BIOVIA regularly receives inquiries about apparently false-negative results in substructure searches of molecules with double bonds. In particular, users often expect the structure (A) in the image below to match structure (B) in a BIOVIA Direct substructure search (SSS) or when using the Substructure Map component in Pipeline Pilot.

These two molecules however to NOT match in a substructure search or in the Substructure Map component, and this is due to the nature of the double bond marked in red in the two molecules. The double bond in molecule (A) is a bare, non-aromatic double bond, whereas the same bond in molecule (B) is an aromatic double bond.

If you want molecule (A) to match molecule (B) in a SSS or a substructure mapping you need to mark the double bond in the query molecule (A) as 'Aromatic' or as 'Double or Aromatic'. You can do that e.g. in BIOVIA Draw.