Bug or just a wrong smiles?

For compounds like 83-34-1, if the smiles is written as


c1ccc2c(C)cnc2c1 MarvinView can display the molecule but cant dearomatize the aromatic bonds. If the smiles is written as c12c(cccc2)[nH]cc1C it works. Is there something wrong with the first smiles I wrote or is this a bug in Marvin?

For 3-methyl-indol the smiles is incorrect, because on aromatic nitrogen atoms the implicit hydrogen has to be defined. For more detail please refer to the documentation of smiles:





http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html#RTFToC29





The correction of the smiles you tried is as follows:





c1ccc2c(C)c[nH]c2c1





but the second smiles you wrote - c12c(cccc2)[nH]cc1C - is also a correct one.

OK thanks- that makes sense- thanks for the quick reply.