Stereo Specification

Basic stereo specification

Enhanced stereo specification

Works in MDL molecule formats: mol, rgf, sdf, rxn etc... and in ChemAxon Extended SMILES format: cxsmiles.

Enhanced stereochemical representation introduces three types of identifiers that can be attached to a stereogenic center. A stereochemical group label is composed from an identifier and a group number. Each stereogenic center marked with wedge bonds belongs to one (and only one) stereochemical group. Grouping allows us to specify relative relationships among stereogenic centers.

Stereochemical group types:

How to specify and view R/S configuration

  1. Draw a chiral molecule.

  2. Click on (select) the asymmetric carbon atom that you want to configure as S or R. Right-click onto the carbon atom pops up the Atom menu. Choose Stereo > R/S and the appropriate configuration.

  3. The relevant bonds will change automatically according to the proper R or S configuration.

  4. To display the stereo label on the asymmetric carbon atom, select View menu > Stereo > R/S Labels > All.

  5. The configuration of the asymmetric carbon atom presents in parentheses as follows.

  6. If you want to remove the stereo label from the the asymmetric carbon atom, choose View menu > Stereo > R/S Labels > None.
  7. If you want to delete stereo representation, right-click on the asymmetric carbon atom and choose Atom menu > Stereo > R/S > Off.

References

[1] http://www.mdl.com/downloads/public/ctfile/ctfile.pdf