Re: [Rdkit-discuss] Hybridization state
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
mailto:jm.nuzill...@univ-reims.fr>> 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
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
ORCID: -0002-5120-2556
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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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/
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Re: [Rdkit-discuss] Hybridization state
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.nuzill...@univ-reims.fr> 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
> Fax : 33 3 26 91 31
> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
>
> ORCID:
> -0002-5120-2556http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>
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> Rdkit-discuss mailing list
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[Rdkit-discuss] Hybridization state
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
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
ORCID: -0002-5120-2556
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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