Shevchuk Roman, Agmon Noam, Rao Francesco
Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany.
Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
J Chem Phys. 2014 Jun 28;140(24):244502. doi: 10.1063/1.4884455.
Proton transfer in macromolecular systems is a fascinating yet elusive process. In the last ten years, molecular simulations have shown to be a useful tool to unveil the atomistic mechanism. Notwithstanding, the large number of degrees of freedom involved make the accurate description of the process very hard even for the case of proton diffusion in bulk water. Here, multi-state empirical valence bond molecular dynamics simulations in conjunction with complex network analysis are applied to study proton transfer in liquid water. Making use of a transition network formalism, this approach takes into account the time evolution of several coordinates simultaneously. Our results provide evidence for a strong dependence of proton transfer on the length of the hydrogen bond solvating the Zundel complex, with proton transfer enhancement as shorter bonds are formed at the acceptor site. We identify six major states (nodes) on the network leading from the "special pair" to a more symmetric Zundel complex required for transferring the proton. Moreover, the second solvation shell specifically rearranges to promote the transfer, reiterating the idea that solvation beyond the first shell of the Zundel complex plays a crucial role in the process.
质子在大分子体系中的转移是一个引人入胜却又难以捉摸的过程。在过去十年中，分子模拟已被证明是揭示原子机制的有用工具。尽管如此，即使对于质子在 bulk 水中扩散的情况，所涉及的大量自由度也使得准确描述该过程变得非常困难。在此，将多态经验价键分子动力学模拟与复杂网络分析相结合，用于研究液态水中的质子转移。利用过渡网络形式，这种方法同时考虑了多个坐标的时间演化。我们的结果表明，质子转移强烈依赖于溶剂化 Zundel 络合物的氢键长度，随着在受体位点形成更短的键，质子转移增强。我们在网络上识别出从“特殊对”到转移质子所需的更对称 Zundel 络合物的六个主要状态（节点）。此外，第二溶剂化层会特异性重排以促进转移，这再次强调了 Zundel 络合物第一溶剂化层之外的溶剂化在该过程中起着关键作用的观点。
