Special cases in stereochemistry

Helicenes belong to a set of structures whose stereochemistry can neither be described by V2 nor by V3 molfiles using up or down bonds to indicate the stereochemistry  (for example by the enhanced stereochemistry of BioVia(Accelrys)). Therefore the P(lus) and M(inus) form cannot be distinguished by using molfiles (or other ASCII based representations). Workaround: To make a duplicate check work and to let them be separated by searches you may define a Sgroup data text field, select the entire molecule on the left and use “P” (=Plus) for the right-handed helix and “M” (=Minus) for the left-handed one.

By using “P” and “M” Heptahelicene can be added to the structure database twice even if the duplicate check on the database is invoked. In case the structure is registered without “P” or “M” it means that you have an unknown stereochemistry and/or the racemate. Note that you already register another compound if you use another vocabulary then P and M, or if you define the Sgroup data text field not over the entire molecule but over a few atoms and/or bonds only. For another example with another dictionary see Automated Structure Modifications and Normalizations