Molecular dynamics simulation of the proton transport in water

Classical Molecular Dynamics with Mobile Protons

An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

Noncontact dipole effects on channel permeation. III. Anomalous proton conductance effects in gramicidin

Proton transport on water wires, of interest for many problems in membrane biology, is analyzed in side-chain analogs of gramicidin A channels. In symmetrical 0.1N HCl solutions, fluorination of channel Trp(11), Trp-(13), or Trp(15) side chains is found to inhibit proton transport, and replacement of one or more Trps with Phe enhances proton transport, the opposite of the effects on K(+) transport in lecithin bilayers. The current-voltage relations are superlinear, indicating that some membrane field-dependent process is rate limiting. The interfacial dipole effects are usually assumed to affect the rate of cation translocation across the channel. For proton conductance, however, water reorientation after proton translocation is anticipated to be rate limiting. We propose that the findings reported here are most readily interpreted as the result of dipole-dipole interactions between channel waters and polar side chains or lipid headgroups. In particular, if reorientation of the water column begins with the water nearest the channel exit, this hypothesis explains the negative impact of fluorination and the positive impact of headgroup dipole on proton conductance.

Special pair dance and partner selection: elementary steps in proton transport in liquid water

Conditional and time-dependent radial distribution functions reveal the details of the water structure surrounding the hydronium during the proton mobility process. Using this methodology for classical multistate empirical valence bond (MS-EVB) and ab initio molecular dynamics trajectories, as well as quantal MS-EVB trajectories, we supply statistical proof that proton hops in liquid water occur by a transition from the H3O+[3H2O] Eigen-complex, via the H5O2+ Zundel-complex, to a H3O+[3H2O] centered on a neighboring water molecule. In the "resting period" before a transition, there is a distorted hydronium with one of its water ligands at a shorter distance and another at a longer distance than average. The identity of this "special partner" interchanges rapidly within the three first-shell water ligands. This is coupled to cleavage of an acceptor-type hydrogen bond. Just before the transition, a partner is selected by an additional translation of the H3O+ moiety in its direction, possibly enabled by loosening of donor-type hydrogen bonds on the opposite side. We monitor the transition in real time, showing how the average structure is converted to a distorted H5O2+ cation constituting the transitional complex for proton hopping between water molecules.

Theoretical models of directional proton molecular transport

The important topic of proton transport through molecular wires is usually associated with the Grotthuss mechanism. In this paper we propose an alternative conductor based on chains of lone pairs. B3LYP/6-31+G** and PW91 DFT calculations on model compounds (1,2,3,4-tetrasubstituted benzenes) show that these compounds could play the role of proton conductors.