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We study the effect of static electric fields of 0.1, 0.4, and 1.0 V/nm on the hydrogen bond structure and dynamics of TIP4P/2005 water at 1 bar and at temperatures between 300 and 200 K using molecular dynamics simulations. At all these temperatures, simulating liquid water with electric fields of 0.1 and 0.4 V/nm has no additional effect on its structural and dynamical changes, which otherwise already take place due to cooling. However, the introduction of 1.0 V/nm field enhances the slowing down of liquid water dynamics, crystallizes it to cubic ice at 240 and 220 K, and amorphizes it at 200 K. At 240 and 220 K, crystallization occurs within 5 and 50 ns, respectively. An electric field of 1 V/nm increases the relaxation times in addition to what cooling does. We note that when liquid water's metastability limit is reached, crystallization is averted and amorphization takes place. Both equilibrium (liquid-solid) and non-equilibrium (liquid-amorphous) transformations are observed at 1 V/nm. Moreover, with an increase in the electric field, H-bonds become stronger. However, the donor-acceptor asymmetry (the difference between the strengths of two donor/acceptor bonds) remains even when crystallization or amorphization takes place. At low temperatures, increasing electric fields on liquid water increases both its crystallization and amorphization tendencies., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Elucidating the underlying mechanisms of water solidification in heterogeneous systems is crucially important for a panoply of applications; gaining such an understanding has also proven to be very challenging to the community. Indeed, one such example lies in clarifying the thermodynamics and kinetics of electro-crystallization in heterogeneous systems, such as micro- and nano-bubble systems. Here, we employ non-equilibrium molecular dynamics of water in heterogeneous environments experiencing direct contact with a propane gas phase at various temperatures in externally applied static electric fields, elucidating significant external-field effects in inducing poly-crystalline cubic-ice formation. This is in stark contrast with recent work on homogeneous cubic-ice electro-nucleation to produce largely fault-free single crystals. We explore the kinetics of heterogeneous cubic-ice electro-nucleation under different field intensities and thermal conditions and provide an overview of time-dependent dynamics of evolution of polycrystallinity.

In the five-decade search for efficient photocatalysts to convert natural sunlight into hydrogen via photoelectrochemical (PEC) dissociation of water, the underlying physics and chemistry of PEC processes taking place at metal-oxide photocatalysts remains relatively poorly understood and is an active area of research by both theorists and experimentalists. This is surely the case for water structuring at metal-oxide surfaces, including their "self-ordering." In this work, we apply classical molecular-dynamics techniques to investigate and classify the structure and ordering of water layers at two TiO 2 surfaces-anatase ⟨101⟩ and rutile ⟨110⟩. We are interested in identifying and classifying layers using local order parameters to distinguish the layered-water superstructure from bulk-like water configurations as observed in liquid water and common ice polymorphs. In particular, we look for the formation of regions with reduced molecular mobility and assess whether they are "ice-like," as has been proposed in recent interpretations in the literature, or, instead, how these interfacial-water structures might be otherwise described. We leverage quantitative and order-parameter analysis techniques to categorize the structural properties of layers of water molecules formed and compare them to both cubic and hexagonal polytypes of bulk ice I, as well as bulk liquid water. In doing so, we propose a general structural recognition/classification framework suitable for identifying and describing molecules at any condensed-state-water interface.

Given methane hydrates' importance in marine sediments, as well as the widespread use of seabed acoustic-signaling methods in oil and gas exploration, the elastic characterization of these materials is particularly relevant. A greater understanding of the properties governing phonon, sound, and acoustic propagation would help to better classify methane-hydrate deposits, aiding in their discovery. Recently, we have published a new nonequilibrium molecular-dynamics (NEMD) methodology to recreate longitudinal and transverse perturbations, observing their propagation through a crystalline lattice by various metrics, to study the underlying S- and P-wave velocities (achieving excellent agreement with experiment) [Melgar et al., J. Phys. Chem. 122(5), 3006-3013 (2018); ibid.150, 084101 (2019)]. Here, we apply these NEMD methods to methane-clathrate systems to study acoustic-propagation characteristics, as well as the lattice elastic behavior. In so doing, we determine S- and P-wave velocities in excellent accord with experiment; we also ascertain the allowable magnitude range of acoustic perturbation and establish a threshold for lattice breakup and hydrate decomposition. Interestingly, upon dissociation, we observe the formation of methane nanobubbles, which agrees with previous studies on the microscopic fundamentals of hydrate dissociation by various means.

