1. In the visualizer window left click on the file drop down menu and select new session. This will reinitialize all of the Cerius2 programs options.

2. Again select ball and stick as the viewing mode, the 3D sketch window should still be present but if it is not click on build in the drop down menu and then select 3D-sketcher and draw another HCN molecule.

3. Now in the sketcher window left click on the angle button so we can change the HCN angle. In the models window left click on the hydrogen then the carbon then the nitrogen to define the angle we will change. Be careful to left click exactly in the center of each atom because where you left click is the exact point the angle will be defined from. After you have defined the angle do not move the mouse outside the model window until after step 4.

4. Now left click and hold in the black portion of the model window and move the mouse up and down to change the HCN angle. Make the angle around 90 degree, it does not have to be exact as this is just a guess for the transition state.

5. If the MOPAC calculation window is not still present, in the left most portion of the visualizer window left click and hold on the light brown box labled BUILDERS1 and from the menu that appears choose QUANTUM1. Then left click on Run to open the MOPAC calculation window.

6. Change the calculation task to Transition State Optimization (geometry optimization to the transition state).

8. Rename the file appropriately (i.e., hcn_ts_search) and change the calculation method from AM1 to PM3.

9. Left click on RUN again a small window will pop up to show that the calcualtion is progessing. When this window disappears the calculation is finished.

10. If the program has found the transition state the HCN molecule should look something like this:

the HCN angle should be round 69 degrees.

10. Analyze the output file and record the heat of formation, enthalpy, heat capacity, and the entropy all at 300 K for the transition state, we will be using this in our calculations later.

11. Now there are some very interesting molecular orbitals that we can view for the transition state, but first for clarity we are going to change a viewing parameter so we can see the atoms a bit more clearly within the molecular orbitals. Left click on surfaces under the analyze section, there is a transparency % selection in the lower left corner or the surfaces window. Type 50 in the blue box and hit enter, then close the window.

13. Now open the orbitals window via the analyze menu and view the molecular orbitals of the transitions state HCN molecule. Notice the second molecular orbital shows the electron sharing between the hydrogen and the nitrogen.

14. Now that we have found the transition state geometry we can run a frequency calculation on it. Change the calculation task to frequency calculation and rename the file and run.

15. Left click on analyze and choose file, the anaylze file window will pop up. Then click on examine file and find and record the heat of formation, enthalpy, heat capacity, and entropy.

15. Go to the vibrations and look at the frequencies of the transition state. The top frequency is negative, which is the imaginary frequency along the direction of reaction that characterizes a transition state.

16. Go ahead and close the vibrations window.

Now let's move on to the products geometry calculation