Miller Thomas F, Vanden-Eijnden Eric, Chandler David
Department of Chemistry, University of California, Berkeley, CA 94720, USA.
Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14559-64. doi: 10.1073/pnas.0705830104. Epub 2007 Aug 28.
With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm)(3) cubes and projecting the atomistic water molecule positions onto this grid. With the coarse-grained field thus defined, the string method in collective variables was used to compute a minimum free-energy pathway (MFEP) for the collapsing chain. These calculations provide a proof of principle for a coarse-grained description of water solvent. Furthermore, the calculated MFEP characterizes the mechanism for the collapse of the hydrated chain by providing a path of maximum likelihood for dynamical trajectories. The reliability of the calculated MFEP was confirmed with the use of conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.
通过对超过10万个原子进行计算机模拟,用边长为0.2纳米的立方体平铺空间,并将原子级水分子位置投影到该网格上,得出了理想化水合链疏水塌缩的机制。在如此定义的粗粒度场中,使用集体变量中的弦方法来计算塌缩链的最小自由能路径(MFEP)。这些计算为水溶剂的粗粒度描述提供了原理证明。此外,计算出的MFEP通过为动力学轨迹提供最大似然路径,表征了水合链塌缩的机制。通过使用传统分子动力学轨迹,证实了计算出的MFEP的可靠性。对MFEP的分析为ten Wolde和Chandler提出的疏水塌缩机制提供了原子层面的确认。特别是,我们表明长度尺度依赖性疏水去湿是所考虑链疏水塌缩中的限速步骤。