title: Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.
abstract: Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
authors.forename: Justin A
authors.identifier: http://orcid.org/0000-0001-6661-8653
authors.initials: JA
authors.lastname: Lemkul
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
authors.forename: Alexander D
authors.identifier: http://orcid.org/0000-0001-8287-6804
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D004247:DNA / Q000737:chemistry*; D044704:DNA, A-Form / Q000737:chemistry; D059371:DNA, B-Form / Q000737:chemistry; D043542:DNA, Z-Form / Q000737:chemistry; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011789:Quantum Theory
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D043542:DNA, Z-Form; D004247:DNA