title: CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.
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.
authors.affiliation: †Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street HSF II, Baltimore, Maryland 21201, United States.|‡Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India.
authors.forename: Madhurima
authors.initials: M
authors.lastname: Jana
authors.affiliation: †Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street HSF II, Baltimore, Maryland 21201, United States.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D003198:Computer Simulation; D005740:Gases / Q000737:chemistry; D008958:Models, Molecular; D010429:Pentoses / Q000737:chemistry*; D011312:Pressure; D011789:Quantum Theory; D055672:Static Electricity; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D005740:Gases; D010429:Pentoses; D014867:Water