In my opinion, if the only fractional value will be 1.5 then non-integer
bond orders aren't worth the pain of breaking compatibility since this
state can be (and is, for rings) represented by setting the aromatic
property of the bond. Perhaps we should provide additional, more
nuanced properties to indicate resonance vs aromaticity?
If there is a reason for fractions other than 1.5, then I think this
should be a separate property entirely (e.g., like formal charges vs
partial charges).
I would point out that although O=CO is represented with a double and
single bond, the oxygens still get an identical partial charge as the
carboxylic acid group is recognized as such:
print(pybel.readstring('smi','O=CO').write('mol2'))
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 7/26/21 5:36 AM, David van der Spoel wrote:
Hi,
maybe this has been discussed earlier, but I would like to hear your
opinion on implementing non-integer bond orders. For e.g. benzene the
average CC bond order would be 1.5, and likewise for COO- groups or NOO
groups. Quantum-chemically such resonant groups turn out to be
symmetrical and e.g. with identical charges on the O in those cases.
When using integer bond orders we are enforcing an asymmetry that is not
there. So would it be worthwhile implementing non-integer bond orders or
is there a workaround that I am overlooking?
Cheers,
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
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