StructureProperty Relationships in Crystal Structures of Polar Molecules

1
Structure-Property Relationships in Crystal
Structures of Polar Molecules
Graham Tizzard Supervisor Mike Hursthouse
2
Background

• No. of different attractive forces determine
  packing in molecular crystals
• London forces, multipolar forces, H- bonding, CT
  forces
• Complex interplay of these repulsion E ? many
  local minima in crystal lattice E
• ? Polymorphism - the existence of more than one
  crystalline form in a substance

3
Polymorphism H-bonding

• H-bonds
• Highest E interactions in molecular crystals ?
  most important attractive force
• Multiple H-bonding sites ? different H-bonding
  topologies ? polymorphism
• However
• Polymorphism also in systems w.out strong H-bonds
  (D H A D N, O, S A N, O, S, Hal)
• Weak H-bonds may exist (C H A, C H p)
• Importance of H-bonding in defining polymorphism
  greatly reduced

4
Aims

• Detailed study of weak or non H-bonding systems
• Especially those w. non-centrosymmetric
  polymorphs
• V. important for development of materials w. NLO
  properties
• Electrostatic interactions expected to exert
  greater influence on xtal structure

5
Dataset

• Constructed from Cambridge Structural Database1
  (CSD) v5.25 (November 2003)
• CSD mined for polymorphic clusters with one
  non-centrosymmetric member
• 835 hits made up of 258 polymorphic clusters
  each comprising of 2-3 different polymorphs

1 F. H. Allen, Acta Crystallogr., B58, 380-388,
2002..
6
Analyses

• XPac2
• Many polymorphic families of a compound show no
  similarity when analysed
• For those that do structure-forming motif may
  be able to be elucidated from results
• Short contact analysis (Mercury v1.2.13)
  modelling of electrostatic charges (Spartan04
  for windows4)
• Correlation between short contact distances
  matching of potentials would suggest these are
  important in a crystal structure

2 XPac T. Gelbrich 2002 University of
Southampton, UK. 3 Mercury v1.2.1 CCDC,
Cambridge, UK. 4 Spartan04 Wavefunction,
Inc. Irvine, CA, USA.
7
4-Bromo-trans-1,4-dihydro-4-tritylbiphenyl
(BAWSAT)
BAWSAT01
BAWSAT
CSD code
monoclinic
orthorhombic
Crystal System
Pc (7)
Pnam (62)
Space Group (No.)
9.011
13.012
a / Å
16.187
17.264
b / Å
8.463
10.431
c / Å
90
90
a / º
108.98
90
ß / º
90
90
? / º
1167.309
2343.211
Cell Volume / Å3
2
4
Z
1.0
0.5
Z
5
5
Reference

• 2 polymorphs identified from CSD BAWSAT
  BAWSAT01
• BAWSAT01 is non-centrosymmetric

5 A. K. Cheetham, M. C. Grossel, J. M. Newsam
J. Am. Chem. Soc. 103 5363 1981.
8
XPac Analysis of BAWSAT

• Views of BAWSAT along the c-axis (top) BAWSAT01
  between the a and c axes (bottom)
• XPac reveals 1d chain along these respective axes
  common to both crystal structures (green)
• In both structures the same chain motif is
  interspaced (in different ways) between the
  original (dark green)
• Is this a structure-forming motif?...

9
Short Contact Electrostatic Charge Analyses of
BAWSAT

• Each molecule in BAWSAT01 (top) BAWSAT (bottom)
  has short contacts w. 8 neighbours
• None of these is particularly strong
• ESC SC data correlation 4/10 wrt. BAWSAT01 0
  wrt. BAWSAT
• Suggests electrostatic interactions unimportant
  in crystal formation
• Other interactions e.g. simple space-filling may
  dictate these structures.

BAWSAT01
Length-VdW / Å
Length / Å
Electrostatic charge 2
Atom2
Electrostatic charge 1
Atom1
-0.086
2.314
0.136779
H24 1
0.130679
H8
-0.086
2.314
0.130679
H8 2
0.136779
H24
-0.08
2.97
-0.117756
Br1 3
0.097207
H3
-0.08
2.97
0.097207
H3 4
-0.117756
Br1
-0.058
2.342
0.120092
H19 5
0.104592
H13
-0.058
2.342
0.104592
H13 6
0.120092
H19
-0.056
2.844
-0.191035
C28 7
0.155091
H4
-0.056
2.844
0.155091
H4 8
-0.191035
C28
-0.041
2.359
0.155091
H4 8
0.136788
H22
-0.041
2.359
0.136788
H22 7
0.155091
H4
BAWSAT
Length-VdW / Å
Length / Å
Electrostatic charge 2
Atom2
Electrostatic charge 1
Atom1
-0.12
2.28
0.155091
H4 1
0.104592
H13
-0.12
2.28
0.104591
H18 2
0.155091
H4
-0.12
2.28
0.104592
H13 3
0.155091
H4
-0.12
2.28
0.155091
H4 4
0.104591
H18
-0.102
2.298
0.097216
H5 5
0.097207
H3
-0.102
2.298
0.097207
H3 6
0.097216
H5
-0.03
2.37
0.104591
H18 7
0.104592
H13
-0.03
2.37
0.104592
H13 8
0.104591
H18
-0.002
2.898
0.078511
C3 5
0.097216
H5
-0.002
2.898
0.097207
H3 5
0.078478
C5
-0.002
2.898
0.097216
H5 4
0.078511
C3
-0.002
2.898
0.078478
C5 4
0.097207
H3
10
2-(a-p-Bromophenyl-ß-nitroethyl)-cyclohexanone
(BPNECH)
BPNECH01
BPNECH
CSD code
orthorhombic
monoclinic
Crystal System
P212121 (19)
P21/c (14)
Space Group (No.)
5.539
5.630
a / Å
8.495
8.560
b / Å
30.777
30.570
c / Å
90
90
a / º
90
90.30
ß / º
90
90
? / º
1448.175
1473.234
Cell Volume / Å3
4
4
Z
1.0
1.0
Z
7
6
Reference

