Neutralization issue

User 674e8cc0a3

12-01-2012 01:01:09

The neutralize action of jc_standardize fails to re-protonate a charged center adjacent to a net neutral, but charge-separated, functional group? E.g.:

select smiles, jc_standardize(smiles, 'config:neutralize..tautomerize outFormat:smiles:u') std_smiles from structures


CC([CH-][N+]([O-])=O)=O CC(=O)[CH-][N+]([O-])=O

[O-][N+]([O-])=CC(C)=O CC(=O)[CH-][N+]([O-])=O

O=[N+](C=C(C)[O-])[O-] CC(=O)C[N+]([O-])=O

The three SMILES are all mesomers of the same deprotonated nitroacetone, but only the "enolate" representation (case 3) is correctly neutralized.

This is JChem in Oracle

ChemAxon e08c317633

19-01-2012 19:50:41

Neutralization mainly means H+ addition or removal. Quote from the documentation: "converts charged atoms to non charged, if it doesn't cause valence errors". Neutralizet does not neutralize mesomeric atoms in the form of A+A- (like nitro). We will extend the documentation with examples.