Neutralizing NH4+ with explicit hydrogens

Hi,

Why is [H][N+]([H])([H])[H] neutralized to [NH4] (a free-radical form) and not N, which is the result of neutralizing [NH4+]?

Moses

"[H][N+]([H])([H])[H]" neutralization should result ammonia ("[H]N([H])[H]"), and this is exactly what I get with Standardizer 5.2.3.1

$ standardize -c "neutralize" "[H][N+]([H])([H])[H]"
[H]N([H])[H]

Zsolt

Zsolt wrote:

"[H][N+]([H])([H])[H]" neutralization should result ammonia ("[H]N([H])[H]"), and this is exactly what I get with Standardizer 5.2.3.1 $ standardize -c "neutralize" "[H][N+]([H])([H])[H]" [H]N([H])[H] Zsolt

 

Hi Zsolt,

I made sure this time to test on the latest JChem (5.2.3_2), using:

 

Molecule m = new MolHandler("[H][N+]([H])([H])[H]");

return (new Standardizer("neutralize")).standardize(m).toFormat("smiles");

 

That does produce [H]N([H])[H]. However, if you do:

 

return (new Standardizer("neutralize")).standardize(m).toFormat("smiles:u");

 

You get [NH4], which is incorrect. You get the same with "smiles:-H". So I guess the problem is not with the Standardizer, but with Molecule's toFormat method or whatever it calls. I also tried:

(new Standardizer("neutralize..removeexplicitH")).standardize(m).toFormat("smiles");

which also returns [NH4]. Finally, I tried this:

 

Molecule m = new MolHandler("[H]N([H])[H]");

return (new Standardizer("removeexplicitH")).standardize(m).toFormat("smiles");

 

and that also returns [NH4], so I'm guessing that's the actual problem. Please let me know if I'm missing something.

 

Moses

 

Hi Moses,

It's indeed a bug. We have fixed it, the fix will be available in JChem 5.2.4.

Thanks for the report.

Zsolt