Collective hydrogen-bond rearrangement dynamics in liquid water

Abstract

We investigate barrier-crossing processes corresponding to collective hydrogen-bond rearrangements in liquid water using Markov state modeling techniques. The analysis is based on trajectories from classical molecular dynamics simulations and accounts for the full dynamics of relative angular and separation coordinates of water clusters and requires no predefined hydrogen bond criterium. We account for the complete 12-dimensional conformational subspace of three water molecules and distinguish five well-separated slow dynamic processes with relaxation times in the picosecond range, followed by a quasi-continuum spectrum of faster modes. By analysis of the Markov eigenstates, these processes are shown to correspond to different collective interchanges of hydrogen-bond donors and acceptors. Using a projection onto hydrogen-bond states, we also analyze the switching of one hydrogen bond between two acceptor water molecules and derive the complete transition network. The most probable pathway corresponds to a direct switch without an intermediate, in agreement with previous studies. However, a considerable fraction of paths proceeds along alternative routes that involve different intermediate states with short-lived alternative hydrogen bonds or weakly bound states.

Graph dynamical networks for unsupervised learning of atomic scale dynamics in materials

“…We have developed a general approach, GDyNets, to understand the atomic scale dynamics in material systems. Despite being widely used in biophysics 31 , fluid dynamics 39 , and kinetic modeling of chemical reactions 40–42 , Koopman models, (or Markov state models 31 , master equation methods 43,44 ) have not been used in learning atomic scale dynamics in materials from MD simulations except for a few examples in understanding solvent dynamics 45–47 . Our approach also differs from several other unsupervised learning methods 48–50 by directly learning a linear Koopman model from MD data.…”

Time-Dependent Friction Effects on Vibrational Infrared Frequencies and Line Shapes of Liquid Water

“…One discerns the stretch band (around 3300 cm –1 for H 2 O and 2400 cm –1 for D 2 O in the aiMD results) and the bend band (at 1650 cm –1 for H 2 O and 1200 cm –1 for D 2 O). The librational absorption band is produced by a large number of different intermolecular vibrational modes 47 that are dominated by rotational vibrations of water molecules in their hydrogen-bond environment (around 700 cm –1 for H 2 O and 550 cm –1 for D 2 O) and by translational vibrations of water molecules against each other around 200 cm –1 for both H 2 O and D 2 O. The agreement between the absorption spectra from aiMD simulations, which fully account for electronic and nuclear polarizations, and from experiments is good, which suggests that the chosen simulation method is well-suited for modeling IR spectra, although the agreement is known to be partly due to a cancellation of approximations in the employed density functional theory (DFT) and the neglect of nuclear quantum effects.…”

Time-dependent friction effects on vibrational infrared frequencies and line shapes of liquid water

“…One discerns the stretch band (around 3300 cm −1 for H 2 O and 2400 cm −1 for D 2 O in the aiMD results) and the bend band (at 1650 cm −1 for H 2 O and 1200 cm −1 for D 2 O). The librational band is produced by a large number of different intermolecular vibrational modes [46] that are dominated by rotational vibrations of water molecules in their hydrogen-bond environment (around 700 cm −1 for H 2 O and 550 cm −1 for D 2 O) and by translational vibrations of water molecules against each other around 200 cm −1 for both H 2 O and D 2 O. The agreement between aiMD simulations, which fully account for electronic and nuclear polarizations, and experimental spectra is good, which suggests that the chosen simulation method is well suited for modeling IR spectra, although the agreement is known to be partly due to a cancellation of approximations in the employed density functional theory (DFT) and the neglect of nuclear quantum effects [47,48].…”