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The advent of air nanobubbles (ANBs) has opened up a wide range of commercial applications spanning industries including wastewater treatment, food processing, biomedical engineering, and agriculture. The implementation of electric field-based air nanobubbles (EF-ANBs) irrigation presents a promising approach to enhance agricultural crop efficiency, concurrently promoting environmentally sustainable practices through reducing fertilizer usage. This study investigated the impact of EF-ANBs on the germination and overall growth of agricultural crops in soil. Results indicate a substantial enhancement in both germination rates and plant growth upon the application of EF-ANBs. Notably, the introduction of ANBs led to a significant enhancement in the germination rate of lettuce and basil, increasing from approximately 20% to 96% and from 16% to 53%, respectively over two days. Moreover, the presence of EF-ANBs facilitates superior hypocotyl elongation, exhibiting a 2.8- and a 1.6-fold increase in the elongation of lettuce and basil, respectively, over a six-day observation period. The enriched oxygen levels within the air nanobubbles expedite aerobic respiration, amplifying electron leakage from the electron transport chain (ETC) and resulting in heightened reactive oxygen species (ROS) production, playing a pivotal role in stimulating growth signaling. Furthermore, the application of EF-ANBs in irrigation surpasses the impact of traditional fertilizers, demonstrating a robust catalytic effect on the shoot, stem, and root length, as well as the leaf count of lettuce plants. Considering these parameters, a single fertilizer treatment (at various concentrations) during EF-ANBs administration, demonstrates superior plant growth compared to regular water combined with fertilizer. The findings underscore the synergistic interaction between aerobic respiration and the generation of ROS in promoting plant growth, particularly in the context of reduced fertilizer levels facilitated by the presence of EF-ANBs. This promising correlation holds significant potential in establishing more sustainability for ever-increasing environmentally conscious agriculture., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgments The authors thank the European Innovation Council Accelerator program and also AquaB Nanobubble Innovations Ltd. for their provision of submersible nanobubble generators; see www.aquab.com and www.aqua-bubble.com for further details., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

In the exploration of the optimal material for achieving the photoelectrochemical dissociation of water into hydrogen, hematite (α-Fe 2 O 3 ) emerges as a highly promising candidate for proof-of-concept demonstrations. Recent studies suggest that the concurrent application of external electric fields could enhance the photoelectrochemical (PEC) process. To delve into this, we conducted nonequilibrium ab initio molecular dynamics (NE-AIMD) simulations in this study, focusing on hematite-water interfaces at room temperature under progressively stronger electric fields. Our findings reveal intriguing evidence of water molecule adsorption and dissociation, as evidenced by an analysis of the structural properties of the hydrated layered surface of the hematite-water interface. Additionally, we scrutinized intermolecular structures using radial distribution functions (RDFs) to explore the interaction between the hematite slab and water. Notably, the presence of a Grotthuss hopping mechanism became apparent as the electric field strength increased. A comprehensive discussion based on intramolecular geometry highlighted aspects such as hydrogen-bond lengths, H-bond angles, average H-bond numbers, and the observed correlation existing among the hydrogen-bond strength, bond-dissociation energy, and H-bond lifetime. Furthermore, we assessed the impact of electric fields on the librational, bending, and stretching modes of hydrogen atoms in water by calculating the vibrational density of states (VDOS). This analysis revealed distinct field effects for the three characteristic band modes, both in the bulk region and at the hematite-water interface. We also evaluated the charge density of active elements at the aqueous hematite surface, delving into field-induced electronic charge-density variations through the Hirshfeld charge density analysis of atomic elements. Throughout this work, we drew clear distinctions between parallel and antiparallel field alignments at the hematite-water interface, aiming to elucidate crucial differences in local behavior for each surface direction of the hematite-water interface., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

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.)

This work presents the effect of hydrogen sulfide gas on the phase behavior of both methane gas hydrate formation and CO 2 gas hydrate formation. For this, the thermodynamic equilibrium conditions for various gas mixtures containing CH 4 /H 2 S and CO 2 /H 2 S are initially found by simulation using PVTSim software. These simulated results are compared using an experimental approach and the available literature. Then, the thermodynamic equilibrium conditions generated by simulation are used for generating Hydrate Liquid-Vapor-Equilibrium (HLVE) curves to understand the phase behavior of gases. Further, the effect of hydrogen sulfide on the thermodynamic stability of methane and carbon dioxide hydrates was studied. It was clearly observed from the results that an increase in H 2 S composition in the gas mixture decreases the stability of CH 4 and CO 2 hydrates., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Gas Hydrate modelling has gained huge attention in the past decade due to its increase in usage for various energy as well as environmental applications at an industrial scale. As the experimental approach is highly expensive and time-consuming, modelling is the best way to predict the conditions before the actual applications at industrial scales. The commercial software currently existing uses the equation of states (EOS) to predict the thermodynamic conditions of gas hydrates. But, in certain cases, the prediction by using EOS fails to predict the hydrate conditions accurately. Therefore, there arose a need for an accurate prediction model to estimate the hydrate formation conditions. So, in this work, an accurate prediction model has been proposed to predict the thermodynamic equilibrium conditions of the gas hydrate formation. The performance of prediction accuracy for the proposed model is compared with those of the SRK equation of state and Peng Robinson (PR) Equation of state. It was observed that in most of the cases the proposed model has predicted the thermodynamic conditions more accurately than the PR and SRK equation of state. This work helps in understanding the limitations of EOS for the prediction hydrate conditions. Also, the current work helps in strengthening the conventional statistical modelling technique to predict the hydrate conditions for a broader range., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint-where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6-7 Å of the surface.

