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?
[The Pub Chem Identifier Exchange Service][1] will certainly assist you for the more standardised names that map to CIDs (that you can download as SMILES)

You can also try Chemicalize.org (if the SMILES download is working)

However, there is (by definition) no solution to ambiguous 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 substitute clean standard ones such as IUPAC names (e.g. Thiolated L-alanine is even google -ve)

 [1]: https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange-help.html