Marvin cannot dearomatize a SMILES.

I tested it in Marvin demo online,  i.e. http://www.chemaxon.com/marvin/sketch/index.php.   After pasting a SMILES,
Cc1nc2ccc(Cl)cc2n1,   I  find that I cannot dearomatize this smiles(
/Structure/Aromatize form/Convert to Kekule form in Marvin). The structure is
valid( /structure/check structure in Marvin). 

 

Could you please check what stops the conversion?  Maybe Marvin is using the default
setting,  this conversion needs specified options for this kind of SMILES, it is fine with me, because I actually use
jchem cartridge to do the conversion.  
please let me know what option I should use in jcf.molconvert

 

 

Thanks

Hi,

The SMILES is missing an implicit Hydrogen atom: Cc1[nH]c2ccc(Cl)cc2n1 .

Our valence check algorithm can't handle aromatic Nitrogen atoms correctly at the moment therefore we always write out the needed implicit Hydrogen atoms in aromatic systems. (eg we generate Cc1[nH]c2ccc(Cl)cc2n1 for this structure). If the smiles is generated by an other application then I suggest to put explicit Hydrogen atoms on the structure on aromatic Nitrogen atoms.

Peter