Enter a molecular formular and optionally further restrictions into the form below. Alternatively, choose one of the examples.
After pressing "START MOLGEN", the corresponding molecular structures will be generated. You can see the number of generated structures as well as the first 1000 structures in the molecule viewer on the right.


Please note that in this online version (a restricted version of MOLGEN 5.0), the computation time is limited to 5 minutes per job. Further, the most powerful restrictions of the commercial versions of MOLGEN, namely the possibilities to prescribe and to forbid the occurence of substructures in the generated structures, are not available in this online version. The filter for aromatic duplicates is turned on by default.

3D placement

You either choose to compute the 3D coordinates (using OpenBabel) on the server, which may fail due to the 5 minutes limit, or do the 3D individually for each structure by clicking on "3D PLACEMENT".

When using MOLGEN online for your scientific publications, please cite

Gugisch, R., Kerber, A., Kohnert, A., Laue, R., Meringer, M., Rücker, C., Wassermann, A.: MOLGEN 5.0, A Molecular Structure Generator (2016) Advances in Mathematical Chemistry and Applications: Revised Edition, 1, pp. 113-138.

Generate all structural isomers of C6H6

Generate all halogenated ethanes.

Generate all chlorinated benzenes

Generate nitrobenzene

Generate all (theoretically possible) structures of mass <=40 with elements C, H, N3, O

Input formula:

Restrictions corresponding to the formula:

2D    3D

3D layout is generated by OpenBabel. Be cautious, 3D placement may be slow.

Restrictions corresponding to the atom states:

Restrictions corresponding to the molecular graph:


0 structures (not started):
Structure 0.