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
Now select the 'Geometry Constraints and Scan' panel
Select all the atoms

You should see '+ N(1) C(2) H(3) (angle)' note in the right panel now:

Click the '+' sign

Now '- N(1) C(2) H(3)' and the two fields as limits for the degree parameter appear.

Enter '180' and '0' in the 'degrees' fields:

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):

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

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

Save the file with as 'HCN_LT' (use the File → Save As command)
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 SCM → Movie command
Select the View → Add Graph command
Use the View → Converged Geometries Only command

You will see the hydrogen atom moving from C to N. You will also see a graph of the energy as function of the LT steps. As the movie is playing a dot shows the corresponding position in the graph.

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.

In the graph, click (without moving!) on the top of the energy graph
Note which geometry has the maximum energy

You should find that at about 60 degree angle the maximum energy is reached. This is Frame 6 (the 7th LT step), see figure:

You can see it more clearly in the output file:

Select the SCM → Output menu command
In the ADFoutput window select the Other Properties → 'LT Path command

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:

Make sure frame 6 is selected in ADFmovie
Use the File → Update Geometry In ADFinput command

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