We have investigated systematically and statistically methanol-concentration effects on methane-hydrate nucleation using both experiment and restrained molecular-dynamics simulation, employing simple observables to achieve an initially homogeneous methane-supersaturated solution particularly favorable for nucleation realization in reasonable simulation times. We observe the pronounced "bifurcated" character of the nucleation rate upon methanol concentration in both experiments and simulation, with promotion at low concentrations and switching to industrially familiar inhibition at higher concentrations. Higher methanol concentrations suppress hydrate growth by in-lattice methanol incorporation, resulting in the formation of "defects", increasing the energy of the nucleus. At low concentrations, on the contrary, the detrimental effect of defects is more than compensated for by the beneficial contribution of CH 3 in easing methane incorporation in the cages or replacing it altogether., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

The thrombin binding aptamer (TBA) is a 15-mer DNA oligonucleotide (5'-GGT TGG TGT GGT TGG-3'), that can form a stable intramolecular antiparallel chair-like G-quadruplex structure. This aptamer shows anticoagulant properties by interacting with one of the two anion binding sites of thrombin, namely the fibrinogen-recognition exosite. Here, we demonstrate that terminal modification of TBA with aromatic fragments such as coumarin, pyrene and perylene diimide (PDI), improves the G-quadruplex stability. The large aromatic surface of these dyes can π-π stack to the G-quadruplex or to each other, thereby stabilizing the aptamer. With respect to the original TBA, monoPDI-functionalized TBA exhibited the most remarkable improvement in melting temperature (ΔT m ≈+18 °C) and displayed enhanced anticoagulant activity., (© 2022 Wiley-VCH GmbH.)

Given its ubiquitous presence in the environment of bio-macromolecules, water is well known to play a fundamental part in biological activity, often as a regulating agent. In parallel, with increasing attention focused on the potential damage of microwave-frequency radiation exposure to human health, the effects of extraneous electric and electromagnetic (e/m) fields on water shells surrounding proteins, and, indeed, biomolecules themselves, are becoming a particularly pertinent issue. In this study, non-equilibrium molecular dynamics simulations of hydrated hen-egg white lysozyme have been performed in both the absence and presence of external electric fields of varying intensity (0.005-0.02 V/Å) and frequency (static, i.e. , zero-frequency, together with oscillating fields of 2.45-100 GHz). By comparing the effect of different electric-field conditions on both the protein's and surrounding hydration layer's dipole moments and their underlying relaxation dynamics, clear and evident non-thermal field effects were observed on the dipolar response of both the protein and hydration layer. This occurred primarily as a consequence of the protein's dipolar alignment with the external field and increased with the growth of field intensity. In addition, it was found that the lag time of dipolar response to the applied field itself, for both the protein and the first hydration sub-shell ( i.e. , directly adsorbed layer), under oscillating fields is longer than that in both the second hydration sub-layer and bulk water, owing to strong direct protein-water adsorption. In that respect, we also probe and discuss the effect of protein-water hydrogen bonds, dissecting the subtleties of "bio-water" dipolar response.

