ArticleJournal of chemical theory and computation2024
Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Discovery of a cryptic aminoacidic triad involved in the temperature adaptation of GH1 enzymes.The FEBS journal · 2026Article
- Thermodynamic Activation Parameters for Chemical Reactions in Enzymes and Solution from Computer Simulations at a Single Temperature.Journal of chemical theory and computation · 2026Article
- Computer Simulations of the Temperature Dependence of Enzyme Reactions.Journal of chemical theory and computation · 2025Review
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2 authors.
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Abstract
Computer simulations of the temperature dependence of enzyme reactions using the empirical valence bond (EVB) method have proven to give very accurate results in terms of the thermodynamic activation parameters. Here, we analyze the reasons for why such simulations are able to correctly capture activation enthalpies and entropies and how sensitive these quantities are to parametrization of the reactive potential energy function. We examine first the solution reference reaction for the enzyme ketosteroid isomerase, which corresponds to the acetate catalyzed deprotonation of the steroid in water. The experimentally determined activation parameters for this reaction turn out to be remarkably well reproduced by the calculations. By modifying the EVB potential so that the activation and reaction free energies become significantly shifted, we show that the activation entropy is basically invariant to such changes and that Δ
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