The computation of 2D-, of 3D-placements, and of stereoisomers

After the generation of the constitutional isomers, you get a sketch of the molecules using a method based on [6], either in form of a tapestry, where several molecules are shown together on the screen, usually 6 of them, or you can get a single molecule on the screen.

  
Figure 1: Molecule tapestry of dioxin isomers

Fig. 1 shows the printed version of a tapestry of dioxin isomers.

The next step is the computation of a placement of that constitutional isomer in space. This is done by an application of the (simplified) MM2-model of Allinger (see. [7]) using an optimization programme. You can watch the result on the screen, rotate it, color it, replace the atoms by little balls, and so on.

Each of the structural isomers may exist in several configurations in space. MOLGEN is capable of generating all possible configurational isomers, again redundancy free (which, of course, also implies the consideration of symmetries).

The notion stereo isomerism is not uniquely defined in chemistry; it should therefore be stated which kinds of effects are taken into account. Primarily there are:

• Chirality of tetravalent atoms, even in rings and spiranes,
• enatiomerism and diastereomerism of allenes including cis/trans-isomerism.

  
Table: Each entry consists of the number of constitutional isomers as in table 1, repeated for the convenience of the reader, and the number of configurational isomers, arising from the first. The row index denotes the number of C-atoms, the column index the number of H-atoms.

In the second step spatial realizations of these isomers are calculated by the application of appropriate geometrical transformations to the placement computed above. (The basics of these calculations, which are again discussed in [9], can be found in [10].) In fig. the four stereoisomers of 1,2,3,4-tetramethylcyclobutane are displayed as an example.

  
Figure: stereoisomers of 1,2,3,4-tetramethylcyclobutane

The cycle structure of the molecule and the position of the stereo-centers sometimes make an accurate transformation impossible. In this case, approximate constructions are performed which can be optimized afterwards.