Fwd: Suggesting CIF data item values

[Brian McMahon]

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 wishes
Timo


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 at chemie.uni-hamburg.de>
> To:     bm at 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
> 
> 
>