[Rdkit-discuss] Inchi/smiles conversion issue

[Alexis P. <ale...@gm...>]

Dear RdKiters,

Why is it that the stable tautomer of the following structure is lost
during inchi/smiles conversion?


[image: image.png]

mol = Chem.MolFromSmiles(*"Cc1ccc([nH]nc2)c2c1"*)
inchi = Chem.MolToInchi(mol)
mol = Chem.MolFromInchi(inchi)
smiles = Chem.MolToSmiles(mol)
print(smiles)

*==> Cc1ccc2n[nH]cc2c1*



The H has shifted on the wrong Nitrogen…

Interestingly, if you remove the methyl, the shift no longer happens:

mol = Chem.MolFromSmiles(*"c1([nH]nc2)c2cccc1"*)
inchi = Chem.MolToInchi(mol)
mol = Chem.MolFromInchi(inchi)
smiles = Chem.MolToSmiles(mol)print(smiles)
==>  *c1([nH]nc2)c2cccc1*



Same issue for any secondary amides: if you pass the smiles of a secondary
amide, you end-up with the following unstable tautomer:


[image: image.png]

Thanks,



Alexis