[Rdkit-discuss] hybridization of nitrogen in beta-lactam

2021-02-13 Thread Peter St. John 
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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Re: [Rdkit-discuss] hybridization of nitrogen in beta-lactam

2021-02-13 Thread Peter S. Shenkin 
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 
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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Re: [Rdkit-discuss] hybridization of nitrogen in beta-lactam

2021-02-13 Thread Peter St. John 
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  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 
> 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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Re: [Rdkit-discuss] hybridization of nitrogen in beta-lactam

2021-02-13 Thread Paul Emsley 


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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