PES scan, transition state search and Intrinsic Reaction Coordinate¶

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

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

Perform a 1D 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

PES Scan¶

Let us begin by starting up the AMSinput GUI module:

: 1. Start AMSjobs

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

3. In AMSinput, select the DFTB panel: →

To create the Pyrithione molecule:

: Copy-paste the following coordinates in the Molecule Editing Area of AMSinput

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. Make sure the SCC-DFTB model is selected

3. Click on the folder next to Parameter directory and select DFTB.org/3ob-3-1

Your AMSinput window should look like this:

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 (PES scan):

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.

../_images/PES-scan_TS_constraints_1.png

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

: 1. Leave the initial distance at 1.612

2. Set final distance to 1.4

3. Set the number of scan points for coordinate SC-1 to 8

../_images/PES-scan_TS_constraints_2.png

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 AMSjobs window to the front

3. Wait for the calculation to finish…

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

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

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

: With AMSmovie 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 AMSmovie, using either arrow keys or the slider, select Frame number 3

2. Click on File → Update Geometry in Input

This will bring AMSinput 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.

In AMSinput:

: 1. In AMSinput, go to the Main panel

2. Select Task → Single Point

3. Check the Frequencies check button

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 AMSjobs window to the front

3. Wait for the calculation to finish…

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

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

This will open AMSspectra:

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.

Transition state search¶

We are now ready to perform the transition state search calculation.

: 1. Open the AMSinput window of the job “Frequencies”

2. Select Task → Transition State

3. Make sure that the Frequencies option is checked

The main panel should look like this:

: 1. Go to the panel Details → Geometry Optimization

2. Select Initial Hessian → From File

3. click on the folder next to Initial Hessian From:

4. Select the file dftb.rkf in the folder Frequencies.results

We can now run the TS search calculation:

: 1. Click on File → Save As… and give it the name “TS”

2. Click on File → Run . This will bring the AMSjobs window to the front

3. Wait for the calculation to finish…

4. Click on Yes when AMSinput asks whether to “Read new coordinates from…”

You can now visualize the TS search using AMSmovie:

: In AMSjobs select the job TS and select SCM → Movie

And confirm that the there is exactly one imaginary (negative) frequency by inspecting the IR spectra with AMSspectra:

: In AMSjobs select the job TS and select SCM → Spectra

../_images/PES-scan_TS_amsspectra_ts.png

IRC (Intrinsic Reaction Coordinate) calculation¶

: 1. Open the AMSinput window of the job “TS”

2. In the main panel select Task → IRC

3. Untick the Frequencies checkbox

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 AMSjobs window to the front

3. Wait for the calculation to finish…

You can now visualize the IRC path using AMSmovie:

: In AMSjobs 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 AMSjobs 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
---------------------------------------------------------------