Structural Correlations and Motifs in Liquid Water at Selected Temperatures: Ab Initio and Empirical Model Predictions

Liquid Structure and Hydrogen Bonding in Aqueous Hydroxylammonium Nitrate

Hydroxylammonium nitrate (HAN) has emerged as a promising component in ionic liquid-based spacecraft propellants. However, the physicochemical and structural properties of aqueous HAN have been largely overlooked. The purpose of this study is to investigate the hydrogen bonding in aqueous HAN and understand its implications on these properties and the proton transfer mechanism as a function of concentration. Classical polarizable molecular dynamics simulations have been employed with the APPLE&P force field to analyze the geometry of individual hydrogen bonds and the overall hydrogen-bonding network in various concentrations of aqueous HAN. Radial distribution functions (RDFs) and spatial distribution functions (SDFs) indicate the structural arrangement of the species and their hydrogen bonds. Projections of water density and the orientation of its electric dipole moment near the ions provide insight into the hydrogen-bonding network. The incorporation of water into the hydrogen-bonding network at high ion concentrations occurs via interstitial accommodation around the ions immediately outside the first solvation shell. While ion pairs are observed at all concentrations considered, the frequency of Ha···On hydrogen bonds increases substantially with the ion concentration. The findings contribute to a better fundamental understanding of HAN and the precursors of reactivity, crucial to the development of "green" spacecraft propellants.

Revealing the mechanism underlying the effects of γ-aminobutyric acid-dioscorin interactions on dioscorin structure and emulsifying properties by molecular dynamic simulations

Many studies have shown that γ-aminobutyric acid (GABA) exhibits various beneficial biological activities, including gut-modulating, neuro-stimulating, and cardio-protecting activities. Naturally, GABA exists in small amounts in yam, which is primarily synthesized by the decarboxylation of L-glutamic acid in the presence of glutamate decarboxylase. Dioscorin, the major tuber storage protein of yam, has been shown to have good solubility and emulsifying activity. However, how GABA interacts with dioscorin and affects their properties has yet to be clarified. In this research, the physicochemical and emulsifying properties of GABA-fortified dioscorin, which was dried by spray drying and freeze drying, were studied. As results, the freeze-dried (FD) dioscorin produced more stable emulsions, while the spray-dried (SD) dioscorin adsorbed more rapidly to oil/water (O/W) interface. The fluorescence spectroscopy, ultraviolet spectroscopy and circular dichroism spectroscopy showed that GABA changed the structure of dioscorin, by exposing its hydrophobic groups. The addition of GABA significantly promoted the adsorption of dioscorin to the O/W interface and prevented droplets coalescence. The results of molecular dynamics simulation (MD) showed that GABA destroyed the H-bond network between dioscorin and water, increased surface hydrophobicity and finally improved the emulsifying properties of dioscorin.

Temperature Dependence of Hydrogen Bond Networks of Liquid Water: Thermodynamic Properties and Structural Heterogeneity from Topological Descriptors

Topological analyses of hydrogen bond networks were performed based on the complex network and island statistics of liquid water at different temperatures. The influence of temperature on the liquid water structures and the topological properties of the hydrogen bond networks was investigated by Metropolis Monte Carlo simulations with the TIP4P/2005 potential model. The bilinear behavior of the second peak in the radial distribution function with the temperature was properly reproduced by these simulations. The average connectivity also displayed a bilinear behavior consistent with being a local descriptor. The semiglobal average path length (or geodesic distance) descriptor showed an unprecedented trimodal distribution, whose areas were dependent on the temperature. Considering equilibrium between these three sets of networks, standard enthalpy and entropy of equilibrium were determined for the first time, providing new insights into the structural heterogeneities of liquid water with interesting perspectives for modeling these quantitative properties of hydrogen bond networks.

Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations

We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.

Dynamics of Ionic Liquid through Intrinsic Vibrational Probes Using the Dispersion-Corrected DFT Functionals

