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Number 13 - February 2001

ICSD USER'S GROUP NEWSLETTER
(Inorganic Crystal Structure Database)

edited by

I.David Brown
Brockhouse Institute for Materials Research
McMaster University
Hamilton, Ontario, Canada L8S 4M1

Contents
  1. Spacegroup Assignment in the ICSD
  2. ICSD for WWW Update
Contact

Comments for the newsletter should be send to the editor:

idbrown@mcmaster.ca

1. Space group assignments in the Inorganic Crystal Structure Database.

The following email exchange may help to clarify some of the unexpected space group assignments that can be found in the ICSD.

On Fri, 12 May 2000, Michael O'Keeffe wrote:
I have been looking into the occurrence of certain space groups and find that there are VERY many errors. My guess is that MOST of the entries for the pure rotation classes are wrong (the structures reported actually have higher symmetry). Sometimes this is obvious, but sometimes less so. There should be some automatic way of checking the symmetry of each entry. The problem is not trivial as the data base is used to screen for certain symmetry properties such as absence of a center of symmetry. Example: look at F23. Most of the entries obviously have symmetry Fm-3m (NaCl or CaF2 structures). Note that BeO is in there too with the NaCl structure. Obviously wrong on two counts. All the entries for I432 are actually Im-3m. Etc., etc.

David Brown replied:
Thank you for your message which I am copying to Vicky Karen for information. She is the person at NIST who is preparing the new software for the ICSD and she should be kept informed of the kinds of problems people encounter.

The problem you raise about wrong space groups is probably encountered mostly in the cubic space groups and is the result of a policy we adopted early on of reporting the structure as the author reported it. At that point we did not want to risk putting more errors into the database by trying to correct an author's interpretation which we thought might be wrong. (We did try to correct obvious numerical errors). In the early days of crystallography is was customary to report the space group with the *minimum* symmetry necessary to describe the structure. Nowadays we look for the space group with the *maximum* symmetry. Thus early structure determinations of Fm-3m crystals are often reported in F23 because there was no way of knowing for sure that the center of symmetry was present. Another consequence of this policy is that wrong structures are also included in the ICSD (they may, after all, be correct structures obtained from a non-standard sample). Such structures should, however, have pointers to the correct determination (pointers should be included to all determinations of the same compound, but this is not trivial to do).

While I will defend the decision not to try to re-interpret the author's original description, there is certainly an argument (which increases as we get more effective database software) for introducing some standardisation. Bergerhoff has introduced his SICS (Standardised Inorganic Crystal Structures database) in which he has selected the best determination of each structure from the ICSD and has transformed it to a standard setting which allows him to look for similar structures. This is one possible way around the problem, but it does put the user one step away from the original report which may contain important information that might be lost in the standardisation. Another possibility is to introduce into the ICSD new records which contain the reinterpreted information. One could then ask the retrieval programs to use either the standardised records or the original records, but both would be available for inspection.

As you say, preparing the standardised form is not a trivial job, but a couple of dedicated people (Bergerhoff and his team, as well as Allmann as a retirement project) have worked through much of the database trying to clean it up. However, any clean up should leave a record of what has been done so that errors introduced during the editorial reinterpretation can be spotted.

Mike O'Keeffe responed:
Thanks for the quick and detailed response to my note. At the risk of exceeding your patience, may I have a few more words on the question of symmetry and the use of symmetry groups in the description of crystal structures.

Crystallography is in the enviable position of being able to rely on exact mathematical results for its underpinnings, and I think that all of us who care about the subject should treat these basics with respect. The point I raised was not whether NaCl might have symmetry F23 or P1 or no symmetry at all; after all (to be pedantic) we can only prove the absence of symmetry, not its presence. The question I raise is the different one of the symmetry of the REPORTED structure. To say that NaCl with a cubic cell and Z = 4 has symmetry F23 is indefensibly wrong and recognizably wrong (one needs at least one set of general positions for symmetry F23, i.e. Z >= 48). Yes I know that your comuter will generate the NaCl structure using F23 (mine will anyway) but surely that is not the whole point of using symmetry. Some other reasons for caring: (a) I have in front of me an analysis of the frequency of occurrence of space group symmetries in ICSD, clearly its interpretation is open to question. (b) Recently a list of all non-centrosymmetric oxides from ICSD was published. It is likewise greatly corrupted. (c) I am interested in discovering structures based on simple organising principles that are non-centrosymmetric (packings of equivalent cylinders is one), and also in finding if these are used in crystal structures (hence my recent interest in I432). (d) Of course many important physical effects such as second harmonic generation or piezoelectricity are related to (the absence of) symmetry. If software is being written to screen ICSD entries for errors of the sort I refer to, may I call attention to Table 14.2 of the International Tables which appears not to be well known, even to crystallographers. What is needed is a listing of the symmetries of all combinations of Wyckoff positions for all the space groups. ICSD could then report both the space group used by the author and the actual symmetry of the reported structure. I suggest the latter be used as the default for searches.


Michael O'Keeffe
Regents' Professor
Department of Chemistry
Arizona State University
Tempe AZ 85287
Tel: (1) (480) 9653670
Fax: (1) (480) 9652747
http://www.asu.edu/clas/chemistry/faculty/okeefe.htm

 

2. Update on ICSD-for-WWW

Message from Alan Hewat.
The latest 15 Jan 2001 version of ICSD-for-WWW contains several new features requested by users. The new features are described on: http://barns.ill.fr/dif/icsd/news.html and may be tried on the ILL's own server http://barns.ill.fr/dif/icsd/ In particular they include:

1) Acrobat PDF output of calculated and indexed powder patterns (as an alternative to postscript)

2) Chime/PDB 3D-display of structures (as an alternative to VRML)

3) Username/Password access (as an alternative to IP names) see:
http://barns.ill.fr/dif/icsd/icsd-password.html

4) Various minor bug fixes (with thanks to all for reports and suggestions)

The present ICSD-for-WWW database from FIZ-Karlsruhe contains 57,195 entries. If you run your own ICSD-for-WWW server, this version for SGI, Sun and HP servers is available from:
ftp://ftp.ill.fr/pub/dif/icsd/

 

 

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