In view of the recently-predicted hydrogen release from type-II (sII) clathrate hydrates in the general 140-180 K temperature range [ J. Phys. Chem. C , 125 , 8430-8439 (2021)], we have investigated in the present study, by means of microsecond-long non-equilibrium molecular-dynamics simulation, the effect of externally-applied electric fields (both static and alternating) on manipulating and accelerating this H 2 -escape process. In particular, we have found that judiciously-selected electromagnetic fields, in the microwave frequency range, serve to enhance dramatically this H 2 -release rate - crucially, without any breakup of the hydrate lattice itself . Of those studied, we have found that 10 GHz serves as the optimal frequency to maximise hydrogen release, owing to promotion of H 2 -H 2 molecular collisions inside doubly-occupied 5 12 6 4 cages in the sII structure and optimal field-period overlap with intra-cage tetrahedral-site hopping and opportunities for inter-cage passage via hexagonal cage faces. This study opens up the vista of "field engineering" for exquisite kinetic control of large, Grid-(terawatt hour)-scale hydrogen-storage systems., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The interaction between a protein and external electric field (EF) can alter its structure and dynamical behavior, which has a potential impact on the biological function of proteins and cause uncertain health consequences. Conversely, the application of EFs of judiciously selected intensity and frequency can help to treat disease, and optimization of this requires a greater understanding of EF-induced effects underpinning basic protein biophysics. In the present study, chignolin─an artificial protein sufficiently small to undergo fast-folding events and transitions─was selected as an ideal prototype to investigate how, and to what extent, externally applied electric fields may manipulate or influence protein-folding phenomena. Nonequilibrium molecular dynamics (NEMD) simulations have been performed of solvated chignolin to determine the distribution of folding states and their underlying transition dynamics, in the absence and presence of externally applied electric fields (both static and alternating); a key focus has been to ascertain how folding pathways are altered in an athermal sense by external fields. Compared to zero-field conditions, a dramatically different─indeed, bifurcated─behavior of chignolin-folding processes emerges between static- and alternating-field scenarios, especially vis-à-vis incipient stages of hydrophobic-core formation: in alternating fields, fold-state populations diversified, with an attendant acceleration of state-hopping folding kinetics, featuring the concomitant emergence of a new, quasi-stable structure compared to the native structure, in field-shifted energy landscapes.

The high-pressure solid phase of water known as ice VII has recently attracted a lot of attention when its presence was detected in large exoplanets, their icy satellites, and even in Earth's mantle. Moreover, a transition of ice VII to the superionic phase can be triggered by external electric fields. Here, we investigate the dielectric responses of ice VII to applied oscillating electric fields of various frequencies employing non-equilibrium ab initio molecular dynamics. We focus on the dynamical properties of a dipole-ordered ice VII structure, for which we explored external-field-induced electronic polarisation and the vibrational spectral density of states (VDOS). These analyses are important for the understanding of collective motions in the ice-VII lattice and the electronic properties of this exotic water phase.

Natural gas hydrate is a promising future energy source, but it also poses a huge threat to oil and gas production due to its ability to deposit within and block pipelines. Understanding the atomistic mechanisms of adhesion between the hydrate and solid surfaces and elucidating its underlying key determining factors can shed light on the fundamentals of novel antihydrate materials design. In this study, large-scale molecular simulations are employed to investigate the hydrate adhesion on solid surfaces, especially with focuses on the atomistic structures of intermediate layer and their influences on the adhesion. The results show that the structure of the intermediate layer formed between hydrate and solid surface is a competitive equilibrium of induced growth from both sides, and is regulated by the content of guest molecules. By comparing the fracture behaviors of the hydrate-solid surface system with different intermediate structures, it is found that both the lattice areal density of water structure and the adsorption of guest molecules on the interface together determine the adhesion strength. Based on the analysis of the adhesion strength distribution, we have also revealed the origins of the drastic difference in adhesion among different water structures such as ice and hydrate. Our simulation indicates that ice-adhesion strength is approximately five times that of lowest hydrate adhesion strength. This finding is surprisingly consistent with the available experimental results.

C 3 -Symmetric triaminoguanidinium chloride is condensed with N -pentylphenothiazine carboxaldehyde to realise a thermally stable twisted organic salt on a gram scale. It appears as a nonmetallic economic salt having an integrated propeller shape with three tub-like cores and displays efficient reversible mechano- and thermo-fluorochromic behaviour. Unlike previous reports, the designed fluorescent, colorimetric thermometer works over a higher temperature range of 130-170 °C with five distinct colour variations.

The rapid growth of CO 2 emissions in the atmosphere has attracted great attention due to the influence of the greenhouse effect. Aerogels' application for capturing CO 2 is quite promising owing to their numerous advantages, such as high porosity (~95%); these are predominantly mesoporous (20-50 nm) materials with very high surface area (>800 m 2 ∙g -1 ). To increase the CO 2 level of aerogels' uptake capacity and selectivity, active materials have been investigated, such as potassium carbonate, K 2 CO 3 , amines, and ionic-liquid amino-acid moieties loaded onto the surface of aerogels. The flexibility of the composition and surface chemistry of aerogels can be modified intentionally-indeed, manipulated-for CO 2 capture. Up to now, most research has focused mainly on the synthesis of amine-modified silica aerogels and the evaluation of their CO 2 -sorption properties. However, there is no comprehensive study focusing on the effect of different types of aerogels and modification groups on the adsorption of CO 2 . In this review, we present, in broad terms, the use of different precursors, as well as modification of synthesis parameters. The present review aims to consider which kind of precursors and modification groups can serve as potentially attractive molecular-design characteristics in promising materials for capturing CO 2 .

