Research Group - Medium Effects -

Members (and former members):

            e-mail: Estanislao.Silla@uv.es

            e-mail: Juan.L.Pascual@uv.es

            e-mail: Ignacio.Tunon@uv.es

            e-mail: M.Teresa.Roca@uv.es

            e-mail: Ignacio.Tunon@uv.es

            e-mail: Alejandro.Soriano@uv.es

            e-mail: Violeta.Lopez@uv.es

            e-mail: Juan.Aranda@uv.es

            e-mail: Silvia.Ferrer@uv.es

            e-mail: J.Javier.Ruiz@uv.es

Research Interest:

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) )

Some Recent Contributions:

A recent significant paper:   

Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach
J. Javier Ruiz-Pernía, Iñaki Tuñón, Vicente Moliner, James T. Hynes, and Maite Roca
http://dx.doi.org/10.1021/ja801156y

List of Publications in pdf format (actualized up to 2005)

F. R. Tortonda, E. Silla, I. Tuñón, D. Rinaldi, M. F. Ruiz-López . Intramolecular Proton Transfer of Serine in Aqueous Solution. Mechanism and Energetics. Theor. Chem. Acc., 104, 89-95 (2000).

I. Tuñón, E. Silla, M. F. Ruiz-López . On the Tautomerization Process of Glycine in Aqueous Solution. Chem. Phys. Letters, 321, 433-437 (2000). [Abstract]  

S.Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán . A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. J. Phys. Chem. B, 104, 11308-11315 (2000). 

S.Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán . Transition Structure Selectivity in Enzyme catalysis. A QM/MM Study of Chorismate Mutase . Theor. Chem. Acc., 105, 207-212 (2001).

S.Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán. M. J. Field . A Hybrid Potential Reaction Path and Free Energy Study of the Chorismate Mutase Reaction. J. Am. Chem. Soc., 123, 1709-1712 (2001). 

R. Castillo, E. Silla, I. Tuñón . The Role of Protein Flexibility in Enzymatic Catalysis. A QM/MM Study of the Deacylation Reaction in Class A ß-Lactamases . J. Am. Chem. Soc. 124, 1809-1816 (2002). [Abstract]

A. Soriano, E. Silla, I. Tuñón . Quantum Mechanics-Molecular Mechanics Study of Dissociative Electron Transfer: The Methylchloride Radical Anion in Aqueous  Solution . J. Chem. Phys. 116, 6102-6110 (2002). [Abstract]    

N. Diaz, D. Suárez, T. L. Sordo, I. Tuñón, E. SIlla. Water-Assited Alkaline Hydrolysis of Monobactams: A Theoretical Study. Chem. Eur. J. 8, 859-867 (2002). 

S. Martí, V. Moliner, I. Tuñón, I. H. Williams. QM/MM calculations of kinetic isotope effects in the chorismate mutase active site. Org. Biomol. Chem. 1, 483-487 (2003) 

S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán. Preorganization and Reorganization as Related Factors in Enzyme Catalysis. The Chorismate Mutase Case. Chem. Eur. J. 9, 984-991 (2003). [Abstract]

F. J. Ramírez, I. Tuñón, J. A. Collado, E. Silla. Structural and Vibrational Study of the Tautomerism of Histamine Free-Base in Solution. J. Am. Chem. Soc. 125, 2328-2340 (2003). [Abstract]

M. Roca, S. Martí, J. Andrés, V. Moliner, I. Tuñón, J. Bertrán, I. H. Williams Theoretical Modelling of Enzyme Catalytic Power: Analysis of Cratic and Electrostatic Factors in Cathecol O-MethylTransferase. J. Am. Chem. Soc. 125, 7726-7737 (2003). [Abstract]