Structural Isomer Generation is one of the backbones of chemistry and small molecule sciences. The problem is that exhaustive structural isomer generation is in general solved, but the number of isomers (less than 2000u) is larger than 10^40. This refers to the number of simple alkane isomers of CnH2n+2 only. The number of alkanes can be easily calculated. All other isomers must be generated in-silico in order to count them. Therefore nobody knows the number of all structural isomers. This number is infinite. For less than 2000u the number is course finite and depends on the molecular formula space.


The questions: What is the number of isomers? or How Do You Calculate Number Of Isomers?

Can only be answered: By use of molecular isomer generators. Again. For complex molecules the number of isomers can not be calculated, they must be fully generated in order to count them. There is no mathematical formula to do that. See also Molecular Isomer Generators as part of the Seven Golden Rules project. Two general approaches A) deterministic and B) stochastic (random) processes exist for isomer generation.


  • MOLGEN - general purpose deterministic and very fast structural isomer generator (Uni Bayreuth)
  • CDK - free open source implementation of a deterministic and random structure generator in JAVA
  • SMOG - freely available deterministic molecular isomer generator works under DOS (closed source)
  • ChemAxon Reactor - for combinatorial generation of molecules and reaction modelling
  • SmiLib - open source tool rapid combinatorial library enumeration (Markush)
  • Clever - Pipeline for designing in silico chemical libraries (based on SmiLib) (Markush)
  • OpenMG - uses nauty as graph isomorphism checker (open source) [PDF]


  • Number of structural isomers less than 150u (Markus Meringer) [XLS]