Molecular Dynamics Simulations Of Organic Solvent Based On Coarse-Grained Model

This paper presents a general coarse-grained molecular mechanics model based on electric multipole expansion potential and Gay-Berne (GB) potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic GB function. The charge distribution is represented by electric multipole expansion, including point charge, dipole moment, and quadrupole moment placed at the center of mass. In order to obtain the GB parameters, we firstly make Monte Carlo sampling for four reference configurations based on the Boltzmann distribution. After comparing with the van der Waals potential within the all-atom model, we get the GB parameters. Also after making the fitting of charge, dipole moment, and quadrupole moment with the electric potential obtained from the quantum chemical computations with Gaussian03, we get the electric multipole potential parameters.With the GB-EMP parameters, then, we make the molecular dynamics simulations (MDS) for six kinds of organic solvents, namely, CHCl₃, CH₂Cl₂, C₅H₅N, DMF, DMSO and THF based on the coarse-grained model (CGM), and make comparison with the results within the all-atom model. The CGM can reproduce, on the whole, the results within the all-atom model, but there are some deviations in the simulations within the CGM, in some details, compare with the all-atom model. For the reason, it is because that we only take account of one interaction site in present work. So for the molecules with more complicated, It is necessary to take account how to place the interaction sites, and the situation with multi-sites when one do the MDS within the frame of coarse-grained model. The main advantages of molecular dynamics simulations based on this CGM is that accuracy can be guaranteed. It is more significantly that we can improve the computational efficiency at the same time. Primarily this is due to the use of the GB-EMP interaction instead of pairs of interactions between atoms, making the number of degree of freedom has been greatly reduced. Also another important factor is the neglect of the high-frequency motion of bond, angle and torsion. It increases the simulation time scale. We need to note that the introduction of the dw parameter can give greater control over the"softness"the GB potential. So the CGM in this paper can also be used to simulate more complex molecules. In addition, this CGM can describe the electrostatic potential accurately. We can apply it to a broad range of molecular systems including highly charged biopolymers.