Transition States
Verification of Transition States
Transition states correspond to first order saddle points on the potential energy surface. A characteristic feature of a transition state is that one and only one of the second derivatives in the transition state is negative. The eigenvector with the negative eigenvalue corresponds to the reaction coordinate. Thus, the transition state can be verified by the analysis of Hessian eigenvalues that are printed in the output and by the visualization of vibrational normal modes with programs such as MOLDEN.
- Extract the optimized Z-matrix from the QST2 optimization that you performed earlier. You can use the command tail -50 outputfile to show the last 50 lines that include the optimized Z-matrix
- Perform the frequency analysis (Freq=NoRaman) for this transition state. The frequency calculation must be performed with the same method and basis set as the optimization.
- Open the output file of the frequency calculation with the MOLDEN and display vibrational frequencies Norm. Mode
Solvation Effects on Transition States
Common Homework for All Levels: Extra 3 point credit
Solvation can change the structures and relative energies of transition states. Thus, to study reactions in solution, transition states should be reoptimized in the presence of appropriate solvent model. We will use Polarizable Continuum (PCM) model to reoptimize transition states.
- Modify the input file for the transition state optimization to add the keyword for solvent calculation (SCRF=PCM keyword in Gaussian) and optimize the transition state at the HF/6-31+G(d,p) level (Opt=(TS,CalcFC) keyword in Gaussian). Once the calculation has finished, perform frequency analysis to verify that the structure is indeed the transition state. Compare the structure of the transition state in water and in the gas phase.
- Modify the input files for the starting materials and products to add the keyword for solvent calculation (SCRF=PCM keyword in Gaussian) and optimize these structures at the HF/6-31+G(d,p) level (Opt keyword in Gaussian). Calculate the reaction energy and the reaction activation energy in the solution phase and compare these values with the gas phase values.
- Provide the rationalization for the observed solvent effects.