Not List

We are using the most recent versions of Marvin and JChem. When I do a search on naphthylene with a not list (F, Cl Br, I) in the 1-position ([!#9!#17!#35!#53]c1cccc2ccccc12), I do not find the following structures in my results:





C=CCN1C=NC2=C3C1=CC=C4C=CC(C=C2)=C34


CC1=NC2=CC=C3C4=C(C=CC=C4)C5=C3C2=C(N1)C=C5





I have left them as Kekule structures.





Where does the problem lie?

Dave,





I just tried your smiles structures in JChem 3.1.3 (the latest version), and the smarts query finds them for me.





As far as I know, you store the structures in molfile format in the database, and the query is sent back in mol format in the jsp application. Is this correct?





After some thought, I think I have a suspect: the bond attached to the not list appears to be "single or aromatic" when I import it into marvin, and this correctly finds the structures. However, the same smarts string is generated when I change the "single or aromatic" bond to single. (This generated smarts seems to be incorrect in this case.)





So, if the original drawing contained single bond, the molfile representation of the query would preserve it, and this does not produce a hit, being the targets fused aromatic systems. To pick up these kind of


structures, "single or aromatic" bond types should be used.





Did I reason correctly, or do you see something else going wrong?





If yes, it would be good to see the source of the query which was actually sent to JChem. (I don't think the database structures' format would matter in this case.)





Best regards,


Szabolcs