IFLYSIB   05383
INSTITUTO DE FISICA DE LIQUIDOS Y SISTEMAS BIOLOGICOS
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
LAM: An enhanced Acetonitrile model for Molecular Dynamics studies
Autor/es:
CARLOS LLERENA SUSTER; H. ARIEL ALVAREZ; ANDRÉS N. MCCARTHY
Lugar:
Universidad Nacional de Quilmes
Reunión:
Congreso; 1er Congreso Argentino de Bioinformática y Biología Computacional; 2010
Institución organizadora:
Asociación Argentina de Bioinformática y Biología Computacional
Resumen:
Acetonitrile (C2H3N: methyl cyanide) is a common solvent in many different processes, both for industrial purposes and laboratory studies. Its low viscosity and low chemical reactivity make it a popular choice for liquid chromatography. Acetonitrile plays an important role as the main solvent used in the manufacture of DNA oligonuleotides from monomers. Furthermore, it has been used successfully in the study of enzymes, which mostly maintain their biological activity in this aprotic medium. However, detailed knowledge of how it interacts with these (and other) biological macromolecules still eludes us.Computational methods with atomic scale precision, including molecular dynamics, represent interesting techniques that could provide new data to understand these processes with more detail.In recent years several computer models for Acetonitrile have been developed [1,2,3,4]. Each one of them has major and minor aspects of coincidence with the experimental data. However, none of them is suitable for long computational studies, since their design is expensive in computational time, mainly due to the fact that they all become unstable when subjected to calculations using larger integration steps than 2fs (femtoseconds).In this work, we present a model for Acetonitrile that offers a fully comparable behavior with any of the other four benchmark models but whose behavior is stable and reliable for integration steps up to 4fs. With the purpose of comparing the behavior of the models enthalpy of vaporization, density, self-diffusion coefficient, shear viscosity, dielectric permitivity and isobaric heat capacity were calculated. References:[1] D.M.F. Edwards, P.A. Madden, I.R. McDonald. Mol. Phys., 51, 1141 (1984).[2] W.L. Jorgensen, J.M. Briggs. Mol. Phys., 63, 547 (1988).[3] E. Guardia, R. Pinzon, J. Casulleras, M. Orozco, F.J. Luque. Mol. Simulation, 26, 287 (2001).[4] P. J. Gee and W. F. van Gunsteren. Molecular Physics, Vol. 104, No. 3, 477-483 (2006).