title: A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons.
abstract: Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge-on-spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united-atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self-diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force-field parameters for CH2, CH3, and CH4 moieties.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland.
authors.forename: Oliwia M
authors.initials: OM
authors.lastname: Szklarczyk
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland.
authors.forename: Stephan J
authors.initials: SJ
authors.lastname: Bachmann
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland.
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D003510:Cyclohexanes / Q000737:chemistry; D006838:Hydrocarbons / Q000737:chemistry*; D008055:Lipids / Q000737:chemistry; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D003510:Cyclohexanes; D006838:Hydrocarbons; D008055:Lipids; D011506:Proteins; C506365:Cyclohexane
keywords: COS model; GROMOS; dielectric permittivity; hydrocarbons; molecular dynamics; polarization