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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

  • 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]


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Aim

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

 Polymorphs

 Same (redetermination / republication)

 Minor phase-transition / pseudo-symmetry

 Error


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Simulate Powder Patterns

In-house C++ library


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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.


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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.


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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?


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Polymorph

TINBIB

TINBIB01


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Error

ZOLRAT

ZOLRAT01

P21/a versus P21/n


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Grey Area

What if similarity 0.90 – 0.99?

 Polymorphs

 Same (redetermination / republication)

 Minor phase-transition / pseudo-symmetry

 Error

Sometimes difficult to decide.


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Polymorphs?

BONTON

BONTON02

Geometry of metal coordination different: polymorphs?


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

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)


Searching the csd for polymorphs and pseudo polymorphs jacco van de streek sam motherwell cambridge crystallographic

Acknowledgements

 René de Gelder, University of Nijmegen

 Editors at the CCDC

 All contributors to the CSD


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