Error during format conversion using JChem Web Services

Hello,

 

I have a problem while converting some structures from smiles to inchi/inchikey. In this special case, it concerns aromatic compounds. e.g.: [O-][N+](=O)c1ccc2nncc2c1 cannot be converted to inchi or inchikey. I get a 500 Internal Server Error. However, when I use the Kekule form to represent the pyrazole ring or even the whole structure, I do not get the error anymore. I assume that if the pyrazole ring, when fused to another aromatic ring, cannot be represented in aromatic form. Is it right? Could you give me an explanation for it?

Since it looks like I should dearomatize the structure for conversion purposes, how can I do this with JChem? What are the paramters/options?

Cheers,

 

MrYan

Hello,

This structure you provided is not aromatic because it doesn't follow Hückel's rule. The standard InCHI library (we rely on this in our export) has its own dearomatization method which cannot cope with this electron configuration. You can read about it in this document (page 25): http://www.inchi-trust.org/download/104/InChI_TechMan.pdf

Also note, that ChemAxon's dearomatization methods (https://docs.chemaxon.com/display/SR/Converting+structure+from+aromatic+form+to+Kekule+form) cannot convert this structure to Kekulé form.

This would be the correct SMILES for this particular aromatic structure: [O-][N+](=O)c1ccc2[nH]ncc2c1

It indicates a hydrogen for one of the nitrogen atoms, and represented like this, it can be exported to InCHI and also dearomatized by ChemAxon software.