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AG Tavan - Projects
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Polarizable force fields for molecular mechanics from first principles (Protein dynamics in their native environment) Molecular mechanical (MM) force fields treat atoms as point masses. Forces are derived from semi-empirical potentials that approximate the chemical and electrostatic interactions. Parameters for the potentials are usually derived from quantum mechanical calculations and experiments at various molecular configurations. Classical force fields like i.e. CHARMM [1] use fixed partial charges to describe the Coulomb interactions between molecules and distant parts of large molecules. The choice of values for these charges mimics polarization effects within the average electric field exerted by the environment on a given molecule. For isotropic and homogeneous fluids this mean field approximation may be adequate. However, for amino acids in proteins a fixed parameter set cannot account for the specific and diverse electric environments experienced by these building blocks. Despite the impressive progress in molecular dynamics methods, which calculate forces quantum mechanically (QM) during simulations [2], applications to long-time dynamics of large molecular systems remain computationally unfeasable. In this project, classical force fields including the molecular polarizability are calculated using QM density functional theory and QM/MM hybrid methods. [1] "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations" Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus, J. Comp. Chem., 4(2):187-217, 1983. [2] "Structural, electronic, and bonding properties of liquid water from first principles" P. L. Silvestrelli and M. Parrinello, J. Chem. Phys., 111:3572-3580, 1999.
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Letzte Änderung: 2023-10-31 16:51
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