X-ray and Neutron Scattering of Water

Structure and slow dynamics of protein hydration water with cryopreserving DMSO and trehalose upon cooling

We study, through molecular dynamics simulations, three aqueous solutions with one lysozyme protein and three different concentrations of trehalose and dimethyl sulfoxide (DMSO). We analyze the structural and dynamical properties of the protein hydration water upon cooling. We find that trehalose plays a major role in modifying the structure of the network of HBs between water molecules in the hydration layer of the protein. The dynamics of hydration water presents, in addition to the α-relaxation, typical of glass formers, a slower long-time relaxation process, which greatly slows down the dynamics of water, particularly in the systems with trehalose, where it becomes dominant at low temperatures. In all the solutions, we observe, from the behavior of the α-relaxation times, a shift of the Mode Coupling Theory crossover temperature and the fragile-to-strong crossover temperature toward higher values with respect to bulk water. We also observe a strong-to-strong crossover from the temperature behavior of the long-relaxation times. In the aqueous solution with only DMSO, the transition shifts to a lower temperature than in the case with only lysozyme reported in the literature. We observe that the addition of trehalose to the mixture has the opposite effect of restoring the original location of the strong-to-strong crossover. In all the solutions analyzed in this work, the observed temperature of the protein dynamical transition is slightly shifted at lower temperatures than that of the strong-to-strong crossover, but their relative order is the same, showing a correlation between the motion of the protein and that of the hydration water.

Local and global expansivity in water

The supra-molecular structure of a liquid is strongly connected to its dynamics, which in turn control macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential to understand the thermal evolution of the dynamics ranging from the liquid to the glass. Here, we combine infrared spectroscopy (IR) measurements of the hydrogen (H) bond stretching vibration of water with molecular dynamics simulations and employ a quantitative analysis to extract the inter-molecular H-bond length in a wide temperature range of the liquid. The extracted expansivity of this H-bond differs strongly from that of the average nearest neighbor distance of oxygen atoms obtained through a common conversion of mass density. However, both properties can be connected through a simple model based on a random loose packing of spheres with a variable coordination number, which demonstrates the relevance of supra-molecular arrangement. Furthermore, the exclusion of the expansivity of the inter-molecular H-bonds reveals that the most compact molecular arrangement is formed in the range of ∼316-331K (i.e., above the density maximum) close to the temperature of several pressure-related anomalies, which indicates a characteristic point in the supra-molecular arrangement. These results confirm our earlier approach to deduce inter-molecular H-bond lengths via IR in polyalcohols [Gabriel et al. J. Chem. Phys. 154, 024503 (2021)] quantitatively and open a new alley to investigate the role of inter-molecular expansion as a precursor of molecular fluctuations on a bond-specific level.

Real-space local self-motion of protonated and deuterated water

We report on the self-part of the Van Hove correlation function, the correlation function describing the dynamics of a single molecule, of water and deuterated water. The correlation function is determined by transforming inelastic scattering spectra of neutrons or x rays over a wide range of momentum transfer Q and energy transfer E to space R and time t. The short-range diffusivity is estimated from the Van Hove correlation function in the framework of the Gaussian approximation. The diffusivity has been found to be different from the long-range macroscopic diffusivity, providing information about local atomic dynamics.

Crossover from gas-like to liquid-like molecular diffusion in a simple supercritical fluid

According to textbooks, no physical observable can be discerned allowing to distinguish a liquid from a gas beyond the critical point. Yet, several proposals have been put forward challenging this view and various transition boundaries between a gas-like and a liquid-like behaviour, including the so-called Widom and Frenkel lines, and percolation line, have been suggested to delineate the supercritical state space. Here we report observation of a crossover from gas-like (Gaussian) to liquid-like (Lorentzian) self-dynamic structure factor by incoherent quasi-elastic neutron scattering measurements on supercritical fluid methane as a function of pressure, along the 200 K isotherm. The molecular self-diffusion coefficient was derived from the best Gaussian (at low pressures) or Lorentzian (at high pressures) fits to the neutron spectra. The Gaussian-to-Lorentzian crossover is progressive and takes place at about the Widom line intercept (59 bar). At considerably higher pressures, a liquid-like jump diffusion mechanism properly describes the supercritical fluid on both sides of the Frenkel line. The present observation of a gas-like to liquid-like crossover in the self dynamics of a simple supercritical fluid confirms emerging views on the unexpectedly complex physics of the supercritical state, and could have planet-wide implications and possible industrial applications in green chemistry.

