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Re: Fwd: Suggesting CIF data item values
- To: coredmg@iucr.org
- Subject: Re: Fwd: Suggesting CIF data item values
- From: Brian McMahon <bm@iucr.org>
- Date: Thu, 30 May 2019 12:27:15 +0100
- In-Reply-To: <95eee719-dc59-2cc8-19f2-81355bf2dcec@iucr.org>
- References: <bf819614-0861-e955-66e8-c95c486c5b16@chemie.uni-hamburg.de><95eee719-dc59-2cc8-19f2-81355bf2dcec@iucr.org>
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: http://www.ch.ic.ac.uk/rzepa/talks/vigo11/3.html 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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