α-quartz is one of the most important SiO 2 polymorphs because it is the basis of very common minerals, especially for seabed materials with geoscientific importance. The elastic characterization of these materials is particularly relevant when the properties governing phonon and sound propagation are involved. These studies are especially interesting for oil exploration purposes. Recently, we published a new method that constitutes to the best of our knowledge the first attempt to recreate longitudinal and transversal perturbations in a simulation box to observe their propagation through the crystal by means of a set of descriptors [D. Melgar et al., J. Phys. Chem. C 122, 3006-3013 (2018)]. The agreement with the experimental S- and P-wave velocities was rather excellent. Thus, an effort has been undertaken to deepen the particularities of this new methodology. Here, bearing in mind this encouraging initial methodology-development progress, we deepen our knowledge of the particularities of this new methodology in presenting a systematic investigation of the implementation of the perturbation source. This includes new ways of creating the perturbation, as well as analyzing the possible effects the perturbation amplitude could have on the resultant velocities. In addition, different force fields were tested to describe the interatomic interactions. The lack of dependence of the seismic velocities on the way the perturbation is created and the perturbation amplitude, and the good agreement with the experimental results are the main reasons that allow the definition of this new methodology as robust and reliable. These qualities are consolidated by the physical behavior of the calculated velocities in the presence of vacancies and under stress. The development of this method opens up a new line of research of calculating seismic velocities for geophysically relevant materials in a systematic way, with full control not only on the sample features (composition, porosity, vacancies, stress, etc.) but also on the particularities of perturbation itself, as well as determining optimal system-response metrics.

Human aquaporin 4 has been studied using non-equilibrium molecular dynamics simulations in the absence and presence of pulses of external electric fields. The pulses were 100 ns in duration and 0.005-0.015 V/Å in intensity acting along the pores' axes. Water diffusivity and the dipolar response of various residues of interest within the pores have been studied. Results show relatively little change in levels of water permeability per se within aquaporin channels during axially oriented field impulses, although care must be taken with regard to statistical certainty. However, the spatial variation of water permeability vis-à-vis electric-field intensity within the milieu of the channels, as revealed by heterogeneity in diffusivity-map gradients, indicates the possibility of somewhat enhanced diffusivity, owing to several residues being affected substantially by external fields, particularly for HIS 201 and 95 and ILE 93. This has the effect of increasing slightly intra-pore water diffusivity in the "pore-mouths" locale, albeit rendering it more spatially uniform overall vis-à-vis zero-field conditions (via manipulation of the selectivity filter).

Non-equilibrium molecular-dynamics simulations have been performed for dissolution of planar propane-hydrate/water interfaces in externally-applied electromagnetic (e/m) fields in the microwave to far infrared range (∼2.45-200 GHz) at electric-field intensities up to 2.0 V/nm and at roughly 20 K over/under temperatures vis-à-vis the zero-field propane-hydrate melting point. Upon e/m-field application, there is a field-frequency threshold above which the dissociation rate drops significantly, with a plateau therein for larger-frequencies. It was found that higher intensity and lower frequency facilitates dissociation. Except in the presence of a thermal driving-force, the 10 GHz frequency shows more substantial rate-enhancement effect vis-à-vis static electric fields or, indeed, lower-frequency e/m fields.

The observed anomalous self-diffusivity of ice VII in the region of 10 GPa at ∼400 K has been suggested to arise from a change in proton-hopping mechanism involving a transition from ionic-defect-driven diffusivity to that dominated by diffusion of rotational defects. Here, we report ab initio molecular dynamics to study the structural, hydrogen bonding, electronic, vibrational, and Raman properties of ice VII at this temperature and between 5 and 20 GPa to elucidate any possible hints of intramolecular strain that may serve as precursor events for proton hopping to unfold. We determine such equilibrium properties to be in reasonable agreement with experimental Raman spectra, although we do not detect any water-dissociation and proton-hopping events per se, owing to still-large water-dissociation free-energy barriers.