Adding a secondary complex metal hydride can either kinetically or thermodynamically facilitate dehydrogenation reactions. Adding Mg 2 FeH 6 to LiBH 4 is energetically favoured, since FeB and MgB 2 are formed as stable intermediate compounds during dehydrogenation reactions. Such "hydride destabilisation" enhances H 2 -release thermodynamics from H 2 -storage materials. Samples of the LiBH 4 and Mg 2 FeH 6 with a 2:1 molar ratio were mixed and decomposed under three different conditions (dynamic decomposition under vacuum, dynamic decomposition under a hydrogen atmosphere, and isothermal decomposition). In situ synchrotron X-ray diffraction results revealed the influence of decomposition conditions on the selected reaction path. Dynamic decomposition of Mg 2 FeH 6 -LiBH 4 under vacuum, or isothermal decomposition at low temperatures, was found to induce pure decomposition of LiBH 4 , whilst mixed decomposition of LiBH 4 + Mg and formation of MgB 2 were achieved via high-temperature isothermal dehydrogenation.

The dynamical properties of physically and chemically adsorbed water molecules at pristine hematite-(001) surfaces have been studied by means of nonequilibrium ab initio molecular dynamics (NE-AIMD) in the NVT ensemble at room temperature, in the presence of externally applied, uniform static electric fields of increasing intensity. The dissociation of water molecules to form chemically adsorbed species was scrutinized, in addition to charge redistribution and Grotthus proton hopping between water molecules. Dynamical properties of the adsorbed water molecules and OH - and H 3 O + ions were gauged, such as the hydrogen bonds between protons in water molecules and the bridging oxygen atoms at the hematite surface, as well as the interactions between oxygen atoms in adsorbed water molecules and iron atoms at the hematite surface. The development of Helmholtz charge layers via water breakup at Fe 2 O 3 -hematite/water interfaces is also an interesting feature, with the development of protonic conduction on the surface and more bulk-like water.

It is predicted herewith that the leakage of both hydrogen (H 2 ) and deuterium (D 2 ) from sII clathrate hydrates, borne of guest chemical-potential equalization driving enhanced nonequilibrium intercage hopping, should be observable experimentally. To this end, we have designed simulations to realize and study this process by microsecond molecular dynamics within the temperature range of 150-180 K-for which the hydrate lattice was found to be stable. In this pursuit, we considered initial large-cage (5 12 6 4 ) guest occupancies of 1-4, with single occupation of 5 12 cavities. Examining transient, nonequilibrium intercage hopping, we present a lattice-escape activation energy for the four nominal large-cage occupancies (1-4), by fitting to the hydrate-leakage rate. The intercage hopping of H 2 and D 2 was studied using Markov-chain models and expressed at different temperatures and large-cage occupancies. The free energy of guest "binding" in the large and small cages was also computed for all of the occupancies. Toward equilibrium, following the majority of H 2 /D 2 escape via leakage, the percentage of occupancies was calculated for both H 2 and D 2 for all of the systems for all initial nominal large-cage occupancies; here, not unexpectedly, double occupancies occurred more favorably in large cages and single occupancies dominated in small cages., Competing Interests: The authors declare no competing financial interest., (© 2021 American Chemical Society.)

Clathrate hydrates are nonstoichiometric crystalline inclusion compounds, wherein a water host lattice entraps small guest molecules in cavities, with methane hydrates being the most widespread in nature. Recent studies have shown that proteins and polypeptides produced by micro-organisms can accelerate methane-hydrate formation. However, the role of magnetic fields and chirality in such phenomena is heretofore unclear. Here, we find prima facie evidence of differently oriented magnetic fields of varying strength showing intricate control on the hydrate-formation kinetics by R and S versions of a prototypical aromatic peptide derived from a naturally occurring, hydrate-promoting source. We also discuss the wider implications of these results on chirality in the biosphere and hydrates in the environment.

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.

Gas hydrates have received considerable attention due to their important role in flow assurance for the oil and gas industry, their extensive natural occurrence on Earth and extraterrestrial planets, and their significant applications in sustainable technologies including but not limited to gas and energy storage, gas separation, and water desalination. Given not only their inherent structural flexibility depending on the type of guest gas molecules and formation conditions, but also the synthetic effects of a wide range of chemical additives on their properties, these variabilities could be exploited to optimise the role of gas hydrates. This includes increasing their industrial applications, understanding and utilising their role in Nature, identifying potential methods for safely extracting natural gases stored in naturally occurring hydrates within the Earth, and for developing green technologies. This review summarizes the different properties of gas hydrates as well as their formation and dissociation kinetics and then reviews the fast-growing literature reporting their role and applications in the aforementioned fields, mainly concentrating on advances during the last decade. Challenges, limitations, and future perspectives of each field are briefly discussed. The overall objective of this review is to provide readers with an extensive overview of gas hydrates that we hope will stimulate further work on this riveting field.

