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Re: Final draft of Phase-ID report



Dear David,
I have read and approve the final draft of the Phase-ID report.

I am sorry I have nothing extra to contribute, as my interest is
in organic molecules in the CSD, and have no direct experience of the
complications in high symmetry inorganic compounds.  The only comments I
can make are from the practical viewpoint of uniquely identifying a
polymorph of a given compound in the CSD.

1. The IUPAC chemical identifier

I presume this can be constructed by algorithm from the CSD connectivity
table. This is not a trivial task, and I see in the report
that the IChI string ignores bonds to metals. About 50% of the CSD 
consists organometallic complexes, which give us at CCDC plenty of 
trouble in assigning a
chemical diagram, i.e. our topology description. Much of the ambiguity
depends on the exact nature of the bonding of ligand atoms to the 
metals. Another worrying matter for organic structures is the
placing of H atoms in the topology, this is sometimes  ambiguous in
organometallic complexes, but usually quite precise in CSD descriptions 
for organic salts, and tautomeric forms.

So I imagine in the CSD there will be many compounds with
same sum-formula, same IChI, same space group, and I think then the
discriminating layer must be the reduced cell parameters.



2. Space groups related as chiral pairs

A quick look in the CSD shows 330 entries with setting P41. Of these
there were 18 flagged as having a stereoisomer present in CSD, and
often these are a different space group. However there are 28/330
which are flagged 'absolute configuration', and in some way it would be
best to indicate that this has been determined and the space group
really is P41, not P43 e.g.. AFUTIE, AFUTOK.

There are only about 3000 compounds in the CSD which are present in
two or more polymorphic forms. Very often they are in different space 
groups, but not always, for example indigo (INDIGO, INGIGO02) both 
P21/c, Z=2, can only be distinguished on reduced cell parameters.

3. The Wyckoff sequence

I think this will rarely  be a useful field for
identification of organic crystals.


Yours sincerely,
Sam Motherwell



David Brown wrote:
> ?Dear Colleagues
> 
> Please find attached the final draft of the report of the
> Working Group on Crystallographic Phase Identifiers. It differs
> from the previous draft (#2) only in a few minor editorial
> aspects.
> 
> The next stage is to submit this report to the IUCr
> Commission of Crystallographic Nomenclature who may refer some
> parts back for further consideration or may approve the report as
> it is. When approved by the Commission, it will be posted on the
> web and published in Acta Cryst. over the names of the members of
> the Working Group, namely:
> 
> David Brown (chair)
> *Sidney Abrahams (chair of CCN ex officio at time the
> working group was established)
> +Michael Berndt (Crystal Impact)
> *John Faber (International Center for Diffraction Data)
> *Vicky Karen (National Institute for Science and Technology
> and the Inorganic Crystal Structure Database)
> *Sam Motherwell (Cambridge Crystallographic Data Centre)
> *Jean-Claude Toledano (Chair, CCN working group on Phase
> Transition Nomenclature)
> Pierre Villars (Pauling File)
> *John Westbrook (Protein Databank)
> *Brian McMahon (IUCr, consultant)
> 
> I need therefore to hear from every one of you who has an
> asterisk (*) by his or her name above that you approve the
> report. Please reply to this email or send your reply to phase-
> identifiers@iucr.org. When you send in your approval (or your
> reservations) please keep in mind that you were selected for this
> Working Group because of your membership in the organizations
> listed after your name. Your approval will indicate that, as far
> as you can tell, your organization would be able to implement the
> phase identifier if it wished. I cannot submit the report until I have 
> heard
> from every one of you and until I get your approval I will
> continue to send reminders. YOUR NAME WILL APPEAR ON THE FINAL REPORT.
> 
>

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