This is one of the fastest generators of molecular structures, an award winning scientific software for chemists.

The basic version is available for Windows 7+. Please have a look in the handbook and see the description of the system details.

Developed by Christoph Benecke, Thomas Grüner, Roland Grund, Reinhard Hohberger, Adalbert Kerber, Reinhard Laue, Thomas Wieland.

MOLGEN 4 series

Applications showed that generator efficiency is not the only important topic for molecular structure elucidation. Thus we offer embedded generators with a much more flexible interface in the MOLGEN 4 series: MOLGEN-MS and MOLGEN-QSPR. Advanced restrictions can be passed to the generator that are obtained from spectroscopy and the generated results can be used directly within QSPR/QSAR studies.


Combinatorial chemistry experiments can clearly be optimized through the use of mathematical simulations. Therefore we provided the new version of MOLGEN with several tools for the application in combinatorial chemistry.

A new kind of structure generator has been developed, that allows to construct virtual combinatorial libraries. The input of this structure generator is a mathematical description reactions and reactants. Using a canonical form our software is able to compare combinatorial libraries, in particular for testing whether a given real library is a subset of a constructed virtual library.

In order to predict physical, chemical or biological properties for the virtual libraries, we implemented various molecular descriptors that serve as input for regression analysis. At the moment there are 708 arithmetical, topological and geometrical descriptors included in our software.

Here you find a list of the descriptors inclusive description and source: as html (2,02MB). More information can be found in the handbook (pdf-download) which comes with the software.

Regression analysis correlates molecular descriptors with measured properties of the real library. Regression methods are provided by the statistics package "R" which is accessed directly from MOLGEN's graphical user interface. So far multilinear regression, regression trees, neural networks and support vector machines are available in order to suggest promising candidate structures for the target property.

MOLGEN-QSPR is available for Windows 7+.

A small tour for understanding MOLGEN-QSPR: tour .


The program system MOLGEN-MS is devoted to computer aided molecular structure elucidation. MOLGEN-MS is mainly adapted to low resolution electron impact mass spectra but also includes tools which allow to process high resolution data and results from atomic analysis. Even information gained from IR or NMR interpretation can be added. MOLGEN-MS arose from the idea to provide a database independent tool for molecular structure elucidation in both chemical industry, research and education.

MOLGEN-MS consists of the following main components

  • MSclass (Mass Spectra classification) predicts the presence or absence of substructures from low resolution mass spectra by multivariate classification methods. In the current version there exist 160 classifiers for 85 different substructures or more general structural properties.
  • ElCoCo (elemental composition computation) computes candidates for the molecular formula by recognition of interleaving isotope pattern in low resolution mass spectra.
  • Molin (molgen input converter) serves as interface between MSclass , ElCoCo and MOLGEN and allows user interaction during the elucidation process.
  • MOLGEN (molecular structure generator) is able to compute in an efficient and redundancy free way all the connectivity-isomers that correspond to the molecular formulae proposed by ElCoCo and which fulfill the substructure restrictions obtained from MSclass, prepared by Molin as graphical input.
  • ReNeGe (reaction network generator) constructs according to known ionisation- and fragmentation mechanisms the MS reaction networks for the structure candidates and investigates, how good the experimental spectrum can be fit by the theoretical isotope pattern of the virtual fragments.

MOLGEN-MS is available for Windows 7+.

Take a look at the MOLGEN-MS flowchart or in the online manual.

The module that matches structural formulas and mass spectra is also available as console application MOLGEN-MSF.

Current developments focus on processing high-resolution data from tandem MS and will be available as console application MOLGEN-MS/MS.


MOLGEN 5.0 combines the efficiency of MOLGEN 3 series with the flexibility of the MOLGEN 4 series.

This is a new version which is available with a command line interface. To get an impression of the new features, take a look on molgen online . You can also look into the handbook. For further information, please don't hesitate to contact us.

MOLGEN 5.0 is available for both Linux and Windows systems.

Developed by Ralf Gugisch, Adalbert Kerber, Axel Kohnert, Reinhard Laue, Markus Meringer, Christoph Rücker, Alfred Wassermann.