Clathrate hydrates are nonstoichiometric crystalline inclusion compounds. Water acts as a "host lattice" and traps small guest molecules in stable cavities. One example, methane hydrates, are especially prevalent in situ at the seafloor. Although microorganism-produced proteins and polypeptides, including marine methylotroph porin proteins, can accelerate methane hydrate formation under conditions simulating their natural occurrence at the seafloor, the role that particular peptide sequences play in biocatalytic hydrate kinetics enhancement is unclear, especially the underlying molecular-level mechanisms. Here, we reveal the peptide-focused regulation of microorganisms' role in managing marine hydrates via an approximation mechanism of enzymatic catalysis accelerating hydrate formation. Aside from control of hydrate kinetics per se , we speculate that this peptide-centric mechanistic understanding could lead to a re-evaluation of the extent and geological importance of bioregulation of methane turnover in the biosphere.

In a superionic (SI) ice phase, oxygen atoms remain crystallographically ordered while protons become fully diffusive as a result of intramolecular dissociation. Ice VII's importance as a potential candidate for a SI ice phase has been conjectured from anomalous proton diffusivity data. Theoretical studies indicate possible SI prevalence in large-planet mantles (e.g., Uranus and Neptune) and exoplanets. Here, we realize sustainable SI behavior in ice VII by means of externally applied electric fields, using state-of-the-art nonequilibrium ab initio molecular dynamics to witness at first hand the protons' fluid dance through a dipole-ordered ice VII lattice. We point out the possibility of SI ice VII on Venus, in its strong permanent electric field., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Nanobubbles (NBs) are nanoscopic gaseous domains than can exist on solid surfaces or in bulk liquids. They have attracted substantial attention due to their long-time (meta)stability and a high potential for real-world applications. Using an approach not previously investigated, we exploit surface-electrostatic NB formation and stabilization via application of external electric fields in gas-liquid systems, with the marked result of massively increased gas uptake into the liquid in NB form. The de facto gas solubility enhancement (over many months) ranges from 2.5-fold for oxygen to 30-fold for methane vis-à-vis respective Henry's law values for gas solubility; the more hydrophobic the gas, the more spectacular the increase. Molecular dynamics simulations reveal that the origin of NBs' movement lies in dielectrophoresis, while substantial NB stabilization arises from a surface-polarization interaction., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

The vibrational density of states (VDOS), electronic structure and optical properties of bulk organo lead-halide perovskites, CH 3 NH 3 PbX 3 (where X = Cl, I and Br), very promising and exciting candidate materials for solar-energy applications, have been studied by means of (hybrid) Density Functional Theory (DFT), with and without spin-orbit coupling, and equilibrium Born-Oppenheimer molecular dynamics (BOMD) in the constant-volume, isothermal (NVT) ensemble at 298 K. Particular emphasis has been directed towards the detailed characterisation of optimal hybrid-DFT strategies to reproduce faithfully the band gap, band structure and optical properties vis-à-vis both experiment and more computationally demanding GW calculations ( i.e. , those involving the single-particle Green's function, G, and the screened Coulomb interaction, W). The VDOS was found to feature intimate coupling between the lead and halide atoms, and was dominated by acoustic phonon modes - particularly so for chlorine, suggesting this as the more effective candidate material of the considered halides. Bulk optical properties were also determined. In view of promising 'hybrid' architectures of perovskites adsorbed on titania substrates, further simulations of lead iodide in contact with titania have been performed to assess thermal stability, as well as dynamical and structural properties of these systems. It was found that lattice strain led to some atomic layers in perovskite further from the interface adopting less crystal-like structure and less pronounced phonon spectra., (© 2020 Published by Elsevier Ltd.)

The accurate molecular simulation prediction of vibrational spectra, and other structural, energetic and spectral characteristics, of photo-active metal-oxide surfaces in contact with light-absorbing dyes is an ongoing thorny and elusive challenge in physical chemistry. With this in mind, a molecular-dynamics (MD) simulation were performed by using optimized empirical potentials for a well-representative and prototypical dye-sensitized solar cell (DSC) solvated by a widely-studied room temperature ionic liquid (RTIL), in the guise of a [bmim] + [NTf2] - RTIL solvating an N719-sensitizing dye adsorbed onto 101 anatase-titania. In doing so, important insights were gleaned into how using a RTIL as the electrolytic hole acceptor modulates the dynamical and vibrational properties of a N719 dye, estimating the spectra for the DSC photo-active interface via Fourier transformation of mass-weighted velocity autocorrelation functions from MD. The acquired vibrational spectra were compared with the experiment spectra and those sampled from ab initio molecular dynamics (AIMD); in particular, various empirical-potential spectra generated from MD provide insight into how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction. In any event, careful fitting of empirical force-field models has been shown to be an effective tool in handling DSC vibrational properties, when validated by AIMD and an experiment.

