Keywords: viewmol

## 7.3 Example: Building cyclohexane

Cyclohexane in its chair configuration has a structure which seems quite complicated to generate, but it can easily be built using VIEWMOL's molecule builder. First, start VIEWMOL without any parameter on the command line and press `Cancel` in the file selection box which pops up. You should now have an empty window on your screen. Press the right mouse button within this window and select `Molecule/New molecule ...` from the pop-up menu. The molecule editor will open up. We start building cyclohexane by building one of the tetrahedra:

- Select `C` from the periodic table.
- Click with the left mouse button in VIEWMOL's window. This will place the first carbon atom at the origin.
- Click with the left mouse button on the first carbon atom. This will attach the second carbon atom to the first.
- Click with the left mouse button on the second carbon atom. This will attach the third carbon atom to the second.
- Select `H` from the periodic table and click twice on the central carbon atom. The molecule should now look like the left one in the Figure.

To continue building cyclohexane we have to remember that the torsion angles among the carbon atoms alternate between gauche and -gauche which can be determined easily by looking at the Newman projection:

- Select `C` again and set the default torsion angle to gauche.
- Click on one of the end carbon atoms. Then select `H` and click on the same carbon atom two more times.
- Change the default torsion angle to -gauche and repeat the last two steps on the just added carbon atom. The molecule should now look like the one in the middle of the Figure.
- Change the default torsion angle to gauche again and add a carbon atom and one hydrogen atom to the last carbon atom. The molecule will now look like the right one in the Figure.
- Change the default torsion angle to trans and add the second hydrogen atom to the carbon atom added last.
- Now change the default torsion angle to -gauche and add one hydrogen atom to the next carbon atom in the ring, then change the default torsion angle to trans and add the second hydrogen atom.
- Finally, complete cyclohexane by adding first a hydrogen with the default set to trans and than a hydrogen with the default set to gauche to the next carbon atom in the ring.

Figure 13: Building cyclohexane