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

>

>(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

>

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.