I would like to take the iupac names or 2 D structures of chemical compounds mentioned in publications which are not free. But these compound names are mentioned in abstract or supporting information which is free.
Are there any copyright issues from the journals concerned if I make use of the iupac names or the 2D struture of the compounds in my in silico research ?
The structures of these compounds are available freely on chemical databases which is in the public domain.
So is it legal to make use of the compound strutures in my computational work which is non-commercial in nature ?
I don't think it is a problem to retrieve the structure of the compound in the available database, because that has been done a lot, but if you ask permission to use it then that is great.
The structures are in the public domain and, most certainly, you can find them free of charge in public online databases such as ChEMBL or PubChem (in fact, I'd rather recommend compiling your data set from these databases than from journals).