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. 2017 Apr;31(4):349-363.
doi: 10.1007/s10822-017-0010-0. Epub 2017 Feb 11.

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

Meagan C Small  1 , Asaminew H Aytenfisu  1 , Fang-Yu Lin  1 , Xibing He  1 , Alexander D MacKerell Jr  2
Affiliations

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

Meagan C Small et al. J Comput Aided Mol Des. 2017 Apr.

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.

Keywords: CHARMM; Electronic polarization; Glycan; Molecular dynamics; Molecular mechanics; Potential energy function.

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Conflict of interest statement

Conflict of Interest: ADM Jr., is co-founder and Chief Scientific Officer of SilcsBio LLC.

Figures

Figure 1
Figure 1
Model compound ketones and aldehydes: acetone (ACO), butanone (BTON), acetaldehyde (AALD), propionaldehyde (PALD), butyraldehyde (BALD) and isobutyraldehyde (IBLD) with corresponding linear sugars D-allose and D-psicose. Methyl, methylene and linear sugar hydroxyl hydrogens are omitted for clarity.
Figure 2
Figure 2
Water interaction pairs for A) acetone (ACO), B) acetaldehyde (AALD), C) butanone (BTON) and D) propionaldehyde (PALD) corresponding to the interacting pairs in Table 2.
Figure 3
Figure 3
Dihedral potential energy scans for A) BTON and B) PALD. QM (black) and MM (red) PES are shown for dihedrals C2-C1-C3-C4 bond for BTON and O-C-CB-CG for PALD.
Figure 4
Figure 4
Dipole moments as a function of time for acetone (ACO), butanone (BTON), acetaldehyde (AALD), and propionaldehyde (PALD) in the gas phase (left column), pure liquid (middle column), and aqueous solution (right column).
Figure 5
Figure 5
Dihedral potential energy scans for D-allose. QM (black) and MM (red) PES are shown for dihedrals containing the O1-C1 bond (top) and C2-O2 bond (bottom).
Figure 6
Figure 6
2-dimensional dihedral potential energy scans for D-psicose. QM (left) and Drude surfaces (right) are shown for dihedrals containing the C1-C2 and C2-C3 bonds.
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