# PES scan, transition state search and IRC¶

In this tutorial we will locate the transition state for Pyrithione tautomerization:

Specifically, we will use AMS in combination with the DFTB Engine to:

• Perform a 1D Potential Energy Surface (PES) scan, a.k.a. linear transit, to locate the initial guess for the subsequent Transition State (TS) search
• Compute the Hessian and normal modes by performing a Frequencies calculation
• Perform a transition state search using the Hessian computed in the previous step
• Compute the Intrinsic Reaction Coordinate (IRC) path connecting the reactant and the product

More informations on these features can be found in the AMS User manual:

## PES Scan¶

Let us begin by starting up the ADFInput GUI module:

2. Click on SCM → New Input. This will open ADFInput

To create the Pyrithione molecule:

Copy-paste the following coordinates in the Molecule Editing Area of ADFInput
13

C      -2.30800400      -0.33458354      -0.03944688
C      -3.55161726      -0.98161691      -0.01806157
C      -3.59405760      -2.37377447       0.06998894
N      -2.43475599      -3.05706858       0.13215278
C      -1.19114674      -2.47716286       0.11543345
C      -1.13146988      -1.07344958       0.02678424
H      -4.47776711      -0.41946857      -0.06866615
H      -4.51286388      -2.95462913       0.09224655
O      -2.42829502      -4.40191846       0.21755293
S       0.09533105      -3.63607352       0.21049529
H      -0.16385857      -0.58321314       0.01095504
H      -2.26672769       0.74932834      -0.10794508
H      -1.26310602      -4.50300286       0.24347732


We now need to select the task and the DFTB parameter set:

1. In the main panel, select Task → PES Scan
2. Click on the folder next to Parameter directory and select DFTB.org/3ob-3-1

Now switch to the “Geometry Constraints and PES Scan” input panel:

In the menu bar, select Model → Geometry Constraints and PES Scan

We will now set up the coordinate along which to scan the potential energy surface:

In the Pyrithione tautomerization, the hydrogen atom bonded to oxygen will cross a small energy barrier and bond to the sulfur atom next to it. We will therefore scan the energy as a function of the H-S distance:

1. Select the H atom attached to O
2. Holding down Shift, select the S atom
3. Click on + next to H(13) S(10) (distance)

This will add the H-S distance as a scan coordinate.

We now need to set the initial value, final value and number of intermediate steps for the H-S distance:

1. Set initial distance to 1.612
2. Set final distance to 1.4
3. Set the number of scan points for coordinate SC-1 to 8

We are now ready to run the calculation:

1. Click on File → Save As... and give it the name “PES_scan”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

After the calculation is completed, we can visualize the results:

In ADFJobs, select the job “PES_scan” then click on SCM → Movie

This will open the ADFMovie program and show the energy profile of the PES scan.

With ADFMovie into focus, use the the right and left arrow keys to go through the frames

As initial guess for the TS search, we pick the geometry corresponding to the highest energy in the PES scan, i.e. frame number 3.

1. In ADFMovie, using either arrow keys or the slider, select Frame number 3
2. Click on File → Update Geometry in Input

This will bring ADFInput to the front update the geometry of the Pyrithione molecule.

## Frequencies calculation¶

It is important to have a good starting Hessian with one imaginary frequency when performing a TS search.

Here we calculate the Hessian matrix that will be used in the subsequent TS search.

1. In ADFInput, go to the Main panel
2. Select Task → Single Point
3. Select Followed by → Frequencies

We can now run the Frequency calculation, which will compute the Hessian and the normal modes:

1. Click on File → Save As... and give it the name “Frequencies”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

When the calculation is finished, we can visualize the normal modes using ADFSpectra:

In ADFJobs select the job “Frequencies” then click on SCM → Spectra

The first mode should have an imaginary frequency (which in the table is shown as a negative frequency). Click on the line in the table corresponding to the imaginary frequency to visualize the mode.

We are now ready to perform the TS search.

## IRC (Intrinsic Reaction Coordinate) calculation¶

1. Open the ADFInput window of the job “TS”
2. In the main panel select Task → IRC
3. Select Followed by → Nothing
4. Click on next to Task → IRC

In the IRC panel you can adjust the options for the Intrinsic Reaction Coordinate calculation. For this example the default options are fine.

We can now run the IRC search calculation:

1. Click on File → Save As... and give it the name “IRC”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

You can now visualize the IRC path using ADFMovie:

In ADFJobs select the job IRC, then select SCM → Movie

A summary of the IRC calculation can be found at the end of the output file:

1. In ADFJobs select the job IRC, then select SCM → Output
2. Scroll until the end of the output file to see the IRC summary:
 ---------------------------------------------------------------
IRC summary
System energy at the TS                  -18.49370493 Hartree
Forward barrier height                     0.00022713 Hartree
Backward barrier height                    0.00245861 Hartree
---------------------------------------------------------------
Rel. energy   Rel. energy    Path coord   RMS gradient
[Hartree]    [kcal/mol]    [Angstrom]    [Hartree/A]
1    -0.0024586        -1.543      -0.47694      0.0000169
2    -0.0024368        -1.529      -0.44378      0.0004731
3    -0.0022943        -1.440      -0.39267      0.0013751
4    -0.0020017        -1.256      -0.33119      0.0022516
5    -0.0015350        -0.963      -0.26152      0.0030561
6    -0.0008980        -0.563      -0.17942      0.0031652
7    -0.0002510        -0.157      -0.10353      0.0025638
8     0.0000000         0.000       0.00000      0.0000251 TS
9    -0.0001465        -0.092       0.10315      0.0012826
10    -0.0002271        -0.143       0.14237      0.0000498
---------------------------------------------------------------