Stereoisomer generation is important in analytical sciences, natural product synthesis and metabolomics. Stereoisomers include tetrahedral (R/S) and double bond isomers (cis/trans). The can be generated with different programs. One of the easiest way is to use Marvin [JAVA Webstart].


Marvin created 512 stereoisomers (2^8) for sucrose and those structures can be saved or other properties can be calculated. A good way of handling those structure files is storing them in Instant-JChem and doing some more calculations there. The number of stereoisomers is usually (2^n) where n refers to chiral centers, but sometimes also less (example: CC(O)C1=C(C(C)O)C(C(C)O)=C1C(C)O has 7 stereoisomers), CC(O)C1C(C(C)O)C(C(C)O)C1C(C)O has 39 stereoisomers see [LIT].


Additional free resources

  • All 32768 maltotriose stereoisomers generated with JChem cxcalc (SMILES zipped) [ZIP]
  • All 50313 stereoisomers (50308 unique) from all 13190 isomers of C8H16O2 (SMILES ZIP) [ZIP] [InChI]

Other tools and links for stereoisomer generation

  • MOLGEN View (Molview.exe) has a routine for calculation of isomers (does not handle all cases, no export)
  • CACTVS can calculate stereoisomers (not all cases)
  • depth-first blog discusses some issues