Software Tools for the Analysis of Z 1 Structures

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Software Tools for the Analysis of Z gt 1
Structures

• A.L.Spek, Utrecht University,
• National Single Crystal Service Facility
• The Netherlands.
• BCA-Meeting, York, April 2003

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Statistics Z gt 1 Structures in CSD

• CSD (Feb. 2003) Entries gt 275000
• Entries with Z gt 1 23711 (10)
• Entries with Z 2 20779
• (No disorder, No errors, No Polymer)
• Organometallic Z 2 6904
• Organic Z 2 9163

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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.

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

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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

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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 ?

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ADDSYM REPORT 2003/1
(25 out of 466)
gt

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

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IUCR CHECKCIF ALERTS
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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.

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ADDSYM REPORT 2003/1

gt

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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.

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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.

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QUATERNION FIT
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Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581
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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

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Concluding Remarks

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