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Understanding water solidification, especially in "No Man's Land" (NML) (150 K < T < 235 K) is crucially important (e.g., upper-troposphere cloud processes) and challenging. A rather neglected aspect of tropospheric ice-crystallite formation is inevitably present electromagnetic fields' role. Here, we employ non-equilibrium molecular dynamics of aggressively quenched supercooled water nano-droplets in the gas phase under NML conditions, in externally applied electromagnetic (e/m) fields, elucidating significant differences between effects of static and oscillating fields: although static fields induce "electro-freezing," e/m fields exhibit the contrary - solidification inhibition. This anti-freeze action extends not only to crystal-ice formation but also restricts amorphisation, i.e., suppression of low-density amorphous ice which forms otherwise in zero-field NML environments. E/m-field applications maintain water in the deeply supercooled state in an "entropic trap," which is ripe for industrial impacts in cryo-freezing, etc.

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

Non-equilibrium molecular-dynamics simulations of bulk methane clathrate hydrates have been conducted in a range of externally applied electromagnetic (e/m) fields. Studies into frequencies of system(or "global")-mass-density fluctuations showed that these clathrates have three major modes: the dominant one is attributable to water molecules' librations and occurs at 720 cm -1 , regardless of any applied e/m fields. One of the more minor system-density fluctuations arises at 10-12 cm -1 and is caused by the propagation of local-density fluctuations; again, this is independent of e/m fields. The final density fluctuation is caused by e/m fields, and it only becomes apparent for field strengths of 1.2 V/nm or higher. The frequency of this mode is always twice the frequency of the applied e/m field. It was shown that the main qualitative features of the translational and librational densities of states (DOSs) were unaffected by the application of e/m fields; however, a slight coupling effect was observed, producing a peak in all DOSs at the frequency of the applied field. This study showed that e/m fields below a certain intensity threshold do not lead to any marked structural distortion or dissociation effect on pre-existing bulk clathrates, in which the hydrogen-bonding structure of the lattice remains intact. This is verified by system-density and configurational-energy values as well as radial distribution functions.

We have performed non-equilibrium molecular dynamics simulations of various TiO 2 /water interfaces at ambient temperature in presence of oscillating electric fields in frequency range 20-100 GHz and RMS intensities 0.05-0.25 V/Å. Although the externally applied fields are by one order of magnitude lower than the intrinsic electric field present on the interfaces (∼1.5-4.5 V/Å), significant non-thermal coupling of rotational and translational motion of water molecules was clearly observed. Enhancement of the motion, manifested by increase of diffusivity, was detected in the first hydration layer, which is known to be heavily confined by adsorption to the TiO 2 surface. Interestingly, the diffusivity increases more rapidly on anatase than on rutile facets where the adsorbed water was found to be more organized and restrained. We observed that the applied oscillating field reduces number of hydrogen bonds on the interface. The remaining H-bonds are weaker than those detected under zero-field conditions; however, their lifetime increases on most of the surfaces when the low-frequency fields are applied. Reduction of adsorption interaction was observed also in IR spectra of interfacial water where the directional patterns are smeared as the intensities of applied fields increase.

Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical transition at a lower temperature (∼200 K) vis-à-vis the zero-field case (∼220 K).

An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

Equilibrium molecular-dynamics (MD) simulations have been performed on metastable sI and sII polymorphs of empty hydrate lattices, in addition to liquid water and ice Ih. The non-polarisable TIP4P-2005, simple point charge model (SPC), and polarisable Thole-type models (TTM): TTM2, TTM3, and TTM4 water models were used in order to survey the differences between models and to see what differences can be expected when polarisability is incorporated. Rigid and flexible variants were used of each model to gauge the effects of flexibility. Power spectra are calculated and compared to density-of-states spectra inferred from inelastic neutron scattering (INS) measurements. Thermodynamic properties were also calculated, as well as molecular-dipole distributions. It was concluded that TTM models offer optimal fidelity vis-à-vis INS spectra, together with thermodynamic properties, with the flexible TTM2 model offering optimal placement of vibrational modes.

Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.

