Neutralization issue

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

SMILES STD_SMILES

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 5.4.1.2 in Oracle 11.2.0.2.0

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.

Zsolt