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
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