Is there a particular problem you are trying to solve where underlying
kekule representation is causing a problem?
On Mon, 26 Jul 2021, 21:28 David Koes, <dk...@pitt.edu> wrote:
> 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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