Miguel wrote:
There is, if we are ever going to make use of it, as in calculating and displaying ESP coloured surfaces.Yes, Jmol will read the a 4th (or 7th) column in an XYZ file as a charge
value
(7th in the case where there are vectors associated with the atoms ... 3 coordinate values + 3 vector coordinate values + 1 charge)
However, Jmol currently interprets this column as a 'formalCharge', not as a 'partialCharge'.
Q: Is there value in having this column support 'partialCharge' in
addition to 'formalCharge'?
What about the partial charges listed in CML files, are they read and stored somewhere?
Q: Please confirm that the range of values for partial charges is > -1 && < 1Partial charges depend on the method to calculate them.
Among the many methods there is one, AIM, that sometimes produces partial charges larger than 1.
(Which is why organic chemists distrust AIM).
Q: Please confirm that I could use the following algorithm to distinguish between partial charge and formal charge for the 'charge' value in (for example) an XYZ file:
if (value > -1 && value < 1) partial charge else if (value is an integer value >= -4 && <= 7) formal charge else error
In 99+ % of the cases this would work; see remark above.
Hens
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