Concentration Fluctuation/Microheterogeneity Duality Illustrated with Aqueous 1,4-Dioxane Mixtures

The structural properties of aqueous 1-4 dioxane mixtures are studied by computer simulations of different water and dioxane force field models, from the perspective of illustrating the link between structural properties at the molecular level and measurable properties such as radiation scattering intensities and Kirkwood-Buff integrals (KBIs). A strategy to consistently correct the KBI obtained from simulations is proposed, which allows us to obtain the genuine KBI corresponding to a given pair of molecular species, in the entire concentration range, and without necessitating excessively large system sizes. The application of this method to the aqueous dioxane mixtures, with an all-atom CHARMM dioxane model and 2 water models, namely, SPC/E and TIP3P, allows one to understand the differences in the structure of the corresponding mixtures at the molecular level, particularly concerning the role of the water aggregates and its model dependence. This study allows us to characterize the dual role played by the concentration fluctuations and the domain segregation, particularly in what concerns the calculated X-ray spectra.

Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry

This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.

Deciphering Density Fluctuations in the Hydration Water of Brownian Nanoparticles via Upconversion Thermometry

We investigate the intricate relationship among temperature, pH, and Brownian velocity in a range of differently sized upconversion nanoparticles (UCNPs) dispersed in water. These UCNPs, acting as nanorulers, offer insights into assessing the relative proportion of high-density and low-density liquid in the surrounding hydration water. The study reveals a size-dependent reduction in the onset temperature of liquid-water fluctuations, indicating an augmented presence of high-density liquid domains at the nanoparticle surfaces. The observed upper-temperature threshold is consistent with a hypothetical phase diagram of water, validating the two-state model. Moreover, an increase in pH disrupts the organization of water molecules, similar to external pressure effects, allowing simulation of the effects of temperature and pressure on hydrogen bonding networks. The findings underscore the significance of the surface of suspended nanoparticles for understanding high- to low-density liquid fluctuations and water behavior at charged interfaces.

Electrofreezing of liquid water at ambient conditions

Water is routinely exposed to external electric fields. Whether, for example, at physiological conditions, in contact with biological systems, or at the interface of polar surfaces in countless technological settings, water responds to fields on the order of a few V Å-1 in a manner that is under intense investigation. Dating back to the 19th century, the possibility of solidifying water upon applying electric fields - a process known as electrofreezing - is an alluring promise that has canalized major efforts since, with uncertain outcomes. Here, we perform long (up to 500 ps per field strength) ab initio molecular dynamics simulations of water at ambient conditions under external electric fields. We show that fields of 0.10 - 0.15 V Å-1 induce electrofreezing to a ferroelectric amorphous phase which we term f-GW (ferroelectric glassy water). The transition occurs after ~ 150 ps for a field of 0.15 V Å-1 and after ~ 200 ps for a field of 0.10 V Å-1 and is signaled by a structural and dynamic arrest and the suppression of the fluctuations of the hydrogen bond network. Our work reports evidence of electrofreezing of bulk liquid water at ambient conditions and therefore impacts several fields, from fundamental chemical physics to biology and catalysis.

Ice-Like Dynamics of Water Clusters

Understanding certain behaviors of water, e.g., its dynamics, is extremely important in various fields. Recently, using 1H nuclear magnetic resonance spectroscopy, we have identified a metastable state of water molecules, i.e., water clusters, in hydrophobic solvents in addition to dissolved water molecules and a small bulk water domain. However, the low abundance of water clusters made observing their dynamics challenging. In this study, the dynamics of water clusters in benzene-d6 were investigated by quasi-elastic neutron scattering measurements using the AGNES time-of-flight spectrometer of the Japan Research Reactor JRR-3. The diffusion dynamics of the hydrogen atoms were much slower than those of bulk water (with a self-diffusion coefficient of 1.15 × 10-9 m2/s at 273 K) and even slower than the upper-limit dynamics at the observable scale (10-10 m2/s). The dynamics of water clusters are slow, "like ice", even at 283-303 K, which is above the freezing point of water (273 K).

Exploring the impact of ions on oxygen K-edge X-ray absorption spectroscopy in NaCl solution using the GW-Bethe-Salpeter-equation approach

X-ray absorption spectroscopy (XAS) is a powerful experimental tool to probe the local structure in materials with the core hole excitations. Here, the oxygen K-edge XAS spectra of the NaCl solution and pure water are computed by using a recently developed GW-Bethe-Salpeter equation approach, based on configurations modeled by path-integral molecular dynamics with the deep-learning technique. The neural network is trained on ab initio data obtained with strongly constrained and appropriately normed density functional theory. The observed changes in the XAS features of the NaCl solution, compared to those of pure water, are in good agreement between experimental and theoretical results. We provided detailed explanations for these spectral changes that occur when NaCl is solvated in pure water. Specifically, the presence of solvating ion pairs leads to localization of electron-hole excitons. Our theoretical XAS results support the theory that the effects of the solvating ions on the H-bond network are mainly confined within the first hydration shell of ions, however beyond the shell the arrangement of water molecules remains to be comparable to that observed in pure water.

