Transition State Optimization
Overview
Transition State Optimization calculations involve locating the first-order saddle points on the potential energy surface. This is required for calculating energy barriers for chemical reactions, reaction rates and analyzing reaction mechanism.
Check the Input and Visualizer section for the allowed input types and how to upload the files.
Modules Available
Three modules are currently available:
Hybrid ML model - Fastest and DFT-accurate using machine learning
DFT - Density Functional Theory (highest accuracy)
Hybrid ML Module Input Fields
Upon selecting the Hybrid ML module, following inputs have to be provided:
Total charge of the molecule (e.g., 0)
Spin mulitplicity = 2S+1 (e.g., 1 for singlet)
Maximum force to be applied for transition state optimization
Threshold parameter for energy change
DFT Module Input Fields
Upon selecting the DFT module, the following inputs must be provided:
Optimization Methods
Any of the methods listed below can be chosen for the transition state optimization:
Quadratic Steepest Descent - A second order method that computes the hessian at every step during the optimization process.
geomeTRIC method - A backend library which provides algorithms for optimizing transition states. It can perform gradient calculations and optionally include vibrational analysis to confirm the transition state.
Berny Algorithm - An optimizer of molecular geometries with respect to the total energy. It takes energy and Cartesian gradients as inputs in each step and returns a new equilibrium structure estimate. An amalgamation of several techniques such as quasi-Newton method, redundant internal coordinates, iterative Hessian approximation, trust region scheme and linear search is implemented in the algorithm.
Eigenvector Following Method - Another quasi-Newton like algorithm.
Nudged Elastic Band - Finds the transition state structure only from the geometries of the reactants and products. The method converges to the minimum energy path and optimizes the saddle-point in the same job.
The first three methods require only the initial guess transition state structure in XYZ format as input. Following inputs must accompany the input structure:
Total charge of the molecule (e.g., 0)
Spin multiplicity = 2S+1 (e.g., 1 for singlet)
Select the basis set family (e.g., Pople, Dunning)
Select the basis set (e.g., 6-31G, 6-31+Gss)
Choose an exchange-correlation functional (e.g., M06)
Note
We have LDA, PBE, PBE0, M06, B3LYP, CAM-B3LYP, and WB97X functionals available right now for the GPU calculations.
If Add Dispersion box is ticked, following additional inputs must be provided:
Select the dispersion correction to be added (e.g., D3ZERO, D3BJ)
If Add Solvent is ticked, following input parameters for solvation models must be provided:
Choose the solvation model (e.g., PCM, SMD)
Select a solvent (e.g., water, ethanol)
In case of Nudged Elastic Band or Eigenvector Following Method, the structures of the reactant, product, and the initial guess transition state (if applicable) must be provided.
Finally, click the Run Calculation button to start the simulation.
Output Details
The following options are available to explore and save the results of your geometry optimization:
To see the optimized transition state structure, select “Molecular Structure” button at the top left and then select Optimized TS from the dropdown above the visualizer.
Click the tsopt_trj to view the trajectory of the transition state optimization by selecting Molecular Structure from the dropdown on the left and tsopt_trj from the dropdown on the right.
Select Vibrational Spectrum from the dropdown on the left above the visualizer to view the vibrational spectrum of the optimized transition state. Imaginary frequencies, if found will be listed above the spectrum.
In the bottom right corner, you can save the “Metadata”.