title: Force field development for organic molecules: modifying dihedral and 1-n pair interaction parameters.
abstract: We comprehensively illustrate a general process of fitting all-atom molecular mechanics force field (FF) parameters based on quantum mechanical calculations and experimental thermodynamic data. For common organic molecules with free dihedral rotations, this FF format is comprised of the usual bond stretching, angle bending, proper and improper dihedral rotation, and 1-4 scaling pair interactions. An extra format of 1-n scaling pair interaction is introduced when a specific intramolecular rotation is strongly hindered. We detail how the preferred order of fitting all intramolecular FF parameters can be determined by systematically generating characteristic configurations. The intermolecular Van der Waals parameters are initially taken from the literature data but adjusted to obtain a better agreement between the molecular dynamics (MD) simulation results and the experimental observations if necessary. By randomly choosing the molecular configurations from MD simulation and comparing their energies computed from FF parameters and quantum mechanics, the FF parameters can be verified self-consistently. Using an example of a platform chemical 3-hydroxypropionic acid, we detail the comparison between the new fitting parameters and the existing FF parameters. In particular, the introduced systematic approach has been applied to obtain the dihedral angle potential and 1-n scaling pair interaction parameters for 48 organic molecules with different functionality. We suggest that this procedure might be used to obtain better dihedral and 1-n interaction potentials when they are not available in the current widely used FF.
authors.affiliation: State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, People's Republic of China; College of Mechanical Science and Engineering, Jilin University, Changchun, 130022, People's Republic of China.
authors.forename: Siyan
authors.initials: S
authors.lastname: Chen
authors.forename: Shasha
authors.initials: S
authors.lastname: Yi
authors.forename: Wenmei
authors.initials: W
authors.lastname: Gao
authors.forename: Chuncheng
authors.initials: C
authors.lastname: Zuo
authors.forename: Zhonghan
authors.initials: Z
authors.lastname: Hu
keywords: force field; molecular dynamics; molecular mechanics; thermodynamics