Egon wrote:
None of the file types that I have seen to date have fractional charges. And that includes CML. I understood Peter to say that CML only defines formalCharge ... an integer value.
Why is this?
Formal charge is a matter of chemoinformatics bookkeeping. Thus sodium chloride is written in SMILES [Na+].[Cl-]. This is absolute - all chemists would agree on this representation. Some organic compounds have + and - charges in the same molecule like [NH3+]CC(=O)[O-] which is the zwitterion of glycine. Because this is fundamental to knowing what the molecule is, it is hardcoded into CML
Experiment and calculation show non-integral charges (perhaps [Na+0.2].[Cl-0.2]. These are a matter of considerable debate - how are they measured, calculated, what volume is used for the integration, etc. There are probably > 50 methods for estimating such charges. Therefore the semantics and ontology have to be resolved by a dictionary showing which convention is used and what it means. In practice, of course, Jmol will get a file with "fractional charge" and you have no idea of the provenance. Only CML can resolve that.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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