Equilibrium molecular-dynamics simulations have been performed for liquid water, and on metastable sI and sII polymorphs of empty hydrate lattices, in addition to ice Ih, in order to study the dynamical properties of librational motion (rotation oscillation) depicted by protons in water molecules. In particular, hydrate lattices were found to display prominent "bifurcated" features, or peaks, at circa 70 and 80-95 meV (or ∼560 and 640-760 cm(-1), respectively), also displayed by ice, in essentially quantitative agreement with experimental neutron-scattering data. However, observed differences in dispersion between these librational modes between these two structures (both hydrate polymorphs vis-à-vis ice), owing primarily to density effects, have been decomposed into contributions arising from angular-velocity dynamics about axes in the local molecular frame of water molecules, with in-plane "wagging" and "twisting" rationalising one mode at ∼70 meV, and out-of-plane motion for the higher-frequency band. This was confirmed explicitly by a type of de facto normal-mode analysis, in which only immediate layers of water molecules about the one under consideration were allowed to move. In contrast, liquid water displayed no marked preference for such local in- or out-of-plane modes characterising librational motion, owing to the marked absence of rigid, pentamers or hexamers therein.

Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein.

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, ∼80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs.

Water has many intriguing and anomalous physical properties that have puzzled and titillated the scientific community for centuries, perhaps none more so than the proposition that water may retain some (permanent) "memory" of conditions (e.g., dilution) or electric fields to which it has been subject. Here, we have performed non-equilibrium molecular dynamics simulations of liquid water in external electric-field nanosecond pulses, at 260-310 K, and gauged significant non-thermal field effects in terms of dipolar response. Response of both system- and individual-dipoles has been investigated, and autocorrelation functions of both show more significant effects in stronger fields, with more sluggish relaxation. Crucially, we show that once the field is removed, the dipoles relax, exhibiting no memory or permanent dipolar alignment. We also quantify the time scales for system dynamical-dipolar properties to revert to zero-field equilibrium behaviour.

Ice crystallisation and melting was studied via massively parallel molecular dynamics under periodic boundary conditions, using approximately spherical ice nano-particles (both "isolated" and as a series of heterogeneous "seeds") of varying size, surrounded by liquid water and at a variety of temperatures. These studies were performed for a series of systems ranging in size from ∼1 × 10(6) to 8.6 × 10(6) molecules, in order to establish system-size effects upon the nano-clusters" crystallisation and dissociation kinetics. Both "traditional" four-site and "single-site" and water models were used, with and without formal point charges, dipoles, and electrostatics, respectively. Simulations were carried out in the microcanonical and isothermal-isobaric ensembles, to assess the influence of "artificial" thermo- and baro-statting, and important disparities were observed, which declined upon using larger systems. It was found that there was a dependence upon system size for both ice growth and dissociation, in that larger systems favoured slower growth and more rapid melting, given the lower extent of "communication" of ice nano-crystallites with their periodic replicae in neighbouring boxes. Although the single-site model exhibited less variation with system size vis-à-vis the multiple-site representation with explicit electrostatics, its crystallisation-dissociation kinetics was artificially fast.

The formation of methane-hydrate precursors at large planar water-methane interfaces has been studied using massively parallel molecular dynamics in systems of varying size from around 10 000 to almost 7 × 10(6) molecules. This process took two distinct steps. First, the concentration of solvated methane clusters increases just inside the aqueous domain via slow diffusion from the methane-water interface, forming "clusters" of solvated methane molecules. Second, the re-ordering process of solvated methane and water molecules takes place in a manner very roughly consistent with the "blob" hypothesis, although with important differences, to form hydrate precursors, necessary for subsequent hydrate nucleation and crystallisation. It was found that larger system sizes serve to promote the formation rate of precursors.

