title: Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations.
abstract: The thermodynamics and kinetics of enzymatically assisted reactions of carbon acids were studied theoretically in this work. Quantum electronic (QE) structure calculations and steered molecular dynamics (SMD) simulations were carried out. Three 3-butenal tautomerization reactions that proceed from the β,γ-unsaturated reactant (R) to the α,β-unsaturated carbon acid product (P) and occur in two elementary steps through an intermediate (I) were studied, ignoring or including the surrounding aqueous medium in the calculations. The Gibbs free energies of activation of the R ⇆ I enolization and I ⇆ P ketonization steps were found to decrease considerably when residues simulating enzymes were introduced into these processes. Although the processes became slightly more favorable thermodynamically when the solution was included in the simulations, they became less favorable kinetically. The results from SMD simulations of these reactions were qualitatively consistent with the values we obtained using QE as well as those found by other authors in similar studies. Our simulations also allowed us to perform a detailed study of these reactions in solution.
authors.affiliation: Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain. santi@unex.es.
authors.forename: Santiago
authors.initials: S
authors.lastname: Tolosa
authors.affiliation: Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Hidalgo
authors.affiliation: Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain.
authors.forename: Jorge A
authors.initials: JA
authors.lastname: Sansón
mesh_terms: D000465:Algorithms; D002255:Carbonic Acid / Q000737:chemistry*; D002384:Catalysis; D008962:Models, Theoretical; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012996:Solutions; D013816:Thermodynamics
chemical_list: D012996:Solutions; D002255:Carbonic Acid
keywords: Enzymatic reactions in solution; Quantum electronic calculations; SMD simulations
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