Structural Properties Of Liquid Water Research Articles

Simulating the isotropic Raman spectra of O-H stretching mode in liquid H2O based on a machine learning potential: the influence of vibrational couplings.

In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that the DP model exhibits DFT-level accuracy, and the DeePMD simulation is a promising approach for modeling the structural properties of liquid water. Based on the DeePMD simulation trajectories, we calculated the isotropic Raman spectra of the O-H stretching mode using the surface-specific velocity-velocity correlation function (ssVVCF), showing that the DeePMD/ssVVCF approach can correctly capture the bimodal characteristics of the experimental Raman spectra, with one peak located near 3400 cm-1 and the other near 3250 cm-1. The success of the DeePMD/ssVVCF approach should be credited to (1) the DFT-level accuracy of the DP model for H2O, (2) the ssVVCF formulation considering the coupling between vibrational modes, and (3) non-Condon effects. Furthermore, the DeePMD simulations revealed that the anharmonic interactions between the coupled water molecules in the first and second hydration shells should play an essential role in the strong mixing of the H-O-H bending mode and the O-H stretching mode, leading to the delocalization of the O-H stretching band. In particular, increasing the strength of hydrogen bonds would enhance the bend-stretch coupling, leading to the red-shifting of the O-H vibrational spectra and the increase in the intensity of the shoulder around 3250 cm-1.

Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface

A mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning. It is possible thanks to the structural properties of interfacial water. These properties include the ability to create high-volume aggregates of water molecules. They can appear near and be anchored to both the ice-binding plane of the antifreeze molecule and the ice surface. When an AFP approaches the growing face of ice, these high-volume, ordered structures near the ice and near the AFP molecule merge together smoothly, but only if the proper distance between the ice and the AFP is ensured. If this is not the case, the resulting merged structure is deformed from its preferred shape and as a result a force occurs that attempts to correct the positioning of the protein. Only then the crystallization of the merged aggregate can proceed unhampered which results in binding of the AFP molecule onto the ice. • The molecular mechanism of interaction of antifreeze proteins with the surface of ice remains unclear. • The existence of long-ranged, water-mediated interactions between the AFP molecule and the ice surface is demonstrated. • These interactions affect the positioning of the AFP molecule relatively to the ice and influence the adsorption process. • Observed behavior is explained by evoking specific structural properties of liquid water.

Isotope effects in liquid water via deep potential molecular dynamics

A comprehensive microscopic understanding of ambient liquid water is a major challenge for ab initio simulations as it simultaneously requires an accurate quantum mechanical description of the underlying potential energy surface (PES) as well as extensive sampling of configuration space. Due to the presence of light atoms (e.g. or ), nuclear quantum fluctuations lead to observable changes in the structural properties of liquid water (e.g. isotope effects), and therefore provide yet another challenge for ab initio approaches. In this work, we demonstrate that the combination of dispersion-inclusive hybrid density functional theory (DFT), the Feynman discretised path-integral (PI) approach, and machine learning (ML) constitutes a versatile ab initio based framework that enables extensive sampling of both thermal and nuclear quantum fluctuations on a quite accurate underlying PES. In particular, we employ the recently developed deep potential molecular dynamics (DPMD) model – a neural-network representation of the ab initio PES – in conjunction with a PI approach based on the generalised Langevin equation (PIGLET) to investigate how isotope effects influence the structural properties of ambient liquid and . Through a detailed analysis of the interference differential cross sections as well as several radial and angular distribution functions, we demonstrate that this approach can furnish a semi-quantitative prediction of these subtle isotope effects.

Effects of dispersion interactions on the structure, polarity, and dynamics of liquid-vapor interface of an aqueous NaCl solution: Results of first principles simulations at room temperature.

The effects of dispersion interaction on the structure, polarity, and dynamics of liquid-vapor interface of a concentrated (5.3M) aqueous NaCl solution have been investigated through first-principles simulations. Among the structural properties, we have investigated the inhomogeneous density profiles of molecules, hydrogen bond distributions, and orientational profiles. On the dynamical side, we have calculated diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion of molecules. The polarity of water molecules across the interface is also calculated. Our simulation results are compared with those when no dispersion corrections are included. It is found that the inclusion of dispersion correction predicts an overall improvement of the structural properties of liquid water. The current study reveals a faster relaxation of hydrogen bonds, diffusion, and rotational motion for both interfacial and bulk molecules compared to the results when no such dispersion corrections are included. The dynamics of vibrational frequency fluctuations are also calculated which capture the relaxation of hydrogen bond fluctuations in the bulk and interfacial regions. Generally, the hydrogen bonds at the interfaces are found to have longer lifetimes due to reduced cooperative effects.