A superstructure can elicit versatile new properties in materials by breaking their original geometrical symmetries. It is an important topic in the layered graphene-like two-dimensional transition metal dichalcogenides, but its origin remains unclear. Using diamond-anvil cell techniques, synchrotron X-ray diffraction, X-ray absorption, and first-principles calculations, we show that the evolution from weak van der Waals bonding to Heisenberg covalent bonding between layers induces an isostructural transition in quasi-two-dimensional 1 T -type VSe 2 at high pressure. Furthermore, our results show that high pressure induces a novel superstructure at 15.5 GPa rather than suppresses it as it would normally, which is unexpected. It is driven by Fermi-surface nesting, enhanced by pressure-induced distortion. The results suggest that the superstructure not only appears in the two-dimensional structure but also can emerge in the pressure-tuned three-dimensional structure with new symmetry and develop superconductivity.

We present a novel derivation of the multipole interaction (energies, forces and fields) in spherical harmonics, which results in an expression that is able to exactly reproduce the results of earlier Cartesian formulations. Our method follows the derivations of Smith (W. Smith, CCP5 Newsletter 1998, 46 , 18.) and Lin (D. Lin, J. Chem. Phys. 2015, 143 , 114115), who evaluate the Ewald sum for multipoles in Cartesian form, and then shows how the resulting expressions can be converted into spherical harmonics, where the conversion is performed by establishing a relation between an inner product on the space of symmetric traceless Cartesian tensors, and an inner product on the space of harmonic polynomials on the unit sphere. We also introduce a diagrammatic method for keeping track of the terms in the multipole interaction expression, such that the total electrostatic energy can be viewed as a 'sum over diagrams', and where the conversion to spherical harmonics is represented by 'braiding' subsets of Cartesian components together. For multipoles of maximum rank n, our algorithm is found to have scaling of n 3.7 vs. n 4.5 for our most optimised Cartesian implementation.

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.

2-Bromo-4,6-dinitroaniline (BNA) is identified as a domestic-dust pollutant in urban environments, with deleterious atmospheric effects. In the present work, we studied the reaction pathways and kinetics for BNA oxidation by the OH radical using quantum-chemical methods and canonical-variational transition-state theory with small-curvature tunneling correction (CVT/SCT). OH-radial-mediated BNA oxidation was studied by considering OH addition to carbon atoms (C1 to C6) of BNA and H-atom abstraction at the -NH 2 group and carbon atoms (C3 and C5) of BNA by OH radicals. It is observed that an OH-addition reaction is energetically more favorable. In addition, the rate constant was calculated for the favorable initial OH-addition reactions over the temperature range of 278 to 1000 K. The subsequent reactions for the favorable BNA-OH adduct intermediate with O 2 , HO 2 and NO radicals are studied. We have identified the following possible end products from this BNA-oxidation reaction: (i) 2-amino-3-bromo-6-hydroperoxy-5-methyl-1-nitro-cyclohexa-2,4 dienol, (ii) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, (iii) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, (iv) 3-amino-4-bromo-4-hydroperoxy-8-methyl-2-nitro-6,7-dioxa-bicyclo oct-2-en-8-ol, (v) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, and (vi) 3-amino-2-bromo-8-methyl-4-nitro-6,7-dioxa-bicyclo oct-3-ene-2,8-diol.

A crystal structure prediction algorithm for use in periodic boundary conditions with empirical rigid models is presented, which employs (i) unrestricted cutoff radii for the real-space interactions, thus allowing the treatment of even very small unit cells, and (ii) a global-optimization algorithm based on the basin-hopping method of Wales et al. (D. J. Wales and J. P. K. Doye, J. Phys. Chem. A 1997, 101, 5111). The algorithm is then applied to the TIP4P model of water (W. L. Jorgensen et al., J. Chem. Phys. 1983, 79, 926.) in order to find the lowest enthalpy water-ice crystalline structures in the pressure region 0-8000 bar, in unit cells holding in the range of 1-16 molecules, and a database of the 10 lowest enthalpy structures found at pressures 0, 4000, and 8000 bar is presented. The algorithm finds many of the ice polymorphs and, in particular, finds that the lowest energy structure at zero pressure is almost exactly tied between an ice Ic (cubic ice) and ice Ih (hexagonal ice) structure, having near-identical energies.

