Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.

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TitlePolarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.
Publication TypeJournal Article
Year of Publication2015
AuthorsPatel, DS, He, X, Mackerell, AD
JournalJ Phys Chem B
Volume119
Issue3
Pagination637-52
Date Published2015 Jan 22
ISSN1520-5207
KeywordsCarbohydrate Conformation, Molecular Dynamics Simulation, Monosaccharides, Pyrans, Quantum Theory, Rotation, Water
Abstract

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.

DOI10.1021/jp412696m
Alternate JournalJ Phys Chem B
PubMed ID24564643
PubMed Central IDPMC4143499
Grant ListR01 GM070855 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States