Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft...

We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type of interactions among molecules by representing groups of atoms within those molecules in terms of ellipsoids (rather than spheres). Our approach systematically translates an arbitrary underlying all-atom (AA) representation of a molecular system to a multisite ellipsoidal potential within the family of Gay-Berne type potentials. As the method enables arbitrary levels of coarse-graining, or even multiple levels of coarse-graining within a single simulation, we describe the method as a Level of Detail (LoD) model. The LoD model, as integrated into our group's Metropolis Monte Carlo computational package, is also capable of reducing the complexity of the molecular electrostatics by means of a multipole expansion of charges obtained from an AA force field (or directly from electronic structure calculations) of the charges within each ellipsoid. Electronic polarizability may additionally be included. The present CG representation does not include transformation of bonded interactions; ellipsoids are connected at the fully atomistic bond sites by freely rotating links that are constrained to maintain a constant distance. The accuracy of the method is demonstrated for three distinct types of self-assembling or self-organizing molecular systems: (1) the interaction between benzene and perfluorobenzene (dispersion interactions), (2) linear hydrocarbon chains (a system with large conformational flexibility), and (3) the self-organization of ethylene carbonate (a highly polar liquid). Lastly, the method is applied to the interaction of large (∼100 atom) molecules, which are typical of organic nonlinear optical chromophores, to demonstrate the effect of different CG models on molecular assembly.