Nada Hiroki
National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 305-8569, Japan.
Sci Rep. 2020 Mar 13;10(1):4708. doi: 10.1038/s41598-020-61773-x.
The mechanism of how ice crystal form has been extensively studied by many researchers but remains an open question. Molecular dynamics (MD) simulations are a useful tool for investigating the molecular-scale mechanism of crystal formation. However, the timescale of phenomena that can be analyzed by MD simulations is typically restricted to microseconds or less, which is far too short to explore ice crystal formation that occurs in real systems. In this study, a metadynamics (MTD) method was adopted to overcome this timescale limitation of MD simulations. An MD simulation combined with the MTD method, in which two discrete oxygen-oxygen radial distribution functions represented by Gaussian window functions were used as collective variables, successfully reproduced the formation of several different ice crystals when the Gaussian window functions were set at appropriate oxygen-oxygen distances: cubic ice, stacking disordered ice consisting of cubic ice and hexagonal ice, high-pressure ice VII, layered ice with an ice VII structure, and layered ice with an unknown structure. The free-energy landscape generated by the MTD method suggests that the formation of each ice crystal occurred via high-density water with a similar structure to the formed ice crystal. The present method can be used not only to study the mechanism of crystal formation but also to search for new crystals in real systems.
冰晶形成的机制已被许多研究人员广泛研究,但仍是一个悬而未决的问题。分子动力学(MD)模拟是研究晶体形成分子尺度机制的有用工具。然而,MD模拟能够分析的现象的时间尺度通常限制在微秒或更短,这对于探索实际系统中发生的冰晶形成来说太短了。在本研究中,采用了元动力学(MTD)方法来克服MD模拟的这一时间尺度限制。将MD模拟与MTD方法相结合,其中由高斯窗函数表示的两个离散氧-氧径向分布函数用作集体变量,当高斯窗函数设置在适当的氧-氧距离时,成功再现了几种不同冰晶的形成:立方冰、由立方冰和六方冰组成的堆积无序冰、高压冰VII、具有冰VII结构的层状冰以及结构未知的层状冰。MTD方法生成的自由能景观表明,每种冰晶的形成都是通过与形成的冰晶结构相似的高密度水发生的。本方法不仅可用于研究晶体形成机制,还可用于在实际系统中寻找新的晶体。