• 2 polymorphs identified from CSD BPNECH
  BPNECH01
• BPNECH01 is non-centrosymmetric

6 M. Calligaris, F. Giordano, L. Randaccio
Ric. Sci., Parte 1 36 1333 1966. 7 D.
Seebach, I. M. Lyapkalo, R. Dahinden Helv Chim
Acta 82 1829 1999.
11
XPac Analysis of BPNECH

• Views of BPNECH (top) and BPNECH01 (bottom) along
  the b-axis
• XPac reveals 2d sheet along these respective axes
  common to both crystal structures (green)
• In BPNECH both highlighted sheets (green dark
  green) are identical
• In BPNECH01 second sheet highlighted (red) is
  same sheet structure after a 21 screw operation

12
Short Contact Electrostatic Charge Analyses of
BPNECH
BPNECH01
Length-VdW
Length
Electrostatic charge 2
Atom2
Electrostatic charge 1
Atom1

• Each molecule in BPNECH01 (top) and BPNECH
  (bottom) has short contacts w. 8 / 9 neighbours
  respectively
• Short contacts are stronger on the whole than in
  BAWSAT BAWSAT01
• ESC SC data correlate in both polymorphs
• Suggests that electrostatic interactions may be
  significant in formation of both crystal systems

-0.222
2.498
0.166816
H13 1
-0.434661
O2
-0.222
2.498
-0.434661
O2 2
0.166816
H13
-0.212
2.508
-0.434661
O2 2
0.203696
H12
-0.212
2.508
0.203696
H12 1
-0.434661
O2
-0.124
2.596
0.130828
H1 3
-0.434661
O2
-0.124
2.596
-0.434661
O2 4
0.130828
H1
-0.084
2.636
0.106818
H7 5
-0.447545
O1
-0.084
2.636
-0.447545
O1 6
0.106818
H7
-0.063
2.987
-0.05641
Br1 7
0.093177
H5
-0.063
2.987
0.093177
H5 8
-0.05641
Br1
-0.059
2.661
0.12995
H2 1
-0.451598
O3
-0.059
2.661
-0.451598
O3 2
0.12995
H2
BPNECH
Length-VdW
Length
Electrostatic charge 2
Atom2
Electrostatic charge 1
Atom1
-0.326
2.394
-0.434661
O2 1
0.130828
H1
-0.326
2.394
0.130828
H1 2
-0.434661
O2
-0.27
2.45
0.1308283
H13 3
-0.434661
O2
-0.27
2.45
-0.434661
O2 4
0.1308283
H13
-0.224
2.496
-0.434661
O2 4
0.1308282
H12
-0.224
2.496
0.1308282
H12 3
-0.434661
O2
-0.145
2.575
-0.451598
O3 4
0.12995
H2
-0.145
2.575
0.12995
H2 3
-0.451598
O3
-0.096
2.624
-0.447545
O1 5
0.106818
H7
-0.096
2.624
0.106818
H7 6
-0.447545
O1
-0.057
3.313
-0.05641
Br1 7
-0.447545
O1
-0.057
3.313
-0.447545
O1 7
-0.05641
Br1
-0.048
2.672
-0.434661
O2 4
0.06238
H9
-0.048
2.672
0.06238
H9 3
-0.434661
O2
-0.029
2.691
0.062736
H3 8
-0.451598
O3
-0.029
2.691
-0.451598
O3 9
0.062736
H3
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Comments I

• Several points worth noting
• Overall analysis involves several techniques -
  hard to draw conclusions using them in isolation
• XPac analysis uses top-down approach - data
  derived from polymorph crystal structures
• Modelling of electrostatic charges is bottom-up
  approach - data derived from molecule
• One goal of Comb-e-Chem project - combine data
  from different analyses to derive novel data
  develop it into meaningful knowledge

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Comments II

• Major bottlenecks throughout project have been
  workflow related
• Data transfer from one application to another
• Driving applications to obtain the data
• Methods of automation investigated
• perl to write data-transfer scripts
• Spreadsheets to automate calculations
• Ultimate aim of providing complete analysis of
  electrostatic interactions of a molecule in
  context of its crystal packing as a single
  callable process

15
Acknowledgements

• Prof. Mike Hursthouse
• The Group Dr. Simon Coles, Dr. Mark Light, Dr.
  Peter Horton, Dr. Ann Bingham, Dr. Thomas
  Gelbrich, Dr. Stefan Christensen, Dr. Yang Li,
  Dr. David Hughes, Suzanna Ward
• EPSRC E-Science project (GR/R67729, Comb-e-Chem)