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Research Group - Medium Effects - web page of the group www.uv.es/efme
Use of continuum models and QM/MM molecular dynamics simulations to study chemical reactions and equilibria in water solution.
Analysis of Potential Energy Surfaces and Free Energy Profiles in the active site of enzymes. To get an insight into the origin of enzymes catalytic power, the enzymatic process is compared with its counterpart in aqueous solution. We have studied chemical reactions catalyzed by Bacillus Subtilis Chorismate Mutase, Cathecolate O-Methyl Transferase, Haloalkane Dehalogenase ... Animation of a Reactive Trajectory
in Chalcone Isomerase
Snapshot of Transition Structure in the BsCM active site
2006 Cover in Chemical Communications
(Potential Energy Surface Exploration of LDH)
This includes the develpoment of new QM/MM couplings, stationary structures searching methods and correction methods for semiempirical Potentials of Mean Force. (see J. Phys. Chem. B, 108, 8427-8433 (2004) & J. Chem. Theor. Comput., 1, 1008-1016 (2005) )
Recent significant papers: Theoretical Study of Phosphodiester Hydrolysis in Nucleotide Pyrophosphatase/Phosphodiesterase. Environmental Effects on the Reaction Mechanism
Violeta López-Canut, Maite Roca, Juan
Bertr
J. Am. Chem. Soc., 2010, 132 (20),
pp 6955–6963
Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris
Juan Aranda, Maite Roca, Violeta López-Canut and Iñaki
Tuñón
J. Phys. Chem. B, 2010, 114 (25),
pp 8467–8473
Predicting an Improvement of Secondary Catalytic Activity of Promiscuos Isochorismate Pyruvate Lyase by Computational Design
Sergio Martí, Juan Andrés, Vicent Moliner, Estanislao Silla,
Iñaki Tuñón, and Juan Bertrán
J. Am. Chem. Soc., 2008, 130 (10),
pp 2894–2895
A Theoretical Analysis of Rate Constants and Kinetic Isotope Effects Corresponding to Different Reactant Valleys in Lactate Dehydrogenase
Silvia Ferrer, Iñaki Tuñón, Sergio Martí, Vicente Moliner,
Mireia Garcia-Viloca, Àngels González-Lafont, and José M. Lluch
J. Am. Chem. Soc., 2006, 128 (51),
pp 16851–16863
Predicting an Improvement of Secondary Catalytic Activity of Promiscuos Isochorismate Pyruvate Lyase by Computational Design
Sergio Martí, Juan Andrés, Vicent Moliner, Estanislao Silla,
Iñaki Tuñón, and Juan Bertrán
J. Am. Chem. Soc., 2008, 130 (10),
pp 2894–2895
Coupling between Protein and Reaction Dynamics in Enzymatic Processes:
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