Electrical noise in electrolytes: a theoretical perspective

Seemingly unrelated experiments such as electrolyte transport through nanotubes, nano-scale electrochemistry, NMR relaxometry and surface force balance measurements, all probe electrical fluctuations: of the electric current, the charge and polarization, the field gradient (for quadrupolar nuclei) and the coupled mass/charge densities. The fluctuations of such various observables arise from the same underlying microscopic dynamics of the ions and solvent molecules. In principle, the relevant length and time scales of these dynamics are encoded in the dynamic structure factors. However, modelling the latter for frequencies and wavevectors spanning many orders of magnitude remains a great challenge to interpret the experiments in terms of physical processes such as solvation dynamics, diffusion, electrostatic and hydrodynamic interactions between ions, interactions with solid surfaces, etc. Here, we highlight the central role of the charge-charge dynamic structure factor in the fluctuations of electrical observables in electrolytes and offer a unifying perspective over a variety of complementary experiments. We further analyze this quantity in the special case of an aqueous NaCl electrolyte, using simulations with explicit ions and an explicit or implicit solvent. We discuss the ability of the standard Poisson-Nernst-Planck theory to capture the simulation results, and how the predictions can be improved. We finally discuss the contributions of ions and water to the total charge fluctuations. This work illustrates an ongoing effort towards a comprehensive understanding of electrical fluctuations in bulk and confined electrolytes, in order to enable experimentalists to decipher the microscopic properties encoded in the measured electrical noise.

Accurate SCC-DFTB Parametrization of Liquid Water with Improved Atomic Charges and Iterative Boltzmann Inversion

This work presents improvements of the description of liquid water within the self-consistent-charge density-functional based tight-binding scheme combining the use of Weighted Mulliken (WMull) charges and optimized O-H repulsive potential through the iterative Boltzmann inversion (IBI) process. The quality of the newly developed models is validated considering pair radial distribution functions (RDFs), as well as other structural, energetic, thermodynamic, and dynamic properties. The use of WMull charges certainly improves the agreement with experimental data, however leading to over-structured RDFs at short distance, that can be further improved by considering an optimized O-H repulsive potential obtained by the IBI process. Three different schemes were used to optimize this potential: (i) optimization including short O-H distances. This led to accurate RDFs as well as improved self-diffusion coefficient and heat of vaporization, while the proton transfer energy barrier is severely deteriorated; (ii) optimization starting at long distance. The proton transfer energy barrier is recovered while the heat of vaporization is deteriorated and the O-H RDF is less accurate at short distance; (iii) optimization within the path-integral molecular dynamics scheme which allows us to exclude nuclear quantum effects from the repulsive potential. The latter potential, in conjunction with the WMull improved atomic charges, provides similar results as (i) for structural, dynamic, and thermodynamic properties while recovering a large part of the proton transfer energy barrier. It therefore offers a good compromise to study both dynamic properties and chemistry within liquid water at a quantum chemical level.

Cation coordination polyhedra lead to multiple lengthscale organization in aqueous electrolytes

Understanding multiple lengthscale correlations in the pair distribution functions (PDFs) of aq. electrolytes is a persistent challenge. Here, the coordination chemistry of polyoxoanions supports an ion-network of cation-coordination polyhedra in NaNO3(aq) and NaNO2(aq) that induce long-range solution structure. Oxygen correlations associated with Na+-coordination polyhedra have two characteristics lengthscales; 3.5-5.5 Å and 5.5-7.5 Å, the latter solely associated oligomers. The PDF contraction between 5.5-7.5 Å observed in many electrolytes is attributed to the distinct O⋯O correlation found in dimers and dimer subunits within oligomers.

Insights into the precipitation kinetics of CaCO3 particles in the presence of polystyrene sulfonate using in situ small-angle X-ray scattering

The formation of calcium carbonate (CaCO3) nanoparticles (NPs) in the presence of polystyrene sulfonate (PSS) as an additive was examined by time-resolved small-angle X-ray scattering (SAXS) in a flow system that mimics experimental conditions used at home facilities where the precipitation can be achieved in a beaker. The experiments were carried out at low concentrations to remain in the dilute regime. A model-independent analysis was performed using the Porod invariant which defines the scale factor, leaving only the distribution of radii as the adjustable parameter. The presence of the PSS additive strongly retards the precipitation of CaCO3 NPs. The formation of NPs reaches a state of equilibrium after a few minutes. Here, it is shown that the concentration of precursors at a fixed PSS concentration plays a key role in determining the size of the NPs obtained. A full analysis of the SAXS patterns was carried out using the Hurd-Flower model to account for the weaker intensity decay than the classical Porod behaviour. The temporal evolution of the particle radii was determined. Wide-angle X-ray scattering experiments carried out simultaneously show that the particles formed have the structure of vaterite with growth consistent with the evolution of the Porod invariant.

