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

# 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

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.

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

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

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 ?

ADDSYM REPORT 2003/1

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(25 out of 466)

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

Communications

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 ...

IUCR CHECKCIF ALERTS

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.

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.

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.

QUATERNION FIT

Cg1 0.946 0.234 0.592

Cg2 0.441 0.253 0.581

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

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.