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(), 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)]
Somewhat relevant:
http://iverson.cm.utexas.edu/courses/310N/POTDSp06/POTDLecture%2017.html
obviously the ring changes things somewhat, but it's basically like a
protein amide bond.
Paul.
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