menucheckCIF procedure
PROC-NAME: CHEMM02 Type_1PURPOSE: To xcheck the moiety formula with the geometry.
PROCEDURE:
Work out the geometry from the _atom_site_ data and xcheck with the moiety formula.
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_chemical_formula_moiety has the identical format to _chemical_formula_sum,
namely C, H, then alphabetical, with the exception that the individual
unconnected independent entities in the structure are listed separately.
A common mistake is to attempt to depict organometallic coordination with
this entry. Such coordination can be given under
_chemical_formula_structural or _chemical_formula_IUPAC if desired, but
must never be given as _chemical_formula_moiety. Furthermore, do not
use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not. Nesting
of parentheses is also not allowed.
Correct examples:
Formulae like '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' and |
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If _chemical_formula_moiety has been given in the correct style, then
there is a discrepancy between the atom counts in one or more of the
moieties and those derived from the atomic coordinates. Check that there is
not a typographical error in _chemical_formula_moiety and that the
actual moieties present in the structure have actually been interpreted
correctly. For example, two groups of atoms might have been expressed as
different moieties, but in the atomic coordinates, after application of
symmetry operations, these moieties were found to generate a single
connected moiety.
Of course, _chemical_formula_moiety must correspond with the true individual molecular moieties present, including any solvent, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. In this case, this message can be ignored. However, be sure that the model is indeed otherwise complete and that no elements have been misassigned. If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z and _chemical_formula_moiety. Also check that the atom site occupancy is correct for the atomic coordinates otherwise a mismatch may be encountered [e.g an atom on a 2-fold axis normally has a site occupancy of 1.0 (but a multiplicity of 0.5)]. Furthermore, the site occupancy for disordered atomic sites should always sum to 1.0 when all of the alternative disordered sites are considered. |