Water self-diffusion and the dipolar response of the selectivity filter within human aquaporin 4 have been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static and alternating electric fields. The pulses were approximately 50 and 100 ns in duration and 0.0065 V/Å in (r.m.s.) intensity and were either static or else 2.45 or 100 GHz in frequency and applied both along and perpendicular to the channels. In addition, the relaxation of the aquaporin, water self-diffusion and gating dynamics following cessation of the impulses was studied. In previous work it was determined that switches in the dihedral angle of the selectivity filter led to boosting of water permeation events within the channels, in the presence of identical external static and alternating electric fields, although applied continuously. Here the application of field impulses (and subsequently, upon removal) has shown that it is the dipolar orientation of the histidine-201 residue in the selectivity filter which governs the dihedral angle, and hence influences water self-diffusion; this constitutes an appropriate order parameter. The dipolar response of this residue to the applied field leads to the adoption of four distinct states, which we modelled as time-homogeneous Markov jump processes, and may be distinguished in the potential of mean force (PMF) as a function of the dipolar orientation of histidine-201. The observations of enhanced "dipolar flipping" of H201 serve to explain increased levels of water self-diffusion within aquaporin channels during, and immediately following, field impulses, although the level of statistical certainty here is lower. Given the appreciable size of the energy barriers evident in PMFs computed directly from deterministic MD (whether in the absence or presence of external fields), metadynamics calculations were undertaken to explore the free-energy landscape of histidine-201 orientation with greater accuracy and precision. These indicate that electric fields do alter the free-energy profile of the H201 side-chain orientation, wherein a perturbation of the symmetric bimodal state evident in the zero-field case is observed. These effects are dependent on the field intensities.

Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

The temporal evolution of two model high-density/low-density (HDL/LDL) interfaces was examined from molecular dynamics (MD) calculations at temperatures close to the predicted second critical point of water for three water models. In all cases, interfacial density equalisation occurred rapidly showing no preference for inhomogenous distribution. A uniform density (of ca. 0.99-1.067 g/cm(3), depending on the potential) was always observed at the interface, indicating the free energy of water in low- and high-density forms is metastable, and that LDL and HDL should not coexist as independent entities at thermodynamic equilibrium. It is reckoned that previous MD studies supporting the "two-liquid" model have an explicit, if inappropriate, assumption of mechanical equilibrium between the two phases. The present result challenges the notion that a second critical point exists, and that LDL/HDL mixtures could be even kinetically metastable.

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.

Molecular dynamics (MD) at the molecular mechanical level and geometry optimisation at the quantum mechanical level have been performed to investigate the transport and fixation of oxygen and carbon dioxide in the cavity of ribulose-1,5-bisphosphate carboxylase/oxygenase, or Rubisco. Multiple MD simulations have been carried out to study the diffusive behaviour of O(2) and CO(2) molecules from the Mg(2+) cation in Rubisco at 298 K and 1 bar, being one step in the overall process of carboxylation/oxygenation in Rubisco. In addition to this work, in order to gain additional perspective on the role of chemical reaction rates and thermodynamics, oxygen, and carbon dioxide uptake mechanisms have also been investigated by the aid of quantum chemical calculations. The results indicate that the activation barrier for carboxylation is slightly lower than that of oxygenation. This agrees qualitatively with experimental findings, and rationalises the observed competition between both catalytic processes in nature. Finally, the longer-lived persistence of CO(2) in the vicinity of the active centre (i.e., slower self-diffusion) may serve to explain, in part, why carboxylation is the more kinetically favoured on an overall basis compared to oxygenation.

UV-Vis spectra are calculated using time-dependent density functional theory for several organic dyes--4-(N, N-dimethylamino) benzonitrile, alizarin, squaraine, polyene-linker dyes, oligothiophene-containing coumarin dyes (NKX series) and triphenylamine-donor dyes. Most of these dyes (except, for the first two) or their derivatives are considered to be promising organic dyes for dye-sensitized solar cells. An accurate description of the photophysics of such dyes is imperative for understanding and creating better dyes. To this end, we studied the dyes within several approximations to the exchange-correlation functional. The chosen functionals--PBE, M06L, B3LYP, M06, CAM-B3LYP, and wB97--represent the various classes of approximations that are currently being used to study material properties. From amongst the six approximations studied here, CAM-B3LYP outperformed the others in its description of charge-transfer excitations in most (though, not all) of the dyes. This study shows why it is difficult to choose a particular functional a priori, especially when starting out with a new dye for solar cell application. A possible way to judge the fitness of an approximation is used in this work and it is shown to provide a good quantitative guideline for subsequent research in this field.

