Re: [Rdkit-discuss] Hybridization state

[Jean-Marc N. <jm....@un...>]

Dear Ivan,

I understand the underlying idea,
even though the result is not the one I expected.

Many thanks for the explanations.

Best regards,

Jean-Marc


Le 26/05/2020 à 14:52, Ivan Tubert-Brohman a écrit :
> Hi Jean-Marc,
>
> RDKit says that the oxygen is sp2 because it has a special rule that 
> considers the conjugation. Whether that is the "true" hybridization 
> for the oxygen could be a long debate; I sometimes hear that it's 
> somewhere between sp2 and sp3, perhaps not as close to sp2 as the 
> nitrogen in amides, but that's all fuzzy and in the end a 
> cheminformatics toolkit needs to have a clear rule.
>
> As far as I can tell here's the relevant code: 
> https://github.com/greglandrum/rdkit/blob/d41752d558bf7200ab67b98cdd9e37f1bdd378de/Code/GraphMol/ConjugHybrid.cpp#L172
>
> I'll quote the comment here (the "case 4" refers to the return value 
> of numBondsPlusLonePairs() for the atom).
>
>         case 4:
>           // potentially SP3, but we'll set it down to SP2
>           // if we have a conjugated bond (like the second O
>           // in O=CO)
>           // we'll also avoid setting the hybridization down to
>           // SP2 in the case of an atom with degree higher than 3
>           // (e.g. things like CP1(C)=CC=CN=C1C, where the P
>           //   has norbs = 4, and a conjugated bond, but clearly should
>           //   not be SP2)
>           // This is Issue276
>
> Hope this helps,
> Ivan
>
> On Tue, May 26, 2020 at 8:10 AM Jean-Marc Nuzillard 
> <jm....@un... <mailto:jm....@un...>> wrote:
>
>     Dear all,
>
>     I recently arrived to this:
>
>     >>> from rdkit import Chem
>     >>> m = Chem.MolFromSmiles("C(=O)OC")
>     >>> for x in m.GetAtoms():
>     ...     if x.GetSymbol() == 'O':
>     ...             print(repr(x.GetHybridization()))
>     ...
>     rdkit.Chem.rdchem.HybridizationType.SP2
>     rdkit.Chem.rdchem.HybridizationType.SP2
>     >>>
>
>     even though an oxygen atom is really SP2 but the other one is SP3.
>     I use version 2020.03.1 of RDKit.
>
>     Best regards,
>
>     Jean-Marc
>
>     -- 
>
>     Dr. Jean-Marc Nuzillard
>     Institute of Molecular Chemistry, CNRS UMR 7312
>     Faculté des Sciences Exactes et Naturelles, Bâtiment 18
>     BP 1039
>     51687 REIMS Cedex 2
>     France
>
>     Tel : 33 3 26 91 82 10
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>
>     ORCID: 0000-0002-5120-2556
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>
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-- 
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/