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Searching the CSD for Polymorphs and Pseudo-polymorphs Jacco van de Streek & Sam Motherwell Cambridge Crystallographic Data Centre, Cambridge, United Kingdom PowerPoint PPT Presentation


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Searching the CSD for Polymorphs and Pseudo-polymorphs Jacco van de Streek & Sam Motherwell Cambridge Crystallographic Data Centre, Cambridge, United Kingdom e -mail: [email protected] CSD.  CSD: Cambridge Structural Database

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Searching the CSD for Polymorphs and Pseudo-polymorphs Jacco van de Streek & Sam Motherwell Cambridge Crystallographic Data Centre, Cambridge, United Kingdom

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  • Searching

  • the

  • CSD

  • for

  • Polymorphs

  • and

  • Pseudo-polymorphs

  • Jacco van de Streek & Sam Motherwell

  • Cambridge Crystallographic Data Centre,

  • Cambridge, United Kingdom

  • e-mail: [email protected]


CSD

  •  CSD: Cambridge Structural Database

  •  3D Atomic coordinates of >300,000 small molecule crystal structures

  •  Sorted by chemical compound

  • Polymorphs are only flagged as such if explicitly indicated in the original publication, or when thought to be obvious

  • Redeterminations / republications of the same structure not flagged


Aim

Given two crystal structures of the same chemical compound, determine if they are:

 Polymorphs

 Same (redetermination / republication)

 Minor phase-transition / pseudo-symmetry

 Error


Comparing Two Crystal Structures

Problems with:

 Different space-group settings, e.g. P21/n and P21/c

 Choice of origin

 Unit-cell differences due to temperature / pressure

 Missed symmetry / pseudo-symmetry

Solution: use simulated powder diffraction patterns


Simulate Powder Patterns

In-house C++ library


Calculate Similarity

Point-by-point measures like R-values are extremely sensitive to peak shifts, e.g. due to temperature.

Therefore, use De Gelder’s measure, which is correctly normalised and less sensitive to peak shifts.

0.84

R. De Gelder, R. Wehrens & J.A. Hageman, J. Comp. Chem.22 (2001) 273-289.


Normalise Unit-Cell Parameters

 Unit-cell parameters determine peak positions

 a, b and c are adjusted to reproduce the “expected” unit-cell volume at 298 K from Hofmann’s average atomic volumes

 Angles kept constant  some discrepancy remains

High T

Low T

Room T

D. Hofmann, Acta Cryst. B58 (2002) 489-493.


High Similarity

If similarity >0.99, the two crystal structures are redeterminations / republications.

This information can be used to eliminate duplicates when doing statistical searches.

We would like to know which of these two crystal structures is “better”.

If at different temperatures / pressures: how do the unit-cell parameters vary as a function of temperature / pressure?


Low Similarity

If similarity <0.90, the two crystal structures are different:

 Polymorphs

 Error

Older literature: misprints & missing minus signs

Newer literature: copy and paste errors

P212121: several “standard” settings / confused with P21212

P21/c, P21/n & P21/a and Pbca & Pcab confusion

# errors small compared to # CSD entries, but large compared to # new polymorphs


Polymorph

TINBIB

TINBIB01


Error

ZOLRAT

ZOLRAT01

P21/a versus P21/n


Grey Area

What if similarity 0.90 – 0.99?

 Polymorphs

 Same (redetermination / republication)

 Minor phase-transition / pseudo-symmetry

 Error

Sometimes difficult to decide.


Polymorphs?

BONTON

BONTON02

Geometry of metal coordination different: polymorphs?


Results & Future work

 174 new pairs of polymorphs identified

 7,000 pairs of redeterminations identified

 Check 3,000 known pairs of polymorphs

 Generate list of unique crystal structures

 Are molecular conformations in polymorphs the same?

 Unit-cell parameters as a function of temperature / pressure

 Find pseudo-polymorphs (solvates)


Acknowledgements

 René de Gelder, University of Nijmegen

 Editors at the CCDC

 All contributors to the CSD


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