structure-property relationships in crystal structures of polar molecules
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Structure-Property Relationships in Crystal Structures of Polar Molecules
Graham Tizzard
Supervisor: Mike Hursthouse
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
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 ∙∙∙ π) Importance of H-bonding in defining polymorphism
greatly reduced
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
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..
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 (Spartan’04 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] Spartan’04; Wavefunction, Inc.; Irvine, CA, USA.
4’-Bromo-trans-1,4-dihydro-4-tritylbiphenyl (BAWSAT)
2 polymorphs identified from CSD: BAWSAT & BAWSAT01
BAWSAT01 is non-centrosymmetric
[5][5]Reference
1.00.5Z’
24Z
1167.3092343.211Cell Volume / Å3
9090γ / º
108.9890β / º
9090α / º
8.46310.431c / Å
16.18717.264b / Å
9.01113.012a / Å
Pc (7)Pnam (62)Space Group (No.)
monoclinicorthorhombicCrystal System
BAWSAT01BAWSATCSD code
[5] A. K. Cheetham, M. C. Grossel, J. M. Newsam; J. Am. Chem. Soc.; 103; 5363; 1981.
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?...
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.
-0.0412.3590.136788H22 :70.155091H4
-0.0412.3590.155091H4 :80.136788H22
-0.0562.8440.155091H4 :8-0.191035C28
-0.0562.844-0.191035C28 :70.155091H4
-0.0582.3420.104592H13 :60.120092H19
-0.0582.3420.120092H19 :50.104592H13
-0.082.970.097207H3 :4-0.117756Br1
-0.082.97-0.117756Br1 :30.097207H3
-0.0862.3140.130679H8 :20.136779H24
-0.0862.3140.136779H24 :10.130679H8
Length-VdW / Å
Length / Å
Electrostatic charge 2
Atom2Electrostatic charge 1
Atom1
BAWSAT01
-0.0022.8980.078478C5 :40.097207H3
-0.0022.8980.097216H5 :40.078511C3
-0.0022.8980.097207H3 :50.078478C5
-0.0022.8980.078511C3 :50.097216H5
-0.032.370.104592H13 :80.104591H18
-0.032.370.104591H18 :70.104592H13
-0.1022.2980.097207H3 :60.097216H5
-0.1022.2980.097216H5 :50.097207H3
-0.122.280.155091H4 :40.104591H18
-0.122.280.104592H13 :30.155091H4
-0.122.280.104591H18 :20.155091H4
-0.122.280.155091H4 :10.104592H13
Length-VdW / Å
Length / Å
Electrostatic charge 2
Atom2Electrostatic charge 1
Atom1
BAWSAT
2-(α-p-Bromophenyl-β-nitroethyl)-cyclohexanone (BPNECH)
2 polymorphs identified from CSD: BPNECH & BPNECH01
BPNECH01 is non-centrosymmetric
[7][6]Reference
1.01.0Z’
44Z
1448.1751473.234Cell Volume / Å3
9090γ / º
9090.30β / º
9090α / º
30.77730.570c / Å
8.4958.560b / Å
5.5395.630a / Å
P212121 (19)P21/c (14)Space Group (No.)
orthorhombicmonoclinicCrystal System
BPNECH01BPNECHCSD code
[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.
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
Short Contact & Electrostatic Charge Analyses of BPNECH
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
-0.0592.661-0.451598O3 :20.12995H2
-0.0592.6610.12995H2 :1-0.451598O3
-0.0632.9870.093177H5 :8-0.05641Br1
-0.0632.987-0.05641Br1 :70.093177H5
-0.0842.636-0.447545O1 :60.106818H7
-0.0842.6360.106818H7 :5-0.447545O1
-0.1242.596-0.434661O2 :40.130828H1
-0.1242.5960.130828H1 :3-0.434661O2
-0.2122.5080.203696H12 :1-0.434661O2
-0.2122.508-0.434661O2 :20.203696H12
-0.2222.498-0.434661O2 :20.166816H13
-0.2222.4980.166816H13 :1-0.434661O2
Length-VdW
LengthElectrostatic charge 2
Atom2Electrostatic charge 1
Atom1
BPNECH01
-0.0292.691-0.451598O3 :90.062736H3
-0.0292.6910.062736H3 :8-0.451598O3
-0.0482.6720.06238H9 :3-0.434661O2
-0.0482.672-0.434661O2 :40.06238H9
-0.0573.313-0.447545O1 :7-0.05641Br1
-0.0573.313-0.05641Br1 :7-0.447545O1
-0.0962.6240.106818H7 :6-0.447545O1
-0.0962.624-0.447545O1 :50.106818H7
-0.1452.5750.12995H2 :3-0.451598O3
-0.1452.575-0.451598O3 :40.12995H2
-0.2242.4960.1308282H12 :3-0.434661O2
-0.2242.496-0.434661O2 :40.1308282H12
-0.272.45-0.434661O2 :40.1308283H13
-0.272.450.1308283H13 :3-0.434661O2
-0.3262.3940.130828H1 :2-0.434661O2
-0.3262.394-0.434661O2 :10.130828H1
Length-VdWLengthElectrostatic charge 2Atom2Electrostatic charge 1Atom1
BPNECH
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
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
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)
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