Computational Chemistry at GVSU

Kinetics and Mechanism

In the wet lab you found (or will find) that step 2 of the iodination of acetone may be the rate determining step (Reference from steph???). We will examine this step in more detail, finding its transition state, and the change in enthalpy, H^‡, in going from the reactants to the transition state (TS).

1. Build each reactant of step 2. Using AM1, geometry optimize each molecule and report its heat of formation, H_f:

Sum all reactant heats of formation: _______________________________________

2. In a similar manner, determine the heats of formation for each product:

Sum all product heats of formation: _______________________________________

3. Find the transition state:

1. Load the model /sgi/chm353/int_h20_ts.msi
2. Do a TS optimization using AM1 (don't forget the charge!)
3. Do a frequency calculation to determine if you are at a transition state (i.e., only one imaginary frequency).
4. If there is more than one significant imaginary frequency, animate the unwanted frequency and click on "step" to stop it somewhere midstream. Do a TS optimization from this point to try to find a minimum for this unwanted normal mode while preserving the maximum for the desired normal mode. Repeat until you locate a valid transition state. (Note: if you are having difficulty finding a transition state, check your charge. If your charge is fine, you may have to obtain a transition state from your instructor).
5. Record the H_f for the transition state:

Transition State heat of formation: _________________________________________

4. Compute the H^‡: _____________________________________

Let's investigate this discrepancy by following the reaction path from TS to products. Unfortunately, "Follow Reaction Path" task doesn't seem to work for this. We will do the same thing using the "Scan Potential Surface" task.

6. Choose a good reaction coordinate that will drive your transition state model to form products. Verify your choice with the instructor.

Reaction coordinate chosen:

Value of the reaction coordinate in the transition state: ___________________________

7. Identify the line in the Z-matrix that corresponds with this reaction coordinate. To do this, choose MOPAC's "Geometry" (not the "Geometry" in the top menu bar) and then "Constraints". A Z-matrix will pop up. Find the appropriate line and verify your choice with the instructor.

Z-matrix line number for the reaction coordinate: _______________________________

8. The transition state optimizations will have left some of the bonds fixed (i.e., not allowed to move during a calculation). These will have an "F" rather than a "V" next to them in the Z-matrix. Allow these bonds to vary by choosing the appropriate line of the Z-matrix and then selecting the "VARY" button for bonds under the Z-matrix.

9. Choose the "Scan Potential Surface" task, and select its "More" button. Enter the Z-matrix line of the reaction coordinate and hit "Enter". This should set the "Start" value to the value in the transition state. Set the "End" value to 10Å and the step # to 80. Run the potential surface scan.

10. More likely than not, you will run into an error message mentioning something about 3 atoms all in a straight line. See the instructor for ways to fix this. This includes changing lines in the Z-matrix. Make sure you do this for the transition state (not the end product of some potential surface scan) and safe each Z-matrix modification (by "File":"Save Model"), so if the new Z-matrix doesn't work, you can start from where you left off.

11. Once you have a potential energy surface, save the graph by choosing the menu deck card "Tables & Graphs" (i.e., where you usually choose "Quantum 1"), and bring the "GRAPHS" card forward. Choose "File ->" and then "Save Graphs".

12. Starting again at the transition state (which requires that you reload your transition state model), calculate the reaction path for going from transition state to reactants. Which reaction coordinate would now be appropriate? Repeat steps 6-11 above.

Reverse reaction coordinate:

Reverse reaction coordinate value in the transition state:___________________________

Z-matrix line number: _____________

13. Ask the instructor to help you "stitch together" your two reaction path graphs. To do this, open each graph file created above in jot. Transfer the data from both sets into one file of x,y data. Add the correct point for your transition state between the two sets of data. Make the reaction coordinate as it goes from transition state to reactants negative, so it will plot to the left of the transition state. Make the "x" for the transition state zero.

For example, if the transition state to reactant was something like (x,y)

1.5 -23

1.6 -24

…

10 -30

and the transition state to product was something like

1.8 -22

1.9 -26

…

10 -29

and the transition state energy was H^‡ = -20, then make the file data read like

-10 -30

…

-1.6 -24

-1.5 -23

0 -20

1.8 -22

1.9 -26

…

10 -29

Transfer these data to a PC (see Useful Information for how to do this). Plot out your data on the PC, with the correct reaction coordinates labelled in the different parts of your graph. Include this graph and this handout, filled out, in your notebook.

15. Compute the computational E_a and compare it to the experimentally determine E_a. Why are these different? Discuss.