I have a list of of names of molecules, some of them rather free-form (e.g "Thiolated L-alanine"). I would like to convert these names into SMILES strings. Is there any tool that could assist with dealing with these ambiguous names?
You can also try Chemicalize.org (if the SMILES download is working)
However, there is (by definition) no solution to ambigous and/or non-standard names (free form as you put it). You will have to eyeball - or better still, find the real person who has invented the free form terms you are having to deal with and get them to substitue clean standard ones such as IUPAC names (e.g. Thiolated L-alanine is even google -ve)