Low-Temperature Dynamics of Water Confined in Unidirectional Hydrophilic Zeolite Nanopores

The dynamical properties of water molecules confined in the unidirectional hydrophilic nanopores of AlPO₄-54 are investigated with quasi-elastic neutron scattering as a function of temperature down to 118 K. AlPO₄-54 has among the largest pores known for aluminophosphates and zeolites (about 1.3 nm), though they are small enough to prevent water crystallization due to the high degree of confinement. Water molecular diffusion into the pore is here measured down to 258 K. Diffusion is slower than in bulk water and has an activation energy of E_a = (20.8 ± 2.8) kJ/mol, in agreement with previous studies on similar confining media. Surprisingly, local hydrogen dynamics associated with water reorientation is measured down to temperatures (118 K), i.e., well below the expected glass transition temperature of bulk water. The reorientational time scale shows the well-known non-Arrhenius behavior down to the freezing of water mass diffusion, while it shows a feeble temperature dependence below. This fast local dynamics, of the order of fractions of nanoseconds, is believed to take place in the dense, highly disordered amorphous water occupying the pore center, indicating its possible plastic nature.

Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding

Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.

Mechanism of Cations Suppressing Proton Diffusion Kinetics for Electrocatalysis

Proton transfer is crucial for electrocatalysis. Accumulating cations at electrochemical interfaces can alter the proton transfer rate and then tune electrocatalytic performance. However, the mechanism for regulating proton transfer remains ambiguous. Here, we quantify the cation effect on proton diffusion in solution by hydrogen evolution on microelectrodes, revealing the rate can be suppressed by more than 10 times. Different from the prevalent opinions that proton transport is slowed down by modified electric field, we found water structure imposes a more evident effect on kinetics. FTIR test and path integral molecular dynamics simulation indicate that proton prefers to wander within the hydration shell of cations rather than to hop rapidly along water wires. Low connectivity of water networks disrupted by cations corrupts the fast-moving path in bulk water. This study highlights the promising way for regulating proton kinetics via a modified water structure.

Kinetics and Mechanisms of Pressure-Induced Ice Amorphization and Polyamorphic Transitions in a Machine-Learned Coarse-Grained Water Model

Water glasses have attracted considerable attention due to their potential connection to a liquid-liquid transition in supercooled water. Here we use molecular simulations to investigate the formation and phase behavior of water glasses using the machine-learned bond-order parameter (ML-BOP) water model. We produce glasses through hyperquenching of water, pressure-induced amorphization (PIA) of ice, and pressure-induced polyamorphic transformations. We find that PIA of polycrystalline ice occurs at a lower pressure than that of monocrystalline ice and through a different mechanism. The temperature dependence of the amorphization pressure of polycrystalline ice for ML-BOP agrees with that in experiments. We also find that ML-BOP accurately reproduces the density, coordination number, and structural features of low-density (LDA), high-density (HDA), and very high-density (VHDA) amorphous water glasses. ML-BOP accurately reproduces the experimental radial distribution function of LDA but overpredicts the minimum between the first two shells in high-density glasses. We examine the kinetics and mechanism of the transformation between low-density and high-density glasses and find that the sharp nature of these transitions in ML-BOP is similar to that in experiments and all-atom water models with a liquid-liquid transition. Transitions between ML-BOP glasses occur through a spinodal-like mechanism, similar to ice crystallization from LDA. Both glass-to-glass and glass-to-ice transformations have Avrami-Kolmogorov kinetics with exponent n = 1.5 ± 0.2 in experiments and simulations. Importantly, ML-BOP reproduces the competition between crystallization and HDA→LDA transition above the glass transition temperature T_g, and separation of their time scales below T_g, observed also in experiments. These findings demonstrate the ability of ML-BOP to accurately reproduce water properties across various regimes, making it a promising model for addressing the competition between polyamorphic transitions and crystallization in water and solutions.

