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Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

Classical equilibrium molecular dynamics simulations have been performed to investigate the diffusive properties of inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 0.05 kbar from 200 K and up to 250-260 K. For mixed H2-THF systems in which there is single H2 occupation of the small cage (labelled "1S1L"), we found that no H2 migration occurs. However, for more densely filled H2-THF and pure-H2 systems, in which there is more than single H2 occupation in the small cage, there is an onset of inter-cage H2 migration events from the small cages to neighbouring cavities at around 200 K. The mean square displacements of the hydrogen molecules were fitted to a mathematical model consisting of an anomalous term and a Fickian component, and nonlinear regression fitting was conducted to estimate long-time (inter-cage) diffusivities. An approximate Arrhenius temperature relationship for the diffusion coefficient was examined and an estimation of the hydrogen hopping energy barrier was calculated for each system.

Extensive equilibrium molecular dynamics simulations have been performed to investigate thermal conduction mechanisms via the Green-Kubo approach for (type II) hydrogen hydrate, at 0.05 kbar and between 30 and 250 K, for both lightly filled H(2) hydrates (1s4l) and for more densely filled H(2) systems (2s4l), in which four H(2) molecules are present in the large cavities, with respective single- and double-occupation of the small cages. The TIP4P water model was used in conjunction with a fully atomistic hydrogen potential along with long-range Ewald electrostatics. It was found that substantially less damping in guest-host energy transfer is present in hydrogen hydrate as is observed in common type I clathrates (e.g., methane hydrate), but more akin in to previous results for type II and H methane hydrate polymorphs. This gives rise to larger thermal conductivities relative to common type I hydrates, and also larger than type II and H methane hydrate polymorphs, and a more crystal-like temperature dependence of the thermal conductivity., (© 2012 American Institute of Physics)

Classical equilibrium molecular dynamics simulations have been performed to investigate dynamical properties of cage radial breathing modes and intra- and inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 0.05 kbar and up to 250 K. For the mixed H(2)-THF system in which there is single H(2) occupation of the small cage (labelled "1SC 1LC"), we find that no H(2) migration occurs, and this is also the case for pure H(2) hydrate with single small-cavity occupation and quadruple occupancy for large cages (dubbed "1SC 4LC"). However, for the more densely filled H(2)-THF and pure-H(2) systems, in which there is double H(2) occupation in the small cage (dubbed "2SC 1LC" and "2SC 4LC," respectively), there is an onset of inter-cage H(2) migration events from the small cages to neighbouring cavities at around 200 K, with an approximate Arrhenius temperature-dependence for the migration rate from 200 to 250 K. It was found that these "cage hopping" events are facilitated by temporary openings of pentagonal small-cage faces with the relaxation and reformation of key stabilising hydrogen bonds during and following passage. The cages remain essentially intact up to 250 K, save for transient hydrogen bond weakening and reformation during and after inter-cage hydrogen diffusion events in the 200-250 K range. The "breathing modes," or underlying frequencies governing the variation in the cavities' radii, exhibit a certain overlap with THF rattling motion in the case of large cavities, while there is some overlap of small cages' radial breathing modes with lattice acoustic modes., (© 2012 American Institute of Physics)

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types. [ABSTRACT FROM AUTHOR]

The intra-cage behaviour of guest H2 and D2 molecules in doubly occupied 51264 cages in structure-II (sII) clathrate hydrates were investigated using classical and path-integral molecular dynamics at 100 K. We probed the structure of tetrahedral sites, proton vibrations, localised molecular rattling timescales at sites, and the jump-diffusion travel of H2 and D2 molecules between sites. The site-diffusion model was correlated with experimental neutron scattering data, and the cage occupancies were then discussed in light of recent state-of-the-art experimental and theoretical findings in the literature. [ABSTRACT FROM AUTHOR]