Note: Assessment of the SCAN+rVV10 functional for the structure of liquid water.

The performance of the SCAN+rVV10 functional in modeling the structural properties of liquid water is studied through constant-volume ab initio molecular dynamics simulations with both classical and quantum nuclei. The radial distribution functions are found to be slightly overstructured with respect to experiment, but overall similar to those achieved with the bare SCAN and the rVV10 functionals. From the pressures calculated during the dynamics, it is inferred that the SCAN+rVV10 functional leads to a noticeable overestimation of the density of liquid water.

Structural Properties of Liquid Water and Ice Ih from Ab-Initio Molecular Dynamics with a Non-Local Correlation Functional

Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice) at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement with experiments for pair distribution functions, in addition to molecular dipole moments, vis-a-vis previous flavours of ab-initio molecular dynamics simulation of water, highlighting the importance of appropriate dispersion. Intramolecular geometry has also been examined, in addition to hydrogen-bonding interactions; it was found that an improved description of dispersion via non-local correlation helps to reduce over-structuring associated with the Perdew-Becke-Ernzerhof (PBE) and other commonly-used functionals.

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed analysis comprising the study of the partial radial distribution functions, various local order indices, the hydrogen-bond network, and the selfdiffusion coefficient. The explicit treatment of the van der Waals interactions leads to an overall improved description of liquid water.

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: templating, molding, and superdiffusion.

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer ("templating" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

Liquid water simulations with the density fragment interaction approach.

We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.

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.

On the suitability of the ILJ function to match different formulations of the electrostatic potential for water-water interactions

Energetic and structural properties of liquid water have been calculated using molecular dynamics simulations in order to investigate the effect of different formulations of the van der Waals (vdW) interaction on the behaviour of liquid water. In particular, two model potentials, the SPC/E using a Lennard Jones (LJ) function and the AMPF using an Improved Lennard Jones function (ILJ) have been considered. The flexibility of the ILJ function in the AMPF model has also been analysed, proving that its vdW component can match different parametrizations of the electrostatic component.

Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring.

Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited

The solvation and transport of the hydrated excess proton is studied using the Car-Parrinello molecular-dynamics (CPMD) simulation method. The simulations were performed using BLYP and HCTH gradient-corrected exchange-correlation energy functionals. The fictitious electronic mass was chosen to be small enough so that the underlying water structural and dynamical properties were converged with respect to this important CPMD simulation parameter. An unphysical overstructuring of liquid water in the CPMD simulations using the BLYP functional resulted in the formation of long-lived hydrogen-bonding structures involving the excess proton and a particular (special) water oxygen. The excess proton was observed to be attracted to the special oxygen through the entire length of the BLYP CPMD simulations. Consequently, the excess proton diffusion was limited by the mobility of the special oxygen in the slowly diffusing water network and, in turn, the excess proton self-diffusion coefficient was found to be significantly below the experimental value. On the other hand, the structural properties of liquid water in the HCTH CPMD simulation were seen to be in better agreement with experiment, although the water and excess proton diffusions were still well below the experimental value.

Thermodynamic and structural properties of liquid water around the temperature of maximum density in a wide range of pressures: A computer simulation study with a polarizable potential model

Computer simulations of liquid water have been performed with the polarizable Brodholt–Sampoli–Vallauri (BSV) potential model at several temperatures around the temperature of maximum density (TMD) in the entire pressure range in which such a density maximum exists in thermodynamically stable liquid water. The temperature and pressure dependence of the thermodynamic and structural properties has been analyzed on the basis of these simulations. We find that the BSV model reproduces most of the important thermodynamic features of water in this temperature and pressure range. The BSV model is also found to reproduce another of the anomalous properties of liquid water, i.e., the isothermal compressibility goes through a minimum when the temperature is increased. On the other hand, it is found that above the TMD the density of the model decreases much faster with increasing temperature than in real water. However, this failure, which is a common feature of the polarizable water models, is rather unimportant in the narrow temperature range studied here. In analyzing the molecular level structure of water as a function of the thermodynamic conditions we find that the increase of the temperature as well as of the pressure has a distorting effect on the tetrahedral hydrogen bonded network, and it causes an increase of the fraction of the interstitial neighbors of the molecules. These changes result in a more compact structure and hence in an increase of the density of the system. When these changes are induced by the temperature, the increasing thermal motion of the molecules can compensate the increase of the density, and the two opposite effects result in the appearance of the density maximum.

