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Re: _chemical_formula[]



Peter Murray-Rust wrote:

> I would be grateful for clarification on the intended and actual use 
> of the _chemical_formula[] Core dictionary items. The dictionary entry 
> includes
> ----------------------
> Definition
>
>    _chemical_formula_ items specify the composition and chemical
>   properties of the compound. The formula data items must agree
>   with those that specify the density, unit-cell and Z values.
>
>
>     _chemical_formula_iupac      '[Mo (C O)4 (C18 H33 P)2]'
>     _chemical_formula_moiety     'C40 H66 Mo O4 P2'
>     _chemical_formula_structural '((C O)4 (P (C6 H11)3)2)Mo'
>     _chemical_formula_sum         'C40 H66 Mo O4 P2'
>     _chemical_formula_weight      768.81
>
> ----------------------
>
> There are at least two different ways of creating such data items:
> - transcription from a chemical logbook or paper where the formula 
> represents the known chemical constitution. This can be derived from 
> knowledge of preparation, analytical measurements, spectra etc.
> - summation of the scattering matter determined by the diffraction 
> experiment.
>
> In many cases these will not agree. This can be due to disorder, 
> unobserved atoms (e.g. H), etc. 

The fact that these formulae should agree with the crystal structure 
suggests that they are determined primarily from the crystal structure.  
Disordered atoms should be included in the atom_site loop together with 
any unobserved atoms (given as dummy atoms).  The correspondence between 
the formula and the cell contents is one of the consistency checks 
performed on papers submitted to Acta Cryst. etc.

> It is important to be able to state the composition of the sample 
> independently of the diffraction experiment. (Indeed if the structure 
> is not solved this is probably all that can be stated!) Such 
> compositions are extremely valuable in publishing crystallography to 
> the chemical community and in internal checks of the CIF. However I 
> gather that some software generates _chemical_formula fields directly 
> from the _atom_site and _symmetry information. 

There is already an item _chemical_formula_analytical where this 
information should be given.  This item corresponds to Peter's 
_chemical_formula_sum_meas below.

>
>
> I think it would be useful to have fields such as:
>     _chemical_formula_iupac_meas
>     _chemical_formula_moiety_meas
>     _chemical_formula_structural_meas
>     _chemical_formula_sum_meas
>     _chemical_formula_weight _meas
>
>     _chemical_formula_iupac_calc
>     _chemical_formula_moiety_calc
>     _chemical_formula_structural_calc
>     _chemical_formula_sum_calc
>     _chemical_formula_weight _calc
>
> This would indicate that the first had been experimentally measured by 
> some means other than diffraction and the second would show that they 
> had been calculated fro the _atom_site + _symmetry information. The 
> current
>     _chemical_formula_iupac
>     _chemical_formula_moiety
>     _chemical_formula_structural
>     _chemical_formula_sum
>     _chemical_formula_weight
> would give no information about the provenance of this information. 

I don't see that there is a need for all of these items.  _*_moiety and 
_*_structural are intended to provide a chemical view of the formula and 
while these two items can be parsed if necessary, there will be better 
ways of describing the chemical view of the crystal content (see the 
next paragraph).  Normally parsing would be restricted to _*_iupac and 
_*_sum.  These are the items that should be the versions of the formula 
identified by how they were obtained.

In connection with another point raised by Peter, I should point out 
that there is a group working on the addition of chemical information to 
CIF.  It will  eventually report to the coreCIF Dictionary Maintenance 
Group but at the moment it is still work in progress.  It is proposing 
items that would specify the bond topology of the molecules (or other 
chemical units) that exist in the crystal (2-D molecular diagram).  The 
chemical properties of these units will be described as well as their 
mapping onto the atoms in the crystal.  In addition, it will be possible 
to describe the ideal geometry of the molecules.  This seems to be close 
to the work that Peter is doing.

David Brown

-- 
Dr. I.D.Brown, Professor Emeritus,
Department of Physics and Astronomy
McMaster University, Hamilton
Ontario, Canada


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