Non-equilibrium molecular dynamics simulations of R and S enantiomers of 1,1-chlorofluoroethane, both for pure liquids and racemic mixtures, have been performed at 298 K in the absence and presence of both electromagnetic (e/m) and circularly polarised electric (CP) fields of varying frequency (100-2200 GHz) and intensity (0.025-0.2 V Å(-1) (rms)). Significant non-thermal field effects were noted in the coupling of rotational and translational motion; for instance, in microwave and far-infrared (MW/IR) e/m fields, marked increases in rotational and translational diffusion vis-à-vis the zero-field case took place at 0.025-0.1 V Å(-1) (rms), with a reduction in translational diffusion vis-à-vis the zero-field case above 0.1 V Å(-1) (rms) above 100 GHz. This was due to enhanced direct coupling of rotational motion with the more intense e/m field at the ideal intrinsic rotational coupling frequency (approximately 700 GHz) leading to such rapidly oscillating rotational motion that extent of translational motion was effectively reduced. In the case of CP fields, rotational and translational diffusion was also enhanced for all intensities, particularly at approximately 700 GHz. For both MW/IR and CP fields, non-linear field effects were evident above around 0.1 V Å(-1) (rms) intensity, in terms of enhancements in translational and rotational motion. Simulation of 90-10 mol. % liquid mixtures of a Lennard-Jones solvent with R and S enantiomer-solutes in MW/IR and CP fields led to more limited promotion of rotational and translational diffusion, due primarily to increased frictional effects. For both e/m and CP fields, examination of the laboratory- and inertial-frame auto- and cross-correlation functions of velocity and angular velocity demonstrated the development of explicit coupling with the external fields at the applied frequencies, especially so in the more intense fields where nonlinear effects come into play. For racemic mixtures, elements of the laboratory- and inertial-frame velocity and angular velocity were found to couple with each other to a lesser extent., (© 2012 American Institute of Physics)

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 large intrinsic bandgap of NiO hinders its potential application as a photocatalyst under visible-light irradiation. In this study, we have performed first-principles screened exchange hybrid density functional theory with the HSE06 functional calculations of N- and C-doped NiO to investigate the effect of doping on the electronic structure of NiO. C-doping at an oxygen site induces gap states due to the dopant, the positions of which suggest that the top of the valence band is made up primarily of C 2p-derived states with some Ni 3d contributions, and the lowest-energy empty state is in the middle of the gap. This leads to an effective bandgap of 1.7 eV, which is of potential interest for photocatalytic applications. N-doping induces comparatively little dopant-Ni 3d interactions, but results in similar positions of dopant-induced states, i.e., the top of the valence band is made up of dopant 2p states and the lowest unoccupied state is the empty gap state derived from the dopant, leading to bandgap narrowing. With the hybrid density functional theory (DFT) results available, we discuss issues with the DFT corrected for on-site Coulomb description of these systems.

Water self-diffusion within human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of external ac and dc electric fields. The computed diffusive (p(d)) and osmotic (p(f)) permeabilities under zero-field conditions are (0.718 ± 0.24) × 10(-14) cm(3) s(-1) and (2.94 ± 0.47) × 10(-14) cm(3) s(-1), respectively; our p(f) agrees with the experimental value of (1.50 ± 0.6) × 10(-14) cm(3) s(-1). A gating mechanism has been proposed in which side-chain dynamics of residue H201, located in the selectivity filter, play an essential role. In addition, for nonequilibrium MD in external fields, it was found that water dipole orientation within the constriction region of the channel is affected by electric fields (e-fields) and that this governs the permeability. It was also found that the rate of side-chain flipping motion of residue H201 is increased in the presence of e-fields, which influences water conductivity further.

Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å(-1). A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-á-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

Water-self-diffusion through single-walled carbon nanotubes (SWCNTs) inserted normal to a phospholipid membrane has been studied using equilibrium and nonequilibrium molecular dynamics simulations in the presence of static and alternating electrical fields. Four different SWCNTs were investigated: (5,5), (6,6), (8,8), and (11,11) and also three arrays of four (6,6) SWCNTs separated by 15, 20, and 25 A, respectively. The (5,5) system shows interesting behavior, where an increase in the applied field frequency in the z direction decreases the water permeation rates, reaching values at higher frequencies similar to zero-field conditions. The (6,6) arrays simulations demonstrated that there is a friction effect, when the nanotubes are closely packed, which retards the movement of the individual water files.