We have conducted non-equilibrium molecular-dynamics (NEMD) simulation to show that externally-applied magnetic fields, including their reversals in direction, have important effects on gas-release dynamics from methane hydrates. In particular, we apply fluctuation-dissipation analysis in the guise of Onsager's hypothesis to study hydrate kinetics at lower applied-field intensities, including temporary hydrate destabilisation in the wake of field-polarity switch; we scale down to the lowest practicable field intensities, of the order of 1 T. We conjecture, that these NEMD-based findings, particularly those involving polarity switch, may have ramifications for superchron-related Earth's magnetic-field polarity swaps affecting methane release into the geosphere, although a good deal of further work would be needed to provide a more definitive causal link., (Copyright © 2019. Published by Elsevier B.V.)

The projection of molecular processes onto a small set of relevant descriptors, the so-called reaction coordinates or collective variables (CVs), is a technique nowadays routinely employed by the biomolecular simulation community. In this work, we implemented two CVs to manipulate the orientation (i.e., angle) (μ⃗ a ) and magnitude (|μ⃗|) of the electric dipole moment. In doing so, we studied the thermodynamics of water orientation under the application of external voltages and the folding of two polypeptides at zero-field conditions. The projection of the free-energy [potential of mean force (PMF)] along water orientation defined an upper limit of around 0.3 V for irrelevant thermodynamic effects. On the other hand, sufficiently strong μ⃗ a restraints applied on 12-alanine (Ala 12 ) triggered structural effects because of the alignment of local dipoles; for lower restraints, a full-body rotation is achieved. The manipulation of |μ⃗| produced strong perturbations on the secondary structure of Ala 12 , promoting an enhanced sampling to its configurational space. Rigorous free-energy calculations in the form of 2-D PMFs for deca-alanine showed the utility of |μ⃗| as a reaction coordinate to study folding in small α helices. As a whole, we propose that the manipulation of both components of the dipole moment, μ⃗ a and |μ⃗|, provides thermodynamics insights into the structural conformation and stability of biomolecules. These new CVs are implemented in the Colvars module, available for NAMD and LAMMPS.

Efficient charge transport has been observed in iodine-doped, iodide-based room-temperature ionic liquids, yielding high ionic conductivity. To elucidate preferred mechanistic pathways for the iodide ( I - )-to-triiodide ( I 3 - ) exchange reactions, we have performed 10 ns reactive molecular-dynamics calculations in the liquid state for 1-butyl-3-methylimidazolium iodide ([BMIM][I]) at 450 to 750 K. Energy-barrier distributions for the iodine-swapping process were determined as a function of temperature, employing a charge-reassignment scheme drawn in part from electronic-structure calculations. Bond-exchange events were observed with rate-determining energy barriers ranging from ~0.19 to 0.23 ± 0.06 eV at 750 and 450 K, respectively, with an approximately Arrhenius temperature dependence for iodine self-diffusivity and reaction kinetics, although diffusion dominates/limits the bond-exchange events. This charge transfer is not dissimilar in energetics to those in solid-state superionic conductors.

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.

Electroporation is a matter of intensive ongoing research interest, and a much-neglected topic in trans-membrane proteins, particularly in view of such promising potential applications in medicine and biotechnology. In particular, selected such novel and exciting applications are predicated on controlling ionic conductivity through electro-pores. Here, we scrutinise the mechanisms of ions' electric conductivity, by means of structural rearrangements, through quasi-stable electro-pores through human-AQP4 as a well-representative prototype of trans-membrane ionic conduction, achieving exquisite control over ionic permeability manipulated by the application of intense static electric fields.

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).

The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystal nucleation processes. Previous work has generally neglected the possibility of the molecular-level dynamics of individual crystal nuclei coupling to local structures. However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have probed the nucleation of prototypical single and multicomponent crystals (specifically, ice and mixed gas hydrates). We establish that local structures can bias the evolution of nascent crystal phases on a nanosecond time scale by, for example, promoting the appearance or disappearance of specific crystal motifs and thus reveal a new facet of crystallization behavior. Moreover, we demonstrate structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Structurally biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.

Electroporation characterization is a topic of intensive interest probed by extensive ongoing research efforts. Usually, these studies are carried out on lipid-bilayer electroporation. Surprisingly, the possibility of water-channel electropore formation across transmembrane proteins themselves, particularly in view of such a promising application, has not yet been elucidated. The present work examines the geometrical and kinetic aspects of electropores and their stability in such a protein milieux (as opposed through the phospholipid membranes) in depth, by means of scrutiny of such a process in human-AQP4 as a well-representative prototype. The residues forming the electropore's walls, organized in loops, reveal the formation mechanism by their dipole alignment and translational response in response to applied axial electric fields in nonequilibrium molecular dynamics simulation. The magnitude of sustaining electric fields (keeping a stable electropore open) were determined. This suggests that transmembrane proteins could play a central role in electroporation applications, e.g., in medicine and biotechnology., Competing Interests: The authors declare no competing financial interest.

