[Cod-bugs] Possibly incorrectly assigned atoms in supplement of Bao et al. (1998)

[Andrius Merkys]

Dear Sean,

many thanks for your detailed answer. I completely agree that for manual
analysis by specialists incorrectly modeled solvent molecules are of
little interest and/or cause no doubt about their possible geometry.
However, we have spotted this issue during automated study of the
geometry in the Crystallography Open Database, and since our software
does not distinguish solvent from other molecules in crystals, this
entry resulted in geometric outliers.

I will contact the corresponding author of the structure via his current
e-mail address in attempt to resolve the issue.

Thank you once more! Andrius Merkys


On 10/08/17 14:11, Sean Conway wrote:
>
> Dear Andrius
>
>  
>
> The following comments are from Anthony Linden:-
>
>  
>
> ============
>
> It is a solvent molecule. I agree that the bond lengths suggest the C/N
>
> might be swapped. But the ellipsoids also show the molecule is
>
> disordered and the disorder has not been modelled. The C ellipsoid is
>
> large and making it N will make things worse unless a disorder model is
>
> developed. We could just say it is apparently disordered and the
>
> identities of the atoms cannot easily be confirmed; making deductions on
>
> just the bond lengths without attempting to modelling the disorder is
>
> probably unproductuve. Although, in Mercury showing short contacts,
>
> there are contacts mostly just to the N for the correct solvent molecule
>
> (there are two), and mostly to the "wrong" C for the one we are worrying
>
> about, so that might support the misassignment.
>
>  
>
> I very much doubt that even if the atom assignment is incorrect that it
>
> has any influence on the geometry of the main molecule. Someone being
>
> really interested in C-H...N contacts for this structure would be the
>
> only real treason to be concerned about it, in my opinion.
>
>  
>
> But to answer Andrius's actual question: there is evidence of disorder
> for this molecule, based on ellipsoid shapes, so the geometry is
> likely to be approximate at best and/or erroneous. Certainly one
> should not interpret those bond lengths as being genuinely
> representative of bonding in MeCN, i.e. it is not something real. It
> is generally believed among practitioners that unusual geometry in any
> organic species is rare and such observations are usually because of
> inadequacies in models rather than real features.
>
> ============
>
>  
>
> I hope that the comments are of help and interest.
>
>  
>
> Best wishes from Chester.
>
> Sean Conway
>
>  
>
> Managing Editor (Acta Cryst. C)
>
> Email: sc at iucr.org
>
> http://journals.iucr.org/c
>
>  
>
> On Thursday, 10 August 2017 12:49:45 BST you wrote:
>
> > Dear Sean Conway,
>
> >
>
> > thank you for your quick reply! I am looking forward to hear the
> decision.
>
> >
>
> > Sincerely,
>
> > Andrius Merkys
>
> >
>
> > On 10/08/17 11:47, Sean Conway wrote:
>
> > > Dear Andrius
>
> > >
>
> > > Many thanks for your message.
>
> > >
>
> > > I will discuss this with the Main Editors of the journal and see
> what they
>
> > > think, i.e. whether a correction is needed or not.
>
> > >
>
> > > I'll get back to you soon with an explanation.
>
> > >
>
> > > Best wishes from Chester.
>
> > > Sean Conway
>
> > >
>
> > > Managing Editor (Acta Cryst. C)
>
> > > Email: sc at iucr.org
>
> > > http://journals.iucr.org/c
>
> > >
>
> > > On Wednesday, 9 August 2017 17:39:26 BST you wrote:
>
> > >> Dear authors,
>
> > >> dear editor,
>
> > >>
>
> > >> I have noticed unusual acetonitrile bond lengths C-C (1 angst.)
> and C-N
>
> > >> (1.45 angst.) in crystal structure in supplement of Bao et al., 1998
>
> > >> (http://scripts.iucr.org/cgi-bin/paper?S0108270198006465,
>
> > >> doi:10.1107/S0108270198006465,
>
> > >> http://www.crystallography.net/cod/2007795.html). To me it seems that
>
> > >> chemical types of N02 and C04 are swapped, resulting in unusually
> short
>
> > >> C-C single bond and long C-N triple bond. I would like to know
> whether
>
> > >> this could be a mistake or a true feature of this crystal structure.
>
> > >>
>
> > >> Yours faithfully,
>
> > >> Andrius Merkys
>
>  
>
>  
>

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania

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