Sulphur stereochemistry representation

Dear Support,





I have two molecules (see chiral_molecule1.mol and chiral_molecule2.mol) with a sulphur atom.


When I compare them with a PERFECT search type for MolSearch, these molecules are the same. In this configuration, molecule is chiral, because of the lone pair of sulphur atom.


As the lone pair is not represented in the molfile the molecule is equals whether a bond if up or down.





My question is: how can I represent the stereochemistry of sulphur with lone pair in order that perfect serach would make a difference between the two molecule.





Thank you for your answer,


Severine

Dear Severine,





I suggest to use an explicit lone pair atom to represent the stereo configuration of the sulphur. You can draw this by using the "LP" button on the More window (Periodic table) or by typing LP. See an example attached.





Please note the R/S labels in Marvin to check whether the stereo configuration is valid or not. (View/Misc/"R/S labels")





There are two issues related to this:





1. There is currently a bug which prevents the proper registration of these chiral compounds, even in the explicit lone pair representation mentioned above. (Inside they behave as no stereo information was specified.) We will notify you when this is fixed.





2. We recommend to use a one-wedged representation around stereo centers, because it is always well-defined. The use of two wedges may be ambiguous. Checking the R/S labels also helps here.





You can still register appropriate lone pair representations into the database, they will be handled properly after the table is regenerated with a future version containing the bugfix.





Best regards,


Szabolcs

Dear Szabolcs,





I thank you so much for your quick answer.


Best regards,


Severine

Dear Severine,





We have implemented the support for this type of stereochemistry.


From the next major JChem release (3.2), these structures will be fully functional.





Best regards,


Szabolcs