Gaussian: Finding the Transition State of Chemical Reaction

Finding the Transition State using Gaussian & Gaussview programs

    Chemical reactions usually include at least three chemical species: reactant, transition state (TS), and products (intermediates are for multistep reactions). The transition state is an imaginative state between the reactant and the product, so the user should have an optimized geometry for the reactant and product! 

Then follow the instructions below to calculate TS.

1. Guess and draw your transition state (TS) structure using Gaussview and create Gaussian input.

2. Calculate the vibrational frequencies of your proposed TS using the Freq keyword. 

3. Open the output file with Gaussview and show the results of the frequency calculation.

4. If the number of Imiganary Frequency is greater than 1, it is not TS, because TS can have only one I.F.

5. Then open Display Vibrations and choose the vibration mode that is not relevant to your desired TS structure. You can click Start Animation to play the vibration of the selected mode.) 

6. Click Manual Displacement and change the values to the lowest value by sliding the button to the leftmost.

7. Click Save Structure. Gaussview will open the new window with an adjusted molecule from the previous window.

8. Save it as a new input and calculate the frequency of the new proposed TS again.

9. If you find a guessed TS structure, which has only 1 imaginary frequency, you can use this structure for optimization of TS to search the saddle point of the state.

How to Remove Imaginary Frequency

    In the geometry optimization of the search of the transition state (TS), a guessed TS must have only one imaginary frequency along the normal mode of vibration. One imaginary frequency indicates that your guessed TS structure is at a saddle point, which is a potential energy maximum rather than a PES minimum. In Gaussian, to gain the precision and accuracy of calculation, the user can fine-tune the convergence criteria to be tighter than the default setting of the program. 

The following keywords are suggested and powerful.

OPT=(Tight) Int=(Grid=Ultrafine) CPHF=(Grid=Fine) FREQ Geom=Check Guess=Read

    Int and CPHF command Gaussian to use a more accurate numerical integration grid (number of points on space) for all steps of calculation. 

Geom=Check and Guess=Read request the calculation to start from the last structure that reads from your checkpoint file, using $OLDCHK keyword. 

Do not forget to remove your Cartesian coordinates (or Z-matrix) before submitting the job since you use Geom=Check and Guess=Read keywords.

Trick to search Transition State quickly and correctly

    What is the fastest and best way to search for the transition state (TS) in a chemical reaction?

With Gaussian, you can use either QST2 or QST3 keyword to use a Synchronous Transit-Guided Quasi-Newton (STQN) method to calculate and optimize the TS structure for each step of a chemical reaction. This method does not require a guess molecule for TS search. You can use this method by preparing only reactant and product structures in the input file. Even if the STQN method can find you the TS quickly, this does not guarantee that the TS structure guessed by QSTn is correct! It may go wrong with the TS of other pathways or reactions. One can use the Berny TS method instead. 

The following step is to use the Berny algorithm to search TS using the Gaussian suite.  Gaussview was used as a molecular editor program and input generator.

1. Have a look carefully at which and how many atoms that involved in your guessed transition state (TS).

2. Mark it and do a calculation using its redundant coordinate.

3. Go to “Redundant Coordinate Editor” in the menu bar of the Gaussview program.

4. Constrain those atoms (from (1)) with the Bond constraint.

5. Choose Hessian as a type of constrained redundant.

6. Set its value to -1 au. This means to tell the Gaussian to force the vibration of a molecule to satisfy the hessian = -1 at the slope.

7. Save it as a new input file for the calculation of the TS search.

8. Add optional for OPT keyword with Opt=(modredundant,CalcAll,TS).

9. Do not calculate vibrational frequency (Freq keyword) together with geometry optimization. You can do this later.

10. When you complete geometry optimization, use the final optimized structure for further vibrational frequency calculation.

11. Compute vibration mode using Freq with the optimized structure from (9).

12. If your guessed TS structure contains only one imaginary frequency, it can be assumed that it is the transition state that you desire.

13. If it still contains >1 imaginary frequency, repeat (1) again. In addition, it can compute TS straightforwardly and produce a correct TS, but it is routine to try several calculations.

Rangsiman Ketkaew