Assignment #12 (Due Wed. April 21)

 

1. Using the accompanying diagram (Report the value you use for the energy barrier) and the equation from lecture calculate the Transition State Theory rate constant for the conversion of the twist-boat form of cyclohexane to the chair form at (NOTE: Assume deltaE= deltaG):

                                                     i.     100K

                                                      ii.     300K

                                                        iii.     600K

                                                        iv.     1200K

2. In PCModel:
1. Build the boat form of cyclohexane (Choose ‘Rings’)

                                                     i.     Choose ‘Query’ and click on 4 adjacent carbons then anywhere on the screen to display the dihedral.

2. Goto ‘Compute’ then ‘Dynam’

                                                     i.     Change the number of steps to 5000 and the initial temperature and bath temperature to 100 K.

                                                      ii.     Run the molecular dynamics simulation

1.     Observe any structural changes/dihedral angle changes during the run. Does the boat appear to convert to the chair at any time?

2.     Erase the final structure (‘Edit’ then ’Erase’)

                                                        iii.     Repeat the molecular dynamics simulation for 300, 600 and 1200K and note the temperature at which the conversion “readily” takes place.

3.  
1. Assuming the rate constants in 1a tell us how many conversions take place per second compute how long between conversions at each temperature?

 

2. Would we observe the transition at lower temperatures by increasing the total simulation time? Explain.