Listar QFA_Articles por autoría "e511e4af-c103-48c6-8ba4-c8d68cf0e967"
Mostrando ítems 1-10 de 10
-
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformatión for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases
Soliman, Mahmoud E. S.; Ruggiero, Giuseppe D.; Ruiz-Pernía, José Javier; Greig, Ian R.; Williams, Ian H. Royal Society of Chemistry (2009)Molecular dynamics simulations have been performed for non-covalent complexes of phenyl b-xylobioside with the retaining endo-b-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. ... -
Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water
Williams, Ian H.; Ruiz-Pernía, José Javier; Tuñón, Iñaki International Union of Pure and Applied Chemistry (2011)2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of ... -
Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution
Ruiz-Pernía, José Javier; Williams, Ian H. Wiley (2012-07)The existence of solvent fluctuations leads to populations of reactant-state (RS) and transition-state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of ... -
Influence of Dielectric Environment upon Isotope Effects onGlycoside Heterolysis: Computational Evaluation and AtomicHessian Analysis
Świderek, Katarzyna; Porter, Alexander J.; Upfold, Catherine M.; Williams, Ian H. American Chemical Society (2019-12-30)Isotope effects depend upon the polarity of the bulk medium in which a chemical process occurs. Implicit solvent calculations with molecule-shaped cavities show that the equilibrium isotope effect (EIE) for heterolysis of ... -
Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling
Świderek, Katarzyna; Tuñón, Iñaki; Williams, Ian H.; Moliner, Vicent American Chemical Society (2018-02)The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three ... -
Mechanism of glycoside hydrolysis: a comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases
Soliman, Mahmoud E. S.; Ruiz-Pernía, José Javier; Greig, Ian R.; Williams, Ian H. Royal Society of Chemistry (2009)Computational simulations have been performed using hybrid quantum-mechanical/ molecular-mechanical potentials to investigate the catalytic mechanism of the retaining endo-b-1, 4-xylanase (BCX) from B. circulans. ... -
QM/MM kinetic isotope effects for chloromethane hydrolysis in water
Ruiz-Pernía, José Javier; Ruggiero, Giuseppe D.; Williams, Ian H. John Wiley & Sons (2013)Computational simulations for chloromethane hydrolysis have been performed using hybrid quantum-mechanical/molecular-mechanical methods with explicit solvation by large numbers of water molecules. In the first part of the ... -
QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects
Kanaan Izquierdo, Natalia; Ruiz-Pernía, José Javier; Williams, Ian H. Royal Society of Chemistry (2008)Sampling of structures from QM/MM molecular dynamics reveals distinct families of reactant-state conformers and yields kinetic isotope effects for reactions in enzyme active sites and in solution, averaged over thermal ... -
Theoretical site-directed mutagenesis. The Asp168Ala mutant of L-Lactate Dehydrogenase
Moliner, Vicent; Ferrer Castillo, Silvia; Silla, Estanislao; Tuñón, Iñaki; Williams, Ian H. Royal Society (Gran Bretanya) (2008)The reduction of pyruvate to lactate catalyzed by the L-Lactate dehydrogenase has been studied in this paper by means of hybrid Quantum Mechanical / Molecular Mechanical simulations. A very flexible molecular model ... -
Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer
Roca, Maite; Williams, Ian H. American Chemical Society (2020-08-19)Isotopic partition-function ratios (IPFRs) computed for transition structures (TSs) of the methyl-transfer reaction catalyzed by catechol O-methyltransferase and modeled by hybrid QM/MM methods are analyzed. The ability ...