Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
J Phys Chem B. 2013 Jun 27;117(25):7546-53. doi: 10.1021/jp403719g. Epub 2013 Jun 19.
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 Crystallogr.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 and 293 K. The calculated unit cell parameters and the intramolecular 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, the hydroxyl group of O7 is found to form bifurcated hydrogen bonds with O6 and O8 of an adjacent molecule, with the interactions dominated by the HO7-O6 interaction. Quantum mechanical calculations support this observation.
天然存在的 6-O-[(R)-1-羧乙基]-α-D-半乳糖吡喃糖的 O-甲基糖苷的结构已通过 100 K 的 X 射线晶体学确定，补充了先前在 293 K 下确定的结构（Acta Crystallogr.1996, C52, 2285-2287）。在晶体环境中对该糖苷进行了分子动力学模拟，在 100 和 293 K 下，在主模拟系统中包含不同数量的单位晶胞。计算的晶胞参数和分子内几何形状（键、角度和二面角）与实验结果吻合良好。原子波动，包括 B 因子和各向异性，在原子基础上的相对值方面具有很好的一致性。此外，波动随模拟系统尺寸的增加而增加，模拟值收敛到低于实验观察值的数值，表明模拟模型没有考虑到实验观察到的 B 因子的所有可能贡献，这可能与模拟时间尺度或尺寸有关。在模拟中，O7 上的羟基被发现与相邻分子的 O6 和 O8 形成分叉氢键，相互作用主要由 HO7-O6 相互作用决定。量子力学计算支持这一观察结果。
