software tools for the analysis of z’ > 1 structures a.l.spek, utrecht university, national...
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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
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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
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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
>
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(25 out of 466)
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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
>
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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’ > 1 structures in the CSD belong to that category
• Archival of the reflection data (Acta Style) in the CCDC strongly advocated.