First principles molecular dynamics simulations have been utilized to study the spectral properties of the protic ionic liquid, methylammonium formate (MAF). All simulations were performed using density functional theory (DFT) and various van der Waals-corrected exchange-correlation functionals. We calculated the vibrational stretch frequency distributions, determined the time-frequency correlations of the intrinsic vibrational probes, the N-H and C-O modes in MAF, and the frequency-structure correlations. We also estimated the average hydrogen-bond lifetimes and orientation dynamics to capture the ultrafast spectral response. The spectroscopic signature of the N-H stretching vibrations using the Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals displays a spectral shift in the lower frequency side, suggesting stronger hydrogen-bonding interactions represented by the gradient approximation functionals than the van der Waals (vdW)-corrected simulations. The carboxylate frequency profiles with the dispersion-corrected representations are almost similar without a significant difference in the normalized distributions. Besides, the COO stretching frequencies at the peak maxima positions of the PBE functionals exhibit a lesser deviation from the experimental data. Spectral diffusion dynamics of the intrinsic vibrational probes on the cationic and anionic sites of the ionic liquid proceed through a short time relaxation of the intact hydrogen bonds followed by an intermediate time constant and a longer time decay indicating the switchover of hydrogen bonds. Dispersion-corrected atom-centered one-electron potential (DCACP) correction added to the BLYP system slows down the picosecond time scales of frequency correlation and the time constants of rotational motion, lengthening the overall system dynamics. The observed trends in the time-dependent decays of frequency fluctuations and the orientation autocorrelation functions correlate with the structural interactions in liquid MAF and hydrogen-bond dynamics. In this study, we examine the predictions made by different density functional treatments comparing the results of the uncorrected BLYP and PBE representations with the semiempirical vdW methods of Grimme and matching our calculated data with the experimental observations.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters and Liquid Water

The incorporation of polarization in multiscale quantum-mechanics/molecular-mechanics (QM/MM) simulations is important for a variety of applications, for example, charge-transfer reactions. A recently developed formalism based on a density functional theory description of the QM region and a potential energy function for H₂O molecules that includes quadrupole as well as dipole polarizability of the MM region is used to simulate liquid water and water clusters. Analysis of the energy, atomic forces, MM polarization, and structure is presented. A quantitative assessment of the QM/MM-MM/MM interaction energy differences of all possible QM/MM configurations of (H₂O)_n clusters shows that the interquartile range of the distributions of the QM/MM binding energies is never more than 20 meV/molecule higher or lower than the binding energies produced with either of the single-model results. Comparing these interaction energy differences with the QM/MM induction differences show that they are not systematically caused by the induced MM moments of our polarizable embedding scheme. Optimized hexamer geometries as well as the liquid water structure are shown to be improved in comparison with results obtained using point-charge based embedding models neglecting polarization.

Ab initio thermodynamics of liquid and solid water

Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations, and proton disorder. This is made possible by combining advanced free-energy methods and state-of-the-art machine-learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments and reliable estimates of the melting points of light and heavy water. We observe that nuclear-quantum effects contribute a crucial [Formula: see text] to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine-learning potentials as an intermediate step.

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H₂O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt₂(P₂O₅H₂)₄]^4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

Signature properties of water: Their molecular electronic origins

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water's crystalline phases and amorphous states. We show that many-body responses arising from water's electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a "strong coupling" approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water's complexity and its molecular origin, predicting water's signature physical properties from ice, through liquid-vapor coexistence, to the critical point.

Electronically coarse-grained model for water

We introduce an electronically coarse-grained description of water representing all long range, many-body electronic responses via an embedded quantum oscillator. Leading-order response coefficients and gas phase electrostatic moments are exactly reproduced. Molecular dynamics, using electronic path integral sampling, shows that this framework is sufficient for a realistic liquid to emerge naturally with transferability extending further to nonambient state points and to the free water surface. The model allows the strength of many-body dispersion and polarization to be adjusted independently and these are found to have significant effects on the condensed phase.

Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections

It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)]. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm(3) while that obtained with dispersion corrections is 1.07 g/cm(3), indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.

Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations

The structure and dynamics of the hydrogen-bond network in heavy water (D(2)O) is studied as a function of the temperature using quantum dynamical simulations. Our approach combines an ab initio-based representation of the water interactions with an explicit quantum treatment of the molecular motion. A direct connection between the calculated linear and nonlinear vibrational spectra and the underlying molecular dynamics is made, which provides new insights into the rearrangement of the hydrogen-bond network in heavy water. A comparison with previous calculations on liquid H(2)O suggests that tunneling does not effectively contribute to the dynamics of the water hydrogen-bond network above the melting point. However, the effects of nuclear quantization are not negligible at all temperatures and become increasingly important near the melting point, which is in agreement with recent experimental analysis of the structural properties of liquid water as well as of the proton momentum distribution in supercooled water.

Accurate predictions of water cluster formation, (H₂O)(n=2-10)

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2-10 water molecules. This approach reveals new low energy conformers for (H(2)O)(n=7,9,10). The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.

