CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.

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TitleCHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.
Publication TypeJournal Article
Year of Publication2015
AuthorsJana, M, Mackerell, AD
JournalJ Phys Chem B
Volume119
Issue25
Pagination7846-59
Date Published2015 Jun 25
ISSN1520-5207
KeywordsComputer Simulation, Gases, Models, Molecular, Pentoses, Pressure, Quantum Theory, Static Electricity, Temperature, Water
Abstract

An empirical all-atom CHARMM polarizable force filed for aldopentofuranoses and methyl-aldopentofuranosides based on the classical Drude oscillator is presented. A single electrostatic model is developed for eight different diastereoisomers of aldopentofuranoses by optimizing the existing electrostatic and bonded parameters as transferred from ethers, alcohols, and hexopyranoses to reproduce quantum mechanical (QM) dipole moments, furanose-water interaction energies and conformational energies. Optimization of selected electrostatic and dihedral parameters was performed to generate a model for methyl-aldopentofuranosides. Accuracy of the model was tested by reproducing experimental data for crystal intramolecular geometries and lattice unit cell parameters, aqueous phase densities, and ring pucker and exocyclic rotamer populations as obtained from NMR experiments. In most cases the model is found to reproduce both QM data and experimental observables in an excellent manner, whereas for the remainder the level of agreement is in the satisfactory regimen. In aqueous phase simulations the monosaccharides have significantly enhanced dipoles as compared to the gas phase. The final model from this study is transferrable for future studies on carbohydrates and can be used with the existing CHARMM Drude polarizable force field for biomolecules.

DOI10.1021/acs.jpcb.5b01767
Alternate JournalJ Phys Chem B
PubMed ID26018564
PubMed Central IDPMC4483154
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