title: Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.
abstract: The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA.
authors.forename: Meagan C
authors.initials: MC
authors.lastname: Small
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA.
authors.forename: Asaminew H
authors.initials: AH
authors.lastname: Aytenfisu
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA.
authors.forename: Fang-Yu
authors.initials: FY
authors.lastname: Lin
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA.
authors.forename: Xibing
authors.initials: X
authors.lastname: He
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA. alex@outerbanks.umaryland.edu.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D000447:Aldehydes / Q000737:chemistry*; D005632:Fructose / Q000737:chemistry*; D005947:Glucose / Q000737:chemistry*; D007659:Ketones / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D000447:Aldehydes; D007659:Ketones; C003243:psicose; D005632:Fructose; C002055:allose; D005947:Glucose
keywords: CHARMM; Electronic polarization; Glycan; Molecular dynamics; Molecular mechanics; Potential energy function