The one-dimensional Schrödinger equation, applied to the H2 intramolecular stretch coordinate in singly to quadruply occupied large cages in extended Type II (sII) hydrogen clathrate hydrate, was solved numerically herein via potential-energy scans from classical molecular dynamics (MD), employing bespoke force-matched H2–water potential. For both occupation cases, the resultant H–H stretch spectra were redshifted by ~350 cm−1 vis-à-vis their classically sampled counterparts, yielding semi-quantitative agreement with experimental Raman spectra. In addition, ab initio MD was carried out systematically for different cage occupations in the extended sII hydrate to assess the effect of differing intra-cage intrinsic electric field milieux on H–H stretch frequencies; we suggest that spatial heterogeneity of the electrostatic environment is responsible for some degree of peak splitting. [ABSTRACT FROM AUTHOR]

The grand challenges in renewable energy lie in our ability to comprehend efficient energy conversion systems, together with dealing with the problem of intermittency via scalable energy storage systems. Relatively little progress has been made on this at grid scale and two overriding challenges still need to be addressed: (i) limiting damage to the environment and (ii) the question of environmentally friendly energy conversion. The present review focuses on a novel route for producing hydrogen, the ultimate clean fuel, from the Sun, and renewable energy source. Hydrogen can be produced by light-driven photoelectrochemical (PEC) water splitting, but it is very inefficient; rather, we focus here on how electric fields can be applied to metal oxide/water systems in tailoring the interplay with their intrinsic electric fields, and in how this can alter and boost PEC activity, drawing both on experiment and non-equilibrium molecular simulation. [ABSTRACT FROM AUTHOR]

• Externally-applied electric fields are shown to boost photo-electrochemical water splitting under certain conditions. • Study of both static and oscillating electric fields. • Experimental and molecular-simulation evidence. • Quantification of AC- and DC-field effects on number of water-lysis events. Given that conversion efficiencies of incident solar radiation to liquid fuels, e.g. , H 2 , are of the order of a few percent or less, as quantified by 'solar to hydrogen' (STH), economically inexpensive and operationally straightforward ways to boost photo-electrochemcial (PEC) H 2 production from solar-driven water splitting are important. In this work, externally-applied static electric fields have led to enhanced H 2 production in an energy-efficient manner, with up to ~30–40% increase in H 2 (bearing in mind field-input energy) in a prototype, open-type solar cell featuring rutile/titania and hematite/iron-oxide (Fe2O 3), respectively, in contact with an alkaline aqueous medium (corresponding to respective relative increases of STH by ~12 and 16%). We have also performed non-equilibrium ab-initio molecular dynamics in both static electric and electromagnetic (e/m) fields, for water in contact with a hematite/iron-oxide (0 0 1) surface, observing enhanced break-up of water molecules, by up to ~70% in the linear-response régime. We discuss the microscopic origin of such enhanced water-splitting, based on experimental and simulation-based insights. In particular, we external-field direction at the hematite surfaces, and scrutinise properties of the adsorbed water molecules and OH– and H 3 O+ species, e.g. , hydrogen bonds between water-protons and the hematite surfaces' bridging oxygen atoms, as well as interactions between oxygen atoms in adsorbed water molecules and underlying iron atoms. [ABSTRACT FROM AUTHOR]

Quartz, as the most stable low-pressure polymorph of silica (SiO 2 ), is widely abundant in Earth's crust and mantle, exhibiting relatively high chemical stability. Although silica is only slightly soluble in water at ambient conditions, producing silicon-based weakly acidic compounds, Shinozaki et al. (2014) have shown recently that water itself can be formed by dissolution of SiO 2 in H 2 fluid under high- temperature and pressure conditions. Here, we have simulated this process via molecular-dynamics techniques based on a reactive force-field description of the Si O 2 / H 2 interface. Diffusion of the H 2 fluid into the quartz crystal lattice was observed upon increasing temperature and pressure, followed by interaction of dissociated, atomic hydrogen with oxygen atoms in the SiO 2 lattice, disrupting the lattice and leading to the formation of water. Interestingly, water is evolved in the subsurface region of the silica, and it remains confined there, isolated from the hydrogen fluid, which corresponds precisely to the ice-like spectroscopic patterns observed experimentally. The over-pressured water formed from quartz and H 2 is a possible trigger for nucleating enigmatic deep earthquakes in the continental mantle lithosphere. [ABSTRACT FROM AUTHOR]