CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides), and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids, and/or lipids when combined with existing CHARMM biomolecular force fields.
Hatcher
Elizabeth
E
Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21201, USA.
Guvench
Olgun
O
Mackerell
Alexander D
AD
D002236:Carbohydrate Conformation; D005632:Fructose / Q000737:chemistry*; D006027:Glycosides / Q000737:chemistry*; D008958:Models, Molecular; D010429:Pentoses / Q000737:chemistry*; D011789:Quantum Theory; D015203:Reproducibility of Results; D014867:Water / Q000737:chemistry
D006027:Glycosides; D010429:Pentoses; D014867:Water; D005632:Fructose
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