Nonequilibrium molecular dynamics simulations have been performed to investigate the thermal-driven breakup of both spherical methane hydrate nanocrystallites (with radii of approximately 18 and 21 A) and planar methane hydrate interfaces in liquid water at 280-340 K. The melting temperatures of each cluster were estimated, and dissociation was observed to be strongly dependent on temperature, with higher dissociation rates at larger overtemperatures vis-a-vis melting. For the 18 and 21 A radius nanocrystals, breakup was also seen to be dependent on cluster size, and different methane compositions (85%, 95%, and 100% of maximum theoretical occupation) in the planar case also lead to slight differences in the initial dissociation rate. In all cases, the diffusion of the methane into the surrounding liquid water was found to be an important step limiting the overall rate of breakup. A simple coupled mass and heat transfer model has been devised for both the spherical and planar hydrate systems that explains these findings, and distinguishes between the role of the overall thermal driving force and methane diffusional mass transfer in controlling the break-up rate.

Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of both external static electric and low-frequency microwave (2.45 GHz) fields of varying intensity. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure relative to the zero-field state, depending on the field conditions, mutation, and orientation with respect to the applied field. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the dipolar alignment of water molecules in both the solvation layer and the bulk was also found to be influential. Substantial differences in behavior were found for proteins with and without overall net charges, particularly with respect to translational motion. Localized motion and perturbation of hydrogen bonds were also found to be evident for charged residues.

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25-0.5 V Arms-1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500 K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.

Nonequilibrium molecular-dynamics simulations have been carried out at 276.65 K and 68 bar for the dissolution of spherical methane hydrate crystallites surrounded by a liquid phase. The liquid was composed of pure water or a water-methane mixture ranging in methane composition from 50% to 100% of the corresponding theoretical maximum for the hydrate and ranged in size from about 1600 to 2200 water molecules. Four different crystallites ranging in size from 115 to 230 water molecules were used in the two-phase systems; the nanocrystals were either empty or had a methane occupation from 80% to 100% of the theoretical maximum. The crystal-liquid systems were prepared in two distinct ways, involving constrained melting of a bulk hydrate system or implantation of the crystallite into a separate liquid phase. The breakup rates were very similar for the four different crystal sizes investigated. The method of system preparation was not found to affect the eventual dissociation rates, despite a lag time of approximately 70 ps associated with relaxation of the liquid interfacial layer in the constrained melting approach. The dissolution rates were not affected substantially by methane occupation of the hydrate phase in the 80%-100% range. In contrast, empty hydrate clusters were found to break up significantly more quickly. Our simulations indicate that the diffusion of methane molecules to the surrounding liquid layer from the crystal surface appears to be the rate-controlling step in hydrate breakup. Increasing the size of the liquid phase was found to reduce the initial delay in breakup. We have compared breakup rates computed using different long-range electrostatic methods. Use of the Ewald, minimum image, and spherical cut-off techniques led to more rapid dissociation relative to the Lekner method.

Nonequilibrium molecular-dynamics (MD) simulations have been performed for the growth and dissolution of a spherical methane hydrate crystallite, surrounded by a saturated water-methane liquid phase, in both the absence and presence of external electromagnetic (e/m) fields in the microwave to far infrared range (5-7500 GHz) at root-mean square (rms) electric field intensities of up to 0.2 V/A. A rigid/polarizable potential was used to model water and a rigid/nonpolarizable model was utilized for methane. In the absence of a field, it was found that the average growth rate of the crystallite was approximately 0.32 water and 0.045 methane molecules per picosecond, evaluated over a 500 ps NPT simulation for three different initial geometries. Upon the application of an e/m field, it was found that no significant deviations from the zero-field crystal growth patterns were observed for rms electric field intensities of less than about 0.1 V/A, regardless of the field frequency. At, and above, this "threshold" intensity, it was found that dissolution took place. The mobility of the molecules in the system was enhanced by the e/m field, to the greatest extent for frequencies of 50-100 GHz. Furthermore, it was observed that there was a systematic frequency variation in the pattern of dipole alignment with the external field and this led to marked differences in the rate of dissolution., ((c) 2004 American Institute of Physics.)