Setting up a reaction kinetics calculation

Information generated by CASTEP as part of the transition state search task enables you to predict the reaction rate coefficient of a chemical reaction. The algorithm is based on transition state theory and involves evaluation of the partition functions of reactant(s), product(s), and transition state. Calculation of a partition function involves obtaining the vibration spectra, this in turn is calculated from the Hessian matrix.

The reaction rate calculation requires three main ingredients:

Transition state search, performed after optimizing geometry of reactants and products
Calculation of the Hessians for all the reaction species
Calculation of the partition functions and reaction rates for forward and reverse reactions

Transition state searching in CASTEP can be performed using either the LST or QST formalism. To optimize the reactant and product structures as part of the TS Search run, check the Optimize reactants and products checkbox on the CASTEP Transition State Search dialog. It is important to set constraints correctly in the initial documents - this has effect both on the cost of the subsequent calculations, and on the accuracy of the results obtained.

To calculate the Hessians for all the reaction species you should check the Calculate partition functions checkbox on the CASTEP Transition State Search dialog. This setting causes vibrational frequencies to be evaluated for reactant, product, and transition state structures. A partial Hessian will be used if there are constrained atoms in the system. Since the calculations rely on finite displacements, the cost can be reduced significantly by fixing coordinates of substrate atoms that are not involved in the surface reaction itself.

The result of the transition state search is an 3D Atomistic Collection Document containing reactant, product, and transition state structures. You can select the "TS" physical system and use the Vibrational Analysis tool to verify the nature of the imaginary mode associated with the reaction.

The reaction rate coefficient can be calculated only if the transition state has exactly one imaginary frequency with its eigenvector along the reaction path.

The 3D Atomistic Collection Document generated will contain all the necessary information to perform the reaction rate calculation itself.

To set up a reaction kinetics calculation

Prepare two documents containing reactant and product structures. Set any necessary fixed atom constraints (fixed atoms should be present in both documents and should have the same coordinates).
Follow the steps required to set up transition state search calculation.
Check the Optimize reactants and products checkbox on the CASTEP Transition State Search dialog, unless you have optimized both structures prior to constructing reaction preview document.
It is recommended to select Ultra-fine for the convergence tolerance for geometry optimization by changing the task to Geometry Optimization, opening CASTEP Geometry Optimization dialog, editing convergence settings, and then changing the task again to TS Search. Such an accurate setting may be necessary to eliminate spurious imaginary modes in the vibrational analysis.
Check the Calculate partition functions checkbox on the CASTEP Transition State Search dialog.
It is recommended to impose more strict convergence criteria than the default values; lack of convergence can result in spurious imaginary modes of the transition state itself.

Setting up a reaction kinetics calculation

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