Observation of a Plastic Crystal in Water-Ammonia Mixtures under High Pressure and Temperature

Solid mixtures of ammonia and water, the so-called ammonia hydrates, are thought to be major components of solar and extra-solar icy planets. We present here a thorough characterization of the recently reported high pressure (P)-temperature (T) phase VII of ammonia monohydrate (AMH) using Raman spectroscopy, X-ray diffraction, and quasi-elastic neutron scattering (QENS) experiments in the ranges 4-10 GPa, 450-600 K. Our results show that AMH-VII exhibits common structural features with the disordered ionico-molecular alloy (DIMA) phase, stable above 7.5 GPa at 300 K: both present a substitutional disorder of water and ammonia over the sites of a body-centered cubic lattice and are partially ionic. The two phases however markedly differ in their hydrogen dynamics, and QENS measurements show that AMH-VII is characterized by free molecular rotations around the lattice positions which are quenched in the DIMA phase. AMH-VII is thus a peculiar crystalline solid in that it combines three types of disorder: substitutional, compositional, and rotational.

Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset

Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.

Transferable Force Fields from Experimental Scattering Data with Machine Learning Assisted Structure Refinement

Deriving transferable pair potentials from experimental neutron and X-ray scattering measurements has been a longstanding challenge in condensed matter physics. State-of-the-art scattering analysis techniques estimate real-space microstructure from reciprocal-space total scattering data by refining pair potentials to obtain agreement between simulated and experimental results. Prior attempts to apply these potentials with molecular simulations have revealed inaccurate predictions of thermodynamic fluid properties. In this Letter, a machine learning assisted structure-inversion method applied to neutron scattering patterns of the noble gases (Ne, Ar, Kr, and Xe) is shown to recover transferable pair potentials that accurately reproduce both microstructure and vapor-liquid equilibria from the triple to critical point. Therefore, it is concluded that a single neutron scattering measurement is sufficient to predict macroscopic thermodynamic properties over a wide range of states and provide novel insight into local atomic forces in dense monatomic systems.

Optical measurement of the picosecond fluid mechanics in simple liquids generated by vibrating nanoparticles: a review

Standard continuum assumptions commonly used to describe the fluid mechanics of simple liquids have the potential to break down when considering flows at the nanometer scale. Two common assumptions for simple molecular liquids are that (1) they exhibit a Newtonian response, where the viscosity uniquely specifies the linear relationship between the stress and strain rate, and (2) the liquid moves in tandem with the solid at any solid-liquid interface, known as the no-slip condition. However, even simple molecular liquids can exhibit a non-Newtonian, viscoelastic response at the picosecond time scales that are characteristic of the motion of many nanoscale objects; this viscoelasticity arises because these time scales can be comparable to those of molecular relaxation in the liquid. In addition, even liquids that wet solid surfaces can exhibit nanometer-scale slip at those surfaces. It has recently become possible to interrogate the viscoelastic response of simple liquids and associated nanoscale slip using optical measurements of the mechanical vibrations of metal nanoparticles. Plasmon resonances in metal nanoparticles provide strong optical signals that can be accessed by several spectroscopies, most notably ultrafast transient-absorption spectroscopy. These spectroscopies have been used to measure the frequency and damping rate of acoustic oscillations in the nanoparticles, providing quantitative information about mechanical coupling and exchange of mechanical energy between the solid particle and its surrounding liquid. This information, in turn, has been used to elucidate the rheology of viscoelastic simple liquids at the nanoscale in terms of their constitutive relations, taking into account separate viscoelastic responses for both shear and compressible flows. The nanoparticle vibrations have also been used to provide quantitative measurements of slip lengths on the single-nanometer scale. Viscoelasticity has been shown to amplify nanoscale slip, illustrating the interplay between different aspects of the unconventional fluid dynamics of simple liquids at nanometer length scales and picosecond time scales.

Experimental Confirmation of the Universal Law for the Vibrational Density of States of Liquids

An analytical model describing the vibrational density of states (VDOS) of liquids has long been elusive, owing to the complexities of liquid dynamics. Nevertheless, Zaccone and Baggioli have recently developed such a model which was proposed to be the universal law for the vibrational density of states of liquids. Distinct from the Debye law, g(ω) ∝ ω², for solids, the universal law for liquids reveals a linear relationship, g(ω) ∝ ω, in the low-energy region. We have confirmed this universal law with experimental VDOS measured by inelastic neutron scattering on real liquid systems including water, liquid metal, and polymer liquids, and have applied this model to extract the effective relaxation rate for the short time dynamics for each liquid. The model has also been further evaluated in the prediction of the specific heat with comparison to existing experimental data as well as with values obtained by different approaches.

