian-2, 3, 4 (Hartree–Fock energy), ------9
Gaussian basis sets (up through aug-cc-pV8Z, in some cases)
MP2/Aug-cc-PVTZbasis set in gaussian 03.
Density functional theory (DFT) is a computational quantum mechanical modelling
method used in physics, chemistry and materials science to investigate the electronic
structure (or nuclear structure) (principally the ground state) of many-body systems, in
particular atoms, molecules, and the condensed phases
Using this theory, the properties of a many-electron system can be determined
by using functionals, i.e. functions of another function, which in this case is the
spatially dependent electron density.
WB97XD falls in a new class of DFT functional known as range-separated
functional, which is capable of capturing both short-rangr and long-range
interactions. B3LYP can only capture short-range interactions because it has
problems with the incorrect 1/r behaviour when r is large (i.e. long range).

Thermogravimetric analysis or thermal gravimetric analysis (TGA) is a
method of thermal analysisin which the mass of a sample
is measured over time as the temperature changes. This measurement provides
information about physical phenomena, such as phase
transitions, absorption, adsorption and desorption; as well as chemical
phenomena including chemisorptions, thermal decomposition, and solid-gas
reactions (e.g., oxidation or reduction
Differential scanning calorimetry, or DSC is a thermoanalytical technique in
which the difference in the amount of heat required to increase
the temperature of a sample and reference is measured as a function of
temperature. Both the sample and reference are maintained at nearly the same
temperature throughout the experiment. Generally, the temperature program for
a DSC analysis is designed such that the sample holder temperature increases
linearly as a function of time. The reference sample should have a well-
defined heat capacity over the range of temperatures to be scanned.

Fourier-transform infrared spectroscopy (FTIR)[1] is a technique used to
obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An
FTIR spectrometer simultaneously collects high-spectral-resolution data over a
wide spectral range.
It relies on inelastic scattering, or Raman scattering, of monochromaticlight,
usually from a laser in the visible, near infrared, or near ultravioletrange. The
laser light interacts with molecular vibrations, phonons or other excitations in the
system, resulting in the energy of the laser photons being shifted up or down. The
shift in energy gives information about the vibrational modes in the
system. Infrared spectroscopy yields similar, but complementary, information.

New Crystalline Phase of (Octaethylporphinato)nickel(II). Effects of pi-pi
Interactions on Molecular Structure and Resonance Raman Spectra- 3920-3021 J. Am.
Chem. Soc., Vol. 110, No. 12, 1988. Theodore D. Brennan,1 W. Robert Scheidt,*1 and John A. Shelnutt*2
Effects of pi -pi Interactions on Molecular Structure and Resonance Raman
Spectra of Crystalline Copper(II) Octaethylporphyrin L. D. Sparks,1 W. Robert Scheldt,*’1 and J.
A. Shelnutt*i+, 2192 Inorganic Chemistry, Vol. 31, No. 11, 1992
IR:
Spectroscopic characterization of triple-decker lanthanide porphyrin sandwich complexes.
Effects of strong. pi.. pi. interactions in extended assemblies
JK Duchowski, DF Bocian - Journal of the American Chemical …, 1990 - ACS Publications

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