Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
J Phys Chem B. 2010 Oct 7;114(39):12501-7. doi: 10.1021/jp105549s.
Proper simulation of dynamic properties, including molecular diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the experimental viscosity of water. Consequently, scaling of simulated diffusion constants of solutes in aqueous solutions is required to effectively compare them with experiment. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concentration dependence of simulated and experimental solution viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concentration dependence of simulated viscosities lags that of experiment, and scaling is not advised. Scaled translational diffusion constants for glucose and the disaccharides trehalose, maltose, and melibiose at low concentration agree nearly quantitatively with experiment, as do NMR (13)C T(1)'s for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concentration. At high concentrations the scaled diffusion constants for glucose and trehalose underestimate and overestimate experiment, respectively. Hydrodynamic bead model calculations indicate a hydration level of approximately 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the analysis.
正确模拟动态特性,包括分子扩散,是经验力场的重要目标。然而,广泛使用的 TIP3P 水模型无法再现水的实验粘度。因此,需要对水溶液中溶质的模拟扩散常数进行缩放,以便有效地将其与实验进行比较。有人提出,在模拟和实验溶液粘度的浓度依赖性平行的情况下,按模型和实际水的粘度比进行缩放是合适的。采用这种方法,可以对 CHARMM 添加剂碳水化合物力场 C35 和 TIP3P 水进行模拟,将葡萄糖和海藻糖的粘度缩放至 20wt%;超过这个值,模拟粘度的浓度依赖性滞后于实验,不建议进行缩放。在低浓度下,葡萄糖和二糖海藻糖、麦芽糖和棉子糖的平移扩散常数与实验几乎完全一致,葡萄糖、海藻糖和麦芽糖的 NMR(13)C T(1)'也符合实验值;这些结果支持在低浓度下使用 C35 模拟糖转运性质。在高浓度下,葡萄糖和海藻糖的缩放扩散常数分别低估和高估了实验值。水动力珠模型计算表明,葡萄糖的水合水平约为 1 个水/羟基。对于二糖,模式则更为复杂,尽管海藻糖的水合程度比麦芽糖多 0.5 到 1,具体取决于分析。