Introduction

The Stereoisomer Generator Plugin is able to enumerate all possible stereoisomers of a given compound. The plugin can handle both tetrahedral- and double-bond-type stereo centers.

An example for stereoisomer generation output in MarvinView (see Fig. 1) and in MarvinSpace (see Fig. 2) can be found below.

Fig. 1 Generated stereoisomers shown in MarvinView

Fig. 2 Generated stereoisomers shown in MarvinSpace

Options

The panel of the plugin has the following options to set:

• Generate

  1. Tetrahedral stereo isomers: only the R/S isomers are generated.

  2. double bond stereo isomers: only E/Z isomers are generated.

  3. both: both R/S and E/Z isomers are generated.

• Generate all stereoisomers: all isomers are generated

• Generate maximum: sets an upper limit for the number of generated isomers. This option gets enabled if not all isomers are generated.

• Protect tetrahedral stereo centers: if checked, stereocenters already pre-set are not included in the stereoisomer generation.

• Protect double bond stereo: if checked, all double bonds with pre-set stereo information remain intact.

• Filter invalid 3D structures: sterically restricted isomers are discarded.

• Display in 3D: results are displayed in a 3D viewer. By default the results are shown in a 2D panel, one for each generated isomer. This option is enabled only if 3D filtering is enabled.

Fig. 3 Options window for stereoisomer calculation

Stereoisomer Generator demo page

You can try our Stereoisomer Generator for free on this demo page.

References

1. Smith, M. B.; March, J. Advanced Organic Chemistry, 5th ed., Wiley Interscience, New York, 2001; pp 1218-1223. ISBN 0471585890