Empirical valence bond
In theoretical chemistry, the Empirical Valence Bond (EVB) approach is an approximation for calculating free-energies of a chemical reaction in condensed-phase. It was first developed by Israeli chemist Arieh Warshel.[1]
This approach can be considered as simplification of the quantum mechanical Valence Bond method in a way that was inspired by the work of Coulson and Danielson, However, the main difference is that the EVB generates potential surfaces from a calibrated Hamiltonian that incorporates the effect of the environment (e.g. the solvent) in a physically rigorous way, as well as provides a rigorous and effective way of obtaining the free energy surface booth in the diabatic and adiabatic representations. This generates microscopic diabatic parabolas that may look like the phenomenological Marcus parabolas (Marcus Theory ) but are obtained from physically based simulations and are used with a typically large mixing term (unlike the case in electron transfer reactions) to generate the adiabatic ground state free energy surface.[2]
Where most methods for reaction free-energy calculations require at least some part of the modeled system to be treated using quantum mechanics, EVB uses a calibrated Hamiltonian to approximate the potential energy surface of a reaction. For a simple 1-step reaction, that typically means that a reaction is modeled using 2 states. These states are valence bond descriptions of the reactants and products of the reaction. The function that gives the ground energy then becomes:
where H11 and H22 are the valence bond descriptions of the reactant and product state respectively, and H12 is the coupling parameter. The H11 and H22 potentials are usually modeled using force field descriptions Ureactants and Uproducts. H12 is a bit trickier as it needs to be parameterized using a reference reaction. This reference reaction can be experimental, typically from a reaction in water or other solvents. Alternatively quantum chemical calculations can be used for calibration.
Free energy calculations
To obtain free-energies from the created ground state energy potential one needs to perform sampling. This can be done using sampling methods like molecular dynamics or Monte Carlo simulations at different states along the reaction coordinates. Typically this is done using a free energy perturbation / umbrella sampling approach.[3]
Application
EVB has been successfully applied to calculating reaction free energies of enzymes.[3] More recently it has been looked at as a tool to study enzyme evolution[4] and to assist in enzyme design.[5]
Software
- Molaris
- Q
- RAPTOR (Rapid Approach for Proton Transport and Other Reactions)
See also
References
- ^ Warshel, Arieh; Weiss, Robert M. (September 1980). "An empirical valence bond approach for comparing reactions in solutions and in enzymes". Journal of the American Chemical Society. 102 (20): 6218–6226. Bibcode:1980JAChS.102.6218W. doi:10.1021/ja00540a008. ISSN 0002-7863.
- ^ Orgel, Leslie E. (1959-01-01). "The Hydrogen Bond". Reviews of Modern Physics. 31 (1): 100–102. doi:10.1103/RevModPhys.31.100. ISSN 0034-6861.
- ^ a b Warshel, Arieh. (1991). Computer modeling of chemical reactions in enzymes and solutions. New York: Wiley. ISBN 0-471-53395-5. OCLC 23016681.
- ^ Åqvist, Johan; Isaksen, Geir Villy; Brandsdal, Bjørn Olav (July 2017). "Computation of enzyme cold adaptation". Nature Reviews Chemistry. 1 (7): 0051. doi:10.1038/s41570-017-0051. ISSN 2397-3358.
- ^ Frushicheva, Maria P; Mills, Matthew JL; Schopf, Patrick; Singh, Manoj K; Prasad, Ram B; Warshel, Arieh (August 2014). "Computer aided enzyme design and catalytic concepts". Current Opinion in Chemical Biology. 21: 56–62. doi:10.1016/j.cbpa.2014.03.022. PMC 4149935. PMID 24814389.