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Software Tools for the Analysis of Z’ > 1 Structures

Software Tools for the Analysis of Z’ > 1 Structures. A.L.Spek, Utrecht University, National Single Crystal Service Facility The Netherlands. BCA-Meeting, York, April 2003. Statistics Z’ > 1 Structures in CSD. # CSD (Feb. 2003) Entries > 275000

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Software Tools for the Analysis of Z’ > 1 Structures

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  1. Software Tools for the Analysis of Z’ > 1 Structures A.L.Spek, Utrecht University, National Single Crystal Service Facility The Netherlands. BCA-Meeting, York, April 2003

  2. Statistics Z’ > 1 Structures in CSD # CSD (Feb. 2003) Entries > 275000 # Entries with Z’ > 1 = 23711 (10%) # Entries with Z’ = 2 = 20779 (No disorder, No errors, No Polymer) # Organometallic Z’ = 2 = 6904 # Organic Z’ = 2 = 9163

  3. Z’ – Classification in CSD • Molecules have different conformations. • Molecules have the same conformation but related by symmetry incompatible with the lattice symmetry. • Molecules are related by pseudo-symmetry compatible with the space group symmetry. • Molecules are related by missed symmetry.

  4. We will look first for cases of missed and pseudo-symmetry using the PLATON software.

  5. PLATON/ADDSYM ANALYSIS • 9163 Z’ = 2 Organic Hits in CSD • ADDSYM  466 Hits (Missed or Pseudo Symmetry Cases) • Some Missed Symmetry Cases already corrected by Dick Marsh et al. • Recent Example of Missed Symmetry in J.A.C.S (2002) 124,11846-11847

  6. Interestingly .. • The paper reporting this structure does not offer any crystallographic information other than the statement: • The molecular structure of 6n is unambiguously clarified by X-ray analysis along with the helpful info: • See supporting Information for DETAILS. • So: Did the referee have a look at this ?

  7. ADDSYM REPORT 2003/1 (25 out of 466) > >

  8. J.A.C.S. 124 (2002) 9052 Communications

  9. And again ... • This two page JACS communication now includes an ORTEP for one of the two independent molecules and: • an acknowledgement to three professors and a PhD for the X-ray structure, discussions and computational assistance…. • A simple submission of the CIF to the Chester CHECKCIF server would have ...

  10. IUCR CHECKCIF ALERTS

  11. NEWSYM • Companion to ADDSYM Analysis • Structure factors calculated from current cell, symmetry and coordinate info. • Determination of the Space Group from the systematic absences in F(calc) • Extinctions in F(calc) may differ from those in F(obs) due to poor data.

  12. ADDSYM REPORT 2003/1 >

  13. Comment • Detailed analysis of near-symmetry is often hampered due to disorder, twinning or poor data • Likely candidates for phase transition upon temperature change • Reflection data needed for detailed analysis • Frequently, only part of the structure obeys the proposed higher symmetry.

  14. Real Z’ = 2 Examples • Molecules with significant conformational differences … • Cases where the local symmetry element relating two independent molecules is incompatible with the lattice symmetry.

  15. QUATERNION FIT

  16. Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581

  17. Observations • Crystallographically independent molecules are often related by pseudo translations in terms of their Center-of-Gravity • Crystallographically independent molecules are often related by pseudo inversion, screw axis or glide planes incompatible with the existing lattice

  18. Concluding Remarks • The PLATON software tools used is available from: http://www.cryst.chem.uu.nl/platon • Not all Z’ > 1 structures in the CSD belong to that category • Archival of the reflection data (Acta Style) in the CCDC strongly advocated.

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