A Benchmark Protocol for DFT Approaches and Data-Driven Models for Halide-Water Clusters

Dissolved ions in aqueous media are ubiquitous in many physicochemical processes, with a direct impact on research fields, such as chemistry, climate, biology, and industry. Ions play a crucial role in the structure of the surrounding network of water molecules as they can either weaken or strengthen it. Gaining a thorough understanding of the underlying forces from small clusters to bulk solutions is still challenging, which motivates further investigations. Through a systematic analysis of the interaction energies obtained from high-level electronic structure methodologies, we assessed various dispersion-corrected density functional approaches, as well as ab initio-based data-driven potential models for halide ion-water clusters. We introduced an active learning scheme to automate the generation of optimally weighted datasets, required for the development of efficient bottom-up anion-water models. Using an evolutionary programming procedure, we determined optimized and reference configurations for such polarizable and first-principles-based representation of the potentials, and we analyzed their structural characteristics and energetics in comparison with estimates from DF-MP2 and DFT+D quantum chemistry computations. Moreover, we presented new benchmark datasets, considering both equilibrium and non-equilibrium configurations of higher-order species with an increasing number of water molecules up to 54 for each F, Cl, Br, and I anions, and we proposed a validation protocol to cross-check methods and approaches. In this way, we aim to improve the predictive ability of future molecular computer simulations for determining the ongoing conflicting distribution of different ions in aqueous environments, as well as the transition from nanoscale clusters to macroscopic condensed phases.

Molecular dynamics simulations of structural and dynamical aspects of DNA hydration water

Water is a remarkable liquid, both because of it is intriguing but also because of its importance. Water plays a key role on the structure and function of biological molecules, but on the other hand also the structure and dynamics of water are deeply influenced by its interactions with biological molecules, specially at low temperatures, where water's anomalies are enhanced. Here we present extensive molecular dynamics simulations of water hydrating a oligonucleotide down to very low temperatures (supercooled water), comparing four water models and analyzing the water structure and dynamics in different domains: water in the minor groove, water in the major groove and bulk water. We found that the water in the grooves is slowed down by the interactions with the nucleic acid and a hints of a dynamic transition regarding translational and orientational dynamics were found, specially for the water models TIP4P/2005 and TIP4P-Ew, which also showed the closest agreement with available experimental data. The behavior of water in such extreme conditions is relevant for the study of cryopreservation of biological tissues.

Broadband Dielectric Spectroscopic Analysis toward Characterization of the Hydration State and Bioprotective Superiority of Trehalose

Alteration of the hydrogen-bond (H-bond) network by trehalose is acknowledged as a bioprotective agent. However, most studies exploring the hydration superiority of the trehalose structure are limited structure are limited by the computational cost or a narrow-range spectrum. In the present study, the structural and dynamical behaviors of the H-bond network of trehalose and maltose solutions were observed and compared with a broadband dielectric spectrum (100 MHz-18 THz) to investigate the influence of the trehalose structure on the bioprotective function. From the relaxation time, the reorientation cooperativity, resonant frequency, and damping constant of water-water vibration, the symmetric structure of trehalose allowed a more significant H-bond strengthening effect and homogeneous aqueous environment. In contrast, the difference in the hydration number between trehalose and maltose was negligible. Thus, the enhanced H-bond strengthening effect and homogeneous aqueous environment owing to the symmetric structure are the essential factors that contribute to the remarkable bioprotective effect of trehalose.

Structural Analysis of Molecular Materials Using the Pair Distribution Function

This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.

Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments

The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.

Long-Range Structures of Amorphous Solid Water

High-energy X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) of amorphous solid water (ASW) were studied during vapor deposition and the heating process. From the diffraction patterns, the oxygen–oxygen pair distribution functions (PDFs) were calculated up to the eighth coordination shell and an r = 23 Å. The PDF of ASW obtained both during vapor deposition at 80 K as well as the subsequent heating are consistent with that of low-density amorphous ice. The formation and temperature-induced collapse of micropores were observed in the XRD data and in the FTIR measurements, more specifically, in the OH stretch and the dangling mode. Above 140 K, ASW crystallizes into a stacking disordered ice, I_sd. It is observed that the fourth, fifth, and sixth peaks in the PDF, corresponding to structural arrangements between 8 and 12 Å, are the most sensitive to the onset of crystallization.

Multiple scattering and resolution effects in small-angle neutron scattering experiments calculated and corrected by the software package MuScatt

This article deals with multiple scattering effects that are important for the method of small-angle neutron scattering (SANS). It considers three channels for the coherent elastic, the incoherent elastic and the incoherent inelastic scattering processes. The first channel contains the desired information on the experiment. Its multiple scattering effects can be desmeared, as shown in the later sections of the article. The other two channels display a nearly constant background as a function of the scattering angle. The incoherent elastic scattering is treated by the theory of Chandrasekhar, allowing for multiple scattering even at large scattering angles. The transfer to a single representative thermalized wavelength by the inelastic scattering - as a simplification - is assumed to happen by a single scattering event. Once the transition to this altered wavelength has happened, further incoherent multiple scattering is considered. The first part of the paper deals with the multiple scattering effects of light water. In the later part of the article, deconvolution algorithms for multiple scattering and instrumental resolution of the elastic coherent signal as implemented in the program MuScatt are described. All of these considerations are interesting for both reactor-based instruments with velocity selectors and time-of-flight SANS instruments and may improve the reliability of the data treatment.