Structural properties of liquid water

Monte Carlo simulations of molecular configurations of liquid water in theNVT-ensemble atT=298 K using unit cells containing 125 and 1000 molecules were, carried out. Comparison of experimental and calculated radial distribution functions suggests the existence of two types of spatial ordering in water. Structural properties of low-energy molecular clusters and associates of closed cycles of H-bonds were determined. The properties of the network of H-bonds can be described by a set of fundamental constants and one free parameter,viz., the probability of bond formation. The existence of long-range correlations in spatial arrangement of both the molecules and the cycles of bonds was established.

Molecular dynamics study of water clusters, liquid, and liquid–vapor interface of water with many-body potentials

The molecular dynamics computer simulation technique is used to develop a rigid, four-site polarizable model for water. The suggested model reasonably describes the important properties of water clusters, the thermodynamic and structural properties of the liquid and the liquid/vapor interface of water. The minimum energy configurations and the binding energies for these clusters are in reasonable agreement with accurate electronic structure calculations. The model predicts that the water trimer, tetramer, and pentamer have cyclic planar minimum energy structures. A prismlike structure is predicted to be lowest in energy for the water hexamer, and a cagelike structure is the second lowest in energy, with an energy of about 0.2 kcal/mol higher than the prismlike structure. The results are consistent with recent quantum Monte Carlo simulations as well as electronic structure calculations. The computed thermodynamic properties for the model, at room temperature, including the liquid density, the enthalpy of vaporization, as well as the diffusion coefficient, are in excellent agreement with experimental values. Structural properties of liquid water, such as the radial distribution functions, neutron, and x-ray scattering intensities, were calculated and critically evaluated against the experimental measurements. In all cases, we found the agreement between the observed data and the computed properties to be quite reasonable. The computed density profile of the water’s liquid/vapor interface shows that the interface is not sharp at a microscopic level and has a thickness of 3.2 Å at 298 K. These results are consistent with those reported in earlier work on the same systems. The calculated surface tension at room temperature is in reasonable agreement with the corresponding experimental data. As expected, the computed average dipole moments of water molecules near the interface are close to their gas phase values, while water molecules far from the interface have dipole moments corresponding to their bulk values.

The dynamics of liquid water: Simulation and submillimeter spectroscopy

Abstract A combination of classical molecular dynamics computer simulation and submillimeter laser and interferometric spectroscopy is used to investigate the dynamical and structural properties of liquid water at 300 K, ϱ = 0.997 gm cm −3 . A new approach to the empirical pair potential, based on the ST2 of Raman and Stillinger has been used to match the low frequency part of the submillimeter spectrum and to generate a range of auto and cross correlation functions. The results from this new atom-atom potential have been compared with those from the work of Stillinger and Rahman and Clementi et al. Broad agreement was obtained and the new potential used to investigate by computer simulation the statistical interdependence of the water molecule's rotation and translation in liquid water at 300 K. This investigation has resulted in the detection of a.c.f.'s of the classical Coriolis, centripetal, and “non uniform” accelerations of the water molecule, together with some of the numerous cross correlations suggested by the rotating frame theory of Langevin diffusion.

A structure model for the lecithin-cholesterol-water membrane

Starting from the structural properties of liquid water and making use of the known bond lengths and orientations of the hydrogen-bonded water molecules, models for the water-lecithin and the water-lecithin-cholesterol systems have been derived. The models are in good agreement with the known properties of the basic cell membrane.

Solute–Water Interactions and the Solubility Behaviour of Long-chain Paraffin Hydrocarbons

THE effect of non-polar groups on the structural properties of liquid water is of interest in several fields of enquiry. The most direct method of studying such systems is by the determination of hydrocarbon solubilities, but, until recently, reliable experimental data have been confined to the four lowest members of the paraffin series1,2. McAuliffe has provided a valuable extension to the existing data by his study of the solubilities of twenty-three aliphatic and aromatic hydrocarbons3. His results show good agreement with earlier data for the C1–C4 paraffins1,2, but his values for the C5–C8 members of the series are lower by more than one order of magnitude than the only other recorded solubilities of these hydrocarbons4.