Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
J Chem Phys. 2012 Jul 14;137(2):024108. doi: 10.1063/1.4732514.
Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied to critically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.
利用分子动力学模拟，并结合自主研发的分裂积分辛方法，我们有效地将水分子的各个自由度解耦，并将它们与相应的恒温器连接。通过这种方式，我们可以在任何给定的旋转、平移和振动温度组合下，阐明水的结构、动力学、光谱和水合性质。研究发现，水介质的旋转温度升高会严重阻碍极性分子的水合作用，以非单调的方式影响离子物种的水合作用，并在一定程度上改善非极性物种的水合作用。由于蛋白质由带电、极性和非极性氨基酸残基组成，因此我们还应用开发的方法学来严格评估这样一种假设，即蛋白质整体水合作用的降低以及各种类型氨基酸残基水合作用之间微妙平衡的改变，为微波增强异常蛋白质折叠和聚集提供了一个合理的物理机制。
