Ok great, thanks for the clarification! I was trying to follow 'S3' in
table 2 of https://doi.org/10.1021/ci300415d, where their criteria was "at
most one sp2 -center in 4-membered rings" which apparently allowed
beta-lactam, but it seems there's more to that characterization than just
total degree.
-- Peter
On Sat, Feb 13, 2021 at 12:15 PM Peter S. Shenkin <shen...@gmail.com> wrote:
> Amide Ns are usually viewed as sp2 because of the resonance RC(=O)-NR2 <->
> RC([O-])=[N+]R2, where R can be H.
>
> Unlike sp3 Ns (amines), amides are not strong H-bond acceptors, though
> both amides and amines are strong donors. This observation is consistent
> with sp2 character.
>
> -P.
>
> On Sat, Feb 13, 2021 at 1:18 PM Peter St. John <peterc.stj...@gmail.com>
> wrote:
>
>> Is there any reason why RDKit says the nitrogen in beta-lactam is
>> SP2-hybridized? I would have assumed it should be SP3. It doesn't seem to
>> be the ring structure, 'C1NC1' lists all the atoms as being SP3.
>>
>>
>>
>> >>> [(atom.GetSymbol(), atom.GetHybridization()) for atom in
>> rdkit.Chem.MolFromSmiles('O=C1CCN1').GetAtoms()]
>>
>> [('O', rdkit.Chem.rdchem.HybridizationType.SP2),
>> ('C', rdkit.Chem.rdchem.HybridizationType.SP2),
>> ('C', rdkit.Chem.rdchem.HybridizationType.SP3),
>> ('C', rdkit.Chem.rdchem.HybridizationType.SP3),
>> ('N', rdkit.Chem.rdchem.HybridizationType.SP2)]
>>
>>
>> Thanks!
>> -- Peter
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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