Step 2: Create a rough approximation for the transition state geometry

The HCN molecule has an CNH isomer. There is an energy barrier between these two states. We are going to find the transition state and calculate its height. To find a better starting point for the transition state search we will perform a linear transit calculation as a rough approximation of the reaction path. We will vary the H-C-N angle in steps between 0 and 180 degrees and optimize bond lengths at each angle.

To set up the linear transit calculation:

Select the "Linear Transit" preset from the 'Main Options' panel
Open the "LinearTransit" panel
Set the number of LT points to 10
Select all atoms

A table will appear in which you can define your LT parameters. In our case HCN angle is the LT parameter. So:

Enter "180" and "0" on the "Angle..." line as limits for the HCN angle parameter
Press the "Add" button

Before running the calculation, we need to do one more thing: reduce the symmetry. This is necessary because intermediate geometries during the linear transit have lower symmetry than the starting C(lin). So:

Change the symmetry from AUTO to NOSYM in the "Symmetry" panel

Note that the "Symmetry" panel is not the button which initially shows 'Nosym' on the top of the drawing area. The "Symmetry" panel is the panel that shows up if one selects 'Symmetry' from the 'Details' Menu.

The set up is complete. Now we will run the LT calculation:

Save the file with as 'HCN_LT' (use the 'Save As' command from the 'File' menu)
Run the calculation 

Running might take a few minues. When the run is finished:

Click "Yes" when asked to read new coordinates

You will see the HCN's isomer, CNH. To see how geometry was changing during the LT run, use ADFmovie:

Select the 'Movie' command from the 'SCM' menu
Use the 'Optimized Geometries Only' command from the 'View' menu

You will see the hydrogen atom moving from C to N.

Somewhere along the path, there is a transition state we are looking for. Note that you needed to use the 'Optimized Geometries Only' command to filter out all the intermediate geometry step, so that you get only the converged geometries for each LT step.

Find the geometry with the maximum energy (hint: use the single-step button)

You should find that at about 60 degree angle the maximum energy is reached. This is Frame 6 (the 7th LT step). You can see it more clearly in the output file:

Select menu 'Output' command from the 'SCM' menu
In the Bob window select the 'LT Path' command from the 'Other Properties' menu

You will see that indeed the geometry number 7 (corresponding to Frame 6 in ADFmovie) has the highest energy. In this particular example the choice of the angle is not very important, but in general you will always want to choose the best approximation for the transition state available.

We will now prepare the search for the transition state starting from this geometry:

Select frame 6 in ADFmovie
Use the 'Update Geometry In ADFinput' command from the 'File' menu

The geometry of HCN in your ADFinput window will be updated to match the geometry currently selected in the ADFmovie window: