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Re: Fwd: Suggesting CIF data item values

As a follow-up to this request, Timo made these additional points:
Dear Brian,
Thank you very much for your quick reply and the further consideration of this case by the respective working group.
Personally, I think that the crystallographer's decision to refine a chiral compound as a particular enantiomer should be described unequivocally within the .cif, especially when relevant parameters like Flack x and the corresponding esd's are not (near-)100 % reliable. One should also think about other methods to determine an absolute configuration, like chiroptical methods. Professor Rzepa (I have no connections to him) obviously suggested an attribute co for _chemical_absolute_configuration to describe that absolute configuration has been determined by chiro-optical procedures, as can be seen here:
Although I am all but an expert for chiro-optical methods, this sounds resonable to me. Or _chemical_absolute_configuration could be added with a property 'other' to allow for a detailed description of the configurational assignment within a subordinate _details data item. However, I am not aware of the intended relationships,  dependencies, and boundaries between _refine_ls_abs_structure_details and _chemical_absolute_configuration.
Best wishesTimo

On 28/05/2019 11:58, Brian McMahon wrote:> Dear Core CIF Group members> > I am forwarding a query I have received, and would be interested to hear> your thoughts on the proposal.> > Regards> Brian> > > -------- Forwarded Message --------> Subject:     Suggesting CIF data item values> Date:     Mon, 27 May 2019 08:39:54 +0200> From:     Timo Stein <timo.stein@chemie.uni-hamburg.de>> To:     bm@iucr.org> > > > Dear Mr. McMahon,> > > I'm writing you to kindly enquire about how to suggest new data values > that are associated with CIF data items. I found the form 'Suggest a new > CIF data item', but I'm not suggesting a new CIF data item, but only a > single property for _chemical_absolute_configuration. The values listed > within coreCIF 2.4.5 involve:> >    * rm - the absolute configuration was assigned on the basis of a>      reference molecule, e.g. a co-crystallized molecule of known>      absolute configuration>    * ad - the absolute configuration was established by anomalous > dispersion>    * rmad - rm + ad>    * syn - absolute configuration of the compound in question is based on>      the chiral information of its synthetical precursor and has not been>      altered>    * unk>    * .> > I suggest to add the property synad to emphasize that ad has been used > to assign a particular absolute configuration _and_ the absolute > configuration is known. As an example, one could think of a scXRD > experiment using Cu irradiation on a crystal comprised of an > /N/-functionalized L-amino acid in trigonal space group /P/32. While the > Flack parameter /x/ should show preference for /P/32 over the > enantiomorphic space group /P/31, its standard deviation might be too > high if a crystal of only mediocre quality containing elements with /Z/ > <= 8 is studied.> > However, if the chemist can ensure that the stereoinformation on > C(alpha) has not been altered during the process of synthesis, > purification, and crystallization of the /N/-functionalized L-amino > acid, _chemical_absolute_configuration synad would be the most > appropriate description on how the absolute configuration was assigned. > The absolute configuration 'was established by reference to an > unchanging chiral centre in the synthetic procedure' (from syn) and > 'confirmed by anomalous-dispersion effects in diffraction measurements > on the crystal' (from rmad).> > Thank you for consideration of this suggestion.> > > Yours sincerely> > Timo Stein> > > _______________________________________________coreDMG mailing listcoreDMG@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg

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