Additional ways of determining absolute configuration.

[James Hester]

Dear Core DMG,

Please see the email below, which we/I have unfortunately left to languish
for more than a year.  In summary, the suggestion can be generalised into
the following:

Three new options are proposed for "_chemical.absolute_configuration",
which specifies how the absolute configuration was assigned to a structure.
The current options are:

         rm
;       'reference molecule' Absolute configuration established by
         the structure determination of a compound containing a
         chiral reference molecule of known absolute configuration.
;
         ad
;       'anomalous dispersion' Absolute configuration established by
         a-d effects in diffraction measurements on the crystal.
;
         rmad
;       'rm + ad' Absolute configuration established by the structure
         determination of a compound containing a chiral reference
         molecule of known absolute configuration and confirmed by
         a-d effects in diffraction measurements on the crystal.
;
         syn
;       'synthetic' Absolute configuration has not been established
         by anomalous-dispersion effects in diffraction measurements on
         the crystal. The enantiomer has been assigned by reference to
         an unchanging chiral centre in the synthetic procedure.
;
         unk
;       'unknown' No firm chemical or a-d evidence for an assignment
         is available. An arbitrary choice of enantiomer has been made.
;
         .         inapplicable

The new options would be:
==============
        synad
;
       'synthetic + ad'. Absolute configuration established by reference to
       an unchanging chiral centre in the synthetic procedure and confirmed
by
         a-d effects in diffraction measurements on the crystal.
;
       co
;
         Absolute configuration has not been established
         by anomalous-dispersion effects in diffraction measurements on
         the crystal. The enantiomer has been assigned by an optical
procedure.
;
       coad
;
       'optical + ad'. Absolute configuration assigned by optical procedure
and confirmed by
         a-d effects in diffraction measurements on the crystal.
;
===============

Please comment on these options. I see no issue with them, but I could
count on one hand the number of times I've attempted an a-d refinement, and
I could count on zero hands the number of times I've attempted an
independent measurement of chirality. For example, is option "co" just the
same as "rm" essentially?

all the best,
James.

On Thu, 30 May 2019 at 21:27, Brian McMahon <bm at iucr.org> wrote:

> 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
> >
> >
> >
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