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.

Molecular-dynamics (MD) simulation of triaxially pressurized ice I h up to 30 kbar at 240 K (with sudden mechanical pressurization from its ambient-pressure structure) has been carried out with both the single-particle mW and atomistic TIP4P-Ice water potentials on systems of up to ∼1 million molecules, for times of the order of 100 ns. It was found that the TIP4P-Ice systems adopted a high-density liquid state above ∼7 kbar, while densification of the mW systems retained essentially crystalline order, owing to a failure for the tetrahedral network to break down appreciably from its ice I h lattice structure. Both are intermediate states adopted along the path toward respective thermodynamically stable states (and with pressure removal show reversion to I h for mW and to supercooled liquid for TIP4P-Ice), similar to recent ice electro-freezing simulations in "No Man's Land". Densification kinetics showed faster mW-system adaptation.

Phase segregation of multicomponent lipid bilayers leads to, under phase-coexistence conditions, domain formation, featuring delimitation by essentially one-dimensional borders. (Micro-)phase segregation of bilayers is proposed to influence the physiological behaviour of cell membranes and provides the driving force for lipid-raft formation. Experiments show a maximum in the electrical-conductivity of membranes at the phase-transition point, which has been conjectured to arise from border-nucleated transmembrane-conducting defects or pores. However, recent electroporation experiments on phase-segregated bilayers demonstrate electro-pore detection in the liquid disordered phase (Ld), wherein they diffuse over macroscopic periods without absorption into the liquid ordered phase (Lo). Here, we scrutinise transmembrane-pore formation via molecular dynamics simulations on a multicomponent phase-segregated bilayer. We find that pores created in Lo domains always migrate spontaneously to the Ld phase, via 'recruitment' of unsaturated lipids to the pore's rim to transport the pore to the fluid phase under a large stress-field driving force. Once in Ld domains, pores migrate towards their centre, never returning or pinning to Lo. These findings are explained by thermodynamics. By comparing the free-energy cost for creating pores in the bulk of Ld and Lo membranes, and in the phase-segregated system, we show that it is always more energetically tractable to create pores in Ld domains, independent of the pore size.

First-principles calculations were carried out to understand how anionic isovalent-atom doping affects the electronic structures and optical properties of α-MoO 3 . The effects of the sulphur and selenium doping at the three unique oxygen sites (O t , O a , and O t ) of α-MoO 3 were examined. We found that the valence p orbitals of Sulphur/Selenium dopant atoms give rise to impurity bands above the valence band maximum in the band structure of α-MoO 3 . The number of impurity bands in the doped material depends on the specific doping sites and the local chemical environment of the dopants in MoO 3 . The impurity bands give rise to the enhanced optical absorptions of the S- and Se-doped MoO 3 in the visible and infrared regions. At low local doping concentration, the effects of the dopant sites on the electronic structure of the material are additive, so increasing the doping concentration will enhance the optical absorption properties of the material in the visible and infrared regions. Further increasing the doping concentration will result in a larger gap between the maximum edge of impurity bands and the conduction band minimum, and will undermine the optical absorption in the visible and infrared region. Such effects are caused by the local geometry change at the high local doping concentration with the dopants displaced from the original O sites, so the resulting impurity bands are no long the superpositions of the impurity bands of each individual on-site dopant atom. Switching from S-doping to Se-doping decreases the gap between the maximum edge of the impurity bands and conduction band minimum, and leads to the optical absorption edge red-shifting further into the visible and infrared regions.

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.

Elucidating water-to-ice freezing, especially in "No Man's Land" (150 K < T < 235 K), is fundamentally important (e.g., predicting upper-troposphere cirrus-cloud formation) - and elusive. An oft-neglected aspect of tropospheric ice-crystallite formation lies in inevitably-present electric fields' role. Exploring nucleation in No Man's Land is technically demanding, owing to rapid nucleation rates, to mention nothing of difficulties of applying relevant electric fields thereto. Here, we tackle these intriguing open questions, via non-equilibrium molecular-dynamics simulations of sub-microsecond formation of rhombus-shaped ice I c nano-crystallites from aggressively-quenched supercooled water nano-droplets in the gas phase, in external static electric fields. We explore droplets' nano-confined geometries and the entropic-ordering agent of external electric fields as a means of realising cubic-ice formation, especially with very few stacking faults and defects.

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.