Return to the Gaussian input window. Click on file and then modify. The Gaussian input window will appear again. Here we need to modify the input file to calculate the transition state. First type =(EF,TS) directly after Opt. This tells Gaussian to perform a eigen value following routine and to optimize the geometry to the transition state.

We need to specify a molecular conformation that is close to what we think is going to be the transitition state. So let's think about what is happening, the hydrogen is moving from the carbon to the nitrogen. Do you think this could happen in a linear fashion? Propbably not, so, as discussed before, the angle H-C-N would more than likely close from 180° to 0°. Therefore the transitition state would more than likely be somewhere between those two extreams, lets use 70°.

Go to the Gaussian Molecule Specification section and input the equilibrium HC and CN bond lengths that were calculated by the geometry optimization on the reactants. Then change the HCN angle to 70°. Now we are ready to calculate the transition state geometry and the associated molecular vibrations.

Run Gaussian, and save your output file.

After the calculation is finished you can view the output by clicking the viewbutton, . This output is pretty large so, click edit in the drop down menus and select find. Then type in "optimized parameters" (without the quotes) as the text you wish to find. This will take you directly to the transition state geometry parameters. As you can see, 70° was not a bad guess since the calculated transition state is 77.5156°. Use the find utility to find where your thermodynamic quantites are in the output by searching for E(UHF) and then enthalpy, record the enthalpy and the Gibbs free energy.

Open molekel and open the transition state calculation output from Gaussian. To see the bond lengths and angles of the molecule, right click in the main window and select geometry and then either distance or angle. Then to display a distance click on any two atoms, to display an angle click on any three atoms that form an angle. To remove the values right click in the main window select geometry and then remove values. The vibrations are animated just as before, but this time we have a special vibration to look at, a negative vibration. This negative vibration is called the imaginary vibration. Animate the negative frequency. This vibration is directly along the reaction path and thus corresponds to the vibration that facilitates the reaction.