title: Network analysis of proton transfer in liquid water.
abstract: 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.
authors.affiliation: Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany.
authors.forename: Roman
authors.initials: R
authors.lastname: Shevchuk
authors.affiliation: Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Noam
authors.initials: N
authors.lastname: Agmon
authors.affiliation: Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany.
authors.forename: Francesco
authors.initials: F
authors.lastname: Rao
mesh_terms: D004058:Diffusion; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D011522:Protons; D014867:Water