Re: [OpenBabel-Devel] Non-integer bond orders for resonant groups

[David v. d. S. <dav...@ic...>]

On 2021-07-27 07:51, Noel O'Boyle wrote:
> Is there a particular problem you are trying to solve where underlying
> kekule representation is causing a problem?
>

Yes, I am extracting bond orders from OB and they go into my force field
code. Different bond orders means different bond properties which in
addition yield different charges in my force field code.

If I understand it correctly the kekulization code checks for resonance
but in order to get the chemistry of single and double bonds right we
had to add over 100 lines to bondtyp.txt, so I am not sure that the code
alone is enough.

If it would be easy to extract the aromaticity of a bond that would be
sufficient for my purpose indeed.

>
> On Mon, 26 Jul 2021, 21:28 David Koes, <dk...@pi...
> <mailto:dk...@pi...>> 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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>


--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org









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