Thermal annealing of cyclohexane derivatives

This example requires Tinker and Tinker should be installed on the same drive as Moilin before Moilin is installed. The Tinker program needs to be installed in the default location which is \program files\tinker if Moilin is to find it.

Load cyclohexane from the Library (alkanes \

The aim here is to watch cyclohexane undergo a chair-chair flip using a bulky t-butyl group in an axial position. In build mode click one of the axial Hs and add four carbons with defult tetrahedral geometry.

Click  to go to the Tinker menu/toolbar. Click the button for a simple optimization. The t-butyl will bend quite a bit but the geometry will not flip. Click to thermally anneal the structure this raises the temperature and then drops it again. You should see the system flip from the starting chair through a boat to the chair with the t-butyl equatorial. If it does not flip (the process uses random movements and is not exactly reproducible) put a second t-butyl group in an axial position at the opposite end of the molecule..

You can use Rasmov to make a movie of this or any other annealing for use in web pages or Powerpoint presentatiuons.