What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on?

The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.

Liquid structure under extreme conditions: high-pressure x-ray diffraction studies

Under extreme conditions of high pressure and temperature, liquids can undergo substantial structural transformations as their atoms rearrange to minimise energy within a more confined volume. Understanding the structural response of liquids under extreme conditions is important across a variety of disciplines, from fundamental physics and exotic chemistry to materials and planetary science.In situexperiments and atomistic simulations can provide crucial insight into the nature of liquid-liquid phase transitions and the complex phase diagrams and melting relations of high-pressure materials. Structural changes in natural magmas at the high-pressures experienced in deep planetary interiors can have a profound impact on their physical properties, knowledge of which is important to inform geochemical models of magmatic processes. Generating the extreme conditions required to melt samples at high-pressure, whilst simultaneously measuring their liquid structure, is a considerable challenge. The measurement, analysis, and interpretation of structural data is further complicated by the inherent disordered nature of liquids at the atomic-scale. However, recent advances in high-pressure technology mean that liquid diffraction measurements are becoming more routinely feasible at synchrotron facilities around the world. This topical review examines methods for high pressure synchrotron x-ray diffraction of liquids and the wide variety of systems which have been studied by them, from simple liquid metals and their remarkable complex behaviour at high-pressure, to molecular-polymeric liquid-liquid transitions in pnicogen and chalcogen liquids, and density-driven structural transformations in water and silicate melts.

Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

[Figure: see text].

Structural investigation of three distinct amorphous forms of Ar hydrate

Three amorphous forms of Ar hydrate were produced using the crystalline clathrate hydrate Ar·6.5H₂O (structure II, Fd3̄m, a ≈ 17.1 Å) as a precursor and structurally characterized by a combination of isotope substitution (³⁶Ar) neutron diffraction and molecular dynamics (MD) simulations. The first form followed from the pressure-induced amorphization of the precursor at 1.5 GPa at 95 K and the second from isobaric annealing at 2 GPa and subsequent cooling back to 95 K. In analogy to amorphous ice, these amorphs are termed high-density amorphous (HDA) and very-high-density amorphous (VHDA), respectively. The third amorph (recovered amorphous, RA) was obtained when recovering VHDA to ambient pressure (at 95 K). The three amorphs have distinctly different structures. In HDA the distinction of the original two crystallographically different Ar guests is maintained as differently dense Ar–water hydration structures, which expresses itself in a split first diffraction peak in the neutron structure factor function. Relaxation of the local water structure during annealing produces a homogeneous hydration environment around Ar, which is accompanied with a densification by about 3%. Upon pressure release the homogeneous amorphous structure undergoes expansion by about 21%. Both VHDA and RA can be considered frozen solutions of immiscible Ar and water in which in average 15 and 11 water molecules, respectively, coordinate Ar out to 4 Å. The local water structures of HDA and VHDA Ar hydrates show some analogy to those of the corresponding amorphous ices, featuring H₂O molecules in 5- and 6-fold coordination with neighboring molecules. However, they are considerably less dense. Most similarity is seen between RA and low density amorphous ice (LDA), which both feature strictly 4-coordinated H₂O networks. It is inferred that, depending on the kind of clathrate structure and occupancy of cages, amorphous states produced from clathrate hydrates display variable local water structures.

Three amorphous forms of Ar clathrate hydrate (pressure-amorphized, annealed and recovered) were characterized by isotope substitution (³⁶Ar) neutron diffraction and molecular dynamics and their local coordinations analyzed and compared to pure ice.

The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

Direct observation of ultrafast hydrogen bond strengthening in liquid water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network¹, including unusually efficient vibrational energy redistribution and relaxation². An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments^2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

A high-accuracy machine-learning water model for exploring water nanocluster structures

Water, the most important molecule on the Earth, possesses many essential and unique physical properties that are far from completely understood, partly due to serious difficulties in identifying the precise microscopic structures of water. Hence, identifying the structures of water nanoclusters is a fundamental and challenging issue for studies on the relationship between the macroscopic physical properties of water and its microscopic structures. For large-scale simulations (at the level of nm and ns) of water nanoclusters, a calculation method with simultaneous accuracy at the level of quantum chemistry and efficiency at the level of an empirical potential method is in great demand. Herein, a machine-learning (ML) water model was utilized to explore the microscopic structural features at different length scales for water nanoclusters with a size up to several nm. The ML water model can be employed to efficiently predict the structures of water nanoclusters with a similar accuracy to that of density functional theory and with substantially lower computational resource demands. To validate the low-lying structure search results with experimental spectral results, an ML water model combined with velocity autocorrelation function analysis was used to simulate the vibrational spectra of water nanoclusters with up to thousands of water molecules. By comparing the simulated and experimentally recorded vibrational spectra, the atomic structures determined by a simulation based on the ML water model are all verified. To demonstrate its ability to represent water's structural evolution at large length and time scales, the ML water model was employed to model the structural evolution during the crystal-liquid transition, and the phase transition temperatures of water clusters with different sizes were precisely predicted. The ML water model provides an efficient theoretical calculation tool for exploring the structures and physical properties of water and their relationships, especially for clusters with relatively large sizes and processes with relatively long durations.

Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water

Understanding the mechanism responsible for the protein low-temperature crossover observed at T≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å^-1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.

Spin diffusion transfer difference (SDTD) NMR: An advanced method for the characterisation of water structuration within particle networks

HYPOTHESIS

The classical STD NMR protocol to monitor solvent interactions in gels is strongly dependent on gelator and solvent concentrations and does not report on the degree of structuration of the solvent at the particle/solvent interface. We hypothesised that, for suspensions of large gelator particles, solvent structuration could be characterised by STD NMR when taking into account the particle-to-solvent ¹H-¹H spin diffusion transfer using the 1D diffusion equation.

EXPERIMENTS

We have carried out a systematic study on effect of gelator and solvent concentrations, and gelator surface charge, affecting the behaviour of the classical STD NMR build-up curves. To do so, we have characterised solvent interactions in dispersions of starch and cellulose-like particles prepared in deuterated water and alcohol/D₂O mixtures.

FINDINGS

The Spin Diffusion Transfer Difference (SDTD) NMR protocol is independent of the gelator and solvent concentrations, hence allowing the estimation of the degree of solvent structuration within different particle networks. In addition, the simulation of SDTD build-up curves using the general one-dimensional diffusion equation allows the determination of minimum distances (r) and spin diffusion rates (D) at the particle/solvent interface. This novel NMR protocol can be readily extended to characterise the solvent(s) organisation in any type of colloidal systems constituted by large particles.

Temperature-dependent dynamic structure factors for liquid water inferred from inelastic neutron scattering measurements

Temperature-dependent dynamic structure factors S(Q, ω) for liquid water have been calculated using a composite model, which is based on the decoupling approximation of the mean square displacement of the water molecules into diffusion and solid-like vibrational parts. The solid-like vibrational part S_vib(Q, ω) is calculated with the phonon expansion method established in the framework of the incoherent Gaussian approximation. The diffusion part S_diff(Q, ω) relies on the Egelstaff-Schofield translational diffusion model corrected for jump diffusions and rotational diffusions with the Singwi-Sjölander random model and Sears expansion, respectively. Systematics of the model parameters as a function of temperature were deduced from quasi-elastic neutron scattering data analysis reported in the literature and from molecular dynamics (MD) simulations relying on the TIP4P/2005f model. The resulting S(Q, ω) values are confronted by means of Monte Carlo simulations to inelastic neutron scattering data measured with IN4, IN5, and IN6 time-of-flight spectrometers of the Institut Laue-Langevin (ILL) (Grenoble, France). A modest range of temperatures (283-494 K) has been investigated with neutron wavelengths corresponding to incident neutron energies ranging from 0.57 to 67.6 meV. The neutron-weighted multiphonon spectra deduced from the ILL data indicate a slight overestimation by the MD simulations of the frequency shift and broadening of the librational band. The descriptive power of the composite model was suited for improving the comparison to experiments via Bayesian updating of prior model parameters inferred from MD simulations. The reported posterior temperature-dependent densities of state of hydrogen in H₂O would represent valuable insights for studying the collective coupling interactions in the water molecule between the inter- and intramolecular degrees of freedom.

Time-of-flight modulated intensity small-angle neutron scattering measurement of the self-diffusion constant of water

The modulated intensity by zero effort small-angle neutron scattering (MI-SANS) technique is used to measure scattering with a high energy resolution on samples normally ill-suited for neutron resonance spin echo. The self-diffusion constant of water is measured over a q–t range of 0.01–0.2 Å−1 and 70–500 ps. In addition to demonstrating the methodology of using time-of-flight MI-SANS instruments to observe diffusion in liquids, the results support previous measurements on water performed with different methods. This polarized neutron technique simultaneously measures the intermediate scattering function for a wide range of time and length scales. Two radio frequency flippers were used in a spin-echo setup with a 100 kHz frequency difference in order to create a high-resolution time measurement. The results are compared with self-diffusion measurements made by other techniques and the general applicability of MI-SANS at a pulsed source is assessed.