Bifurcated Hydrogen Bonding and Asymmetric Fluctuations in aCarbohydrate Crystal Studied via X-ray Crystallography and Computationalanalysis

摘要

The structure of the O-methyl glycoside of the naturally occurring 6-O-[(R)-1-carboxyethyl]-α-d-galactopyranose, C10H18O8, has been determined by X-ray crystallography at 100 K, supplementing the previously determined structure obtained at 293 K (Acta Cryst., 1996, C52, 2285-2287). Molecular dynamics simulations of this glycoside were performed in the crystal environment with different numbers of units cells included in the primary simulation system at both 100 K and 293 K. The calculated unit cell parameters and the intra-molecular geometries (bonds, angles, and dihedrals) agree well with experimental results. Atomic fluctuations, including B-factors and anisotropies, are in good agreement with respect to the relative values on an atom-by-atom basis. In addition, the fluctuations increase with increasing simulation system size, with the simulated values converging to values lower than those observed experimentally indicating that the simulation model is not accounting for all possible contributions to the experimentally observed B-factors which may be related to either the simulation time scale or size. In the simulations thehydroxyl group of O7 is found to form bifurcated hydrogen bonds with O6 and O8of an adjacent molecule, with the interactions dominated by the HO7-O6interaction. Quantum mechanical calculations support this observation.