Influence of individual ionic components on the agglomeration kinetics of silver nanoparticles

The precise characteristic of the agglomeration behavior of colloidal suspensions is of paramount interest to many current studies in nanoscience. This work seeks to elucidate the influence that differently charged salts have on the agglomeration state of a Lee-Meisel-type silver colloid. Moreover, we investigate the influence of the chemical nature of individual ions on their potential to induce agglomeration. Raman spectroscopy and surface-enhanced Raman spectroscopy are used to give insights into mechanistic aspects of the agglomeration process and to assess the differences in the influence of different salts on the agglomeration behavior. Finally, we demonstrate the potential of the measurement procedure used in this work to determine the elementary charge on colloidal NPs.

Probing the Equilibrium Size and Hydrogen Bonding Structure in Aqueous Aerosol Droplets

Comparative measurements on two or more optically trapped aerosol droplets can allow the hygroscopic properties of aerosol to be investigated in exquisite detail. In this paper we consider two methods for assessing the dependence on relative humidity of the water activity and solute concentration in the condensed phase. We demonstrate in this paper that using a control droplet as a microprobe of relative humidity in the vicinity of a second droplet of interest can allow the RH to be determined with an accuracy of between 0.01 to 0.1 %. Not only is such a probe highly responsive, but the accuracy of the RH determination improves with increase in GF or RH, counter to the performance of macroscopic RH probes. We also demonstrate that spontaneous Raman scattering recorded from excitation of the OH stretching vibration in supersaturated solution droplets of sodium chloride shows the considerable perturbation induced by the chloride ion on the hydrogen bonding network. Chloride is recognised as a hydrogen bonding structure breaker and these observations are shown to be consistent with measurements on more dilute solutions.

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE-rich solutions have stronger TFE-water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF(3) groups. The distribution of cluster sizes in solution supports these conclusions.

Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: a first-principles molecular dynamics study

First-principles molecular dynamics calculations performed in a fully converged basis set are used to reveal new details about the mechanism of the anomalous proton-transport process in water, a fundamental question dating back over 200 years. By separating actual structural diffusion from simple rattling events, wherein a proton shuttles forth and back in a hydrogen bond, it is found that the former are driven by a concerted mechanism in which hydronium begins to accept a hydrogen bond from a donor water molecule while the proton-receiving water molecule simultaneously loses one of its acceptor hydrogen bonds. The kinetics of the process are found to be in good agreement with recent experiments.

The properties of water: insights from quantum simulations

The properties of water play a central role in many phenomena of relevance to different areas of science, including physics, chemistry, biology, geology, and climate research. Although well studied for decades, the behavior of water under different conditions and in different environments still remains mysterious and often surprising. In this article, various efforts aimed at providing a comprehensive representation of the water properties at a molecular level through computer modeling and simulation will be described. In particular, the unique role played by the hydrogen-bond network will be examined, first in liquid water, then in the solvation of model biological compounds, and finally in ice, especially highlighting the important effects related to the quantization of the nuclear motion.

Importance of van der Waals interactions in liquid water

We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description of van der Waals interactions in DFT-GGA leads to a softening of liquid water's structure with higher mobility. The results obtained with dispersion-corrected atom-centered potentials are especially encouraging. In particular, the radial distribution functions are in better agreement with experiment, and the self-diffusion coefficient increases by more than three-fold compared with the one predicted by the BLYP functional. This work demonstrates that van der Waals interactions are essential in fine-tuning both structural and dynamical properties of liquid water.

Reversible geminate recombination of hydrogen-bonded water molecule pair

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t(-3/2) asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Anomalies of liquid water at low temperature due to two types of hydrogen bonds

It is believed that water anomalies are related to the hydrogen bonds between water molecules, but the relationship still remains a challenge. Here, by introducing two types of hydrogen bond--strong and weak, we successfully reproduce many liquid water anomalies, particularly the thermodynamic anomalies at supercooled temperature. We find that the exchange of strong and weak H bonds, which enhance the competition between the open and collapsed structures of liquid water, might be the key to those anomalies of supercooled liquid water. Our study is helpful in understanding the hydrogen bond structure in liquid water.

Nuclear quantum effects in water

A path-integral Car-Parrinello molecular dynamics simulation of liquid water and ice is performed. It is found that the inclusion of nuclear quantum effects systematically improves the agreement of first-principles simulations of liquid water with experiment. In addition, the proton momentum distribution is computed utilizing a recently developed open path-integral molecular dynamics methodology. It is shown that these results are in good agreement with experimental data.