On 13/02/2021 18:15, Peter St. John 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(),
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
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,
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
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