Molecular Dynamics Study Of Water Research Articles

A molecular dynamics study of water confined in between two graphene sheets under compression

Several studies have demonstrated interest in creating surfaces with improved water interaction and adaptive properties because the behavior of water confined at the nanoscale plays a significant role in the synthesis of materials for technological applications. Remarkably, confinement at the nanoscale significantly modifies the characteristics of water. We determine the phase diagram of water contained by graphene stack sheets in slab form, at T = 300 K, and for a constant pressure using molecular dynamics simulations. We discover that, as shown in the simulation, water can exist in both the liquid and vapor phases depending on the confining geometry and compressibility ratio. We also pay attention to how stable the interacting liquid is in relation to the pressure of compression that is perpendicular to the graphene sheets. To build this system and analyze its surface interface properties, we also used analytical and electronic scale modeling approaches. The impact of nanoconfinement on internal pressure may be seen in water, and this can be used to create interfacial materials for the creation of environmentally friendly solar cell materials. Our research highlights the intricate, seemingly random behavior of nanoconfined water—behavior that is difficult for graphene to understand. The results obtained offer crucial direction for system design and configuration of materials at the graphene/water interface that can be utilized as a benchmark for other future designs.

Molecular dynamics study of water and ion behaviors of mixed salts solutions on extended quartz surface

The adoption and evolution of water molecules and ions in mixed electrolytes at the surface play vital roles in the physical properties and chemical reactions of SiO2-like corrosion. The effect of salt type and concentration on the structure and dynamics of water molecules and ions at silica surfaces are studied using all-atom molecular dynamics simulations taking the case of the NaCl, MgCl2, and NaCl–MgCl2 aqueous solutions. The ability of ion hydration is in the order of Mg2+ > Na+ > Cl−, being opposite to their hydration Gibbs free energies, which directly influence the weak interaction in the solution and the diffusion rate of the particles. Mg shows stronger destruction to weak interactions than Na does, and ionic hydration of Mg2+ decelerates the self-diffusion coefficient of water molecules significantly due to the enhanced Coulomb effect and the interruption of solution continuity. Meanwhile, the self-diffusion coefficient of particles decreases with the concentration improvement in the single salt solution as increased ionic hydration. In the mixed salt solution, the order of diffusion rate is Cl− > Na+ > Mg2+ as a result of the different confinement effects of the protonated pore. Interestingly, a small amount of Na+ addition can promote the self-diffusion of Mg2+, but a great many of Na+ addition slows the diffusion of Mg2+. This work provides comprehensive insight into the behavior of mixed salt solutions at silica surfaces, shedding light on the practical applications of geological sciences, cultural relics protection, and colloidal sciences.

Theoretical description of water from single-molecule to condensed phase: Recent progress on potential energy surfaces and molecular dynamics

In this work, we review recent progress on the view of potential energy surfaces and molecular dynamics study of water and its related reactions in the last decade or so. Some important gas-phase reactions of water with radicals, chemisorbed dissociative dynamics of water on solid surfaces, and statistical mechanics and vibrational spectrum simulations of water from clusters to the condensed phase have been introduced. The recently developed machine learning techniques, such as the neural networks in a combination of permutational invariant polynomials or fundamental invariants, the atomic neural networks framework, the gaussian approximation potentials with the smooth overlap of atomic position kernel, as well as the many-body expansion framework for the construction of highly accurate potential energy surfaces, have also been discussed. Finally, some suggestions have been provided for further improvement of the potential energy surfaces and dynamics methods of water-related systems.

Molecular dynamics study of water confined in MIL-101 metal–organic frameworks

Molecular dynamics simulations of water adsorbed in Material Institute Lavoisier MIL-101(Cr) metal-organic frameworks are performed to analyze the kinetic properties of water molecules confined in the framework at 298.15 K and under different vapor pressures and clarify the water adsorption mechanism in MIL-101(Cr). The terahertz frequency-domain spectra (THz-FDS) of water are calculated by applying fast Fourier transform to the configurational data of water molecules. According to the characteristic frequencies in the THz-FDS, the dominant motions of water molecules in MIL-101(Cr) can be categorized into three types: (1) low-frequency translational motion (0-0.5 THz), (2) medium-frequency vibrational motion (2-2.5 THz), and (3) high-frequency vibrational motion (>6 THz). Each type of water motion is confirmed by visualizing the water configuration in MIL-101(Cr). The ratio of the number of water molecules with low-frequency translational motion to the total number of water molecules increases with the increase in vapor pressure. In contrast, that with medium-frequency vibrational motion is found to decrease with vapor pressure, exhibiting a pronounced decrease after water condensation has started in the cavities. That with the high-frequency vibrational motion is almost independent of the vapor pressure. The interactions between different types of water molecules affect the THz-FDS. Furthermore, the self-diffusion coefficient and the velocity auto-correlation function are calculated to clarify the adsorption state of the water confined in MIL-101(Cr). To confirm that the general trend of the THz-FDS does not depend on the water model, the simulations are performed using three water models, namely, rigid SPC/E, flexible SPC/E, and rigid TIP5PEw.

Molecular dynamics study of water over Pt/TiO2 Surfaces

Titanium dioxide based catalysts, such as Pt/TiO2, have shown promise as water splitting photocatalysts and have been extensively studied experimentally. However, there are only few computational studies which are essential to understand the mechanistic aspects. We employ Molecular Dynamics (MD) simulations to establish a nanoscale atomistic model of the interfacial interactions of water on anatase (101) and rutile (110) surfaces with Pt atoms adsorbed. The highlight of our model is the large scale: we have simulated systems approximately 30nm x 30nm x 3nm for a time interval spanning over 4ns.

Molecular dynamics study of water and ions transport in nano-pore of layered structure: A case study of tobermorite

Water and ions transport in the cement hydrate determines the durability of cementitious material. Due to the structural similarity, tobermorite, an important mineral analogue of the main phase of cement hydrate, was used to investigate transport behaviour at the molecular level. In this study, the structural and dynamical properties of the water/ions and the tobermorite interface were studied by the molecular dynamics (MD) simulation method. On the (001) surface of tobermorite, water molecules diffusing in the channel between the silicate chains demonstrate a number of structural water features: large density, good orientation preference, ordered interfacial organization and low diffusion rate. The dipole vector of type 1 water molecules point upwards due to the attraction from the calcium sheet, while type 2 water molecules turn downwards due to the restrained H-bonds donated from ONB atoms in the silicate chains. The stable H-bonds connected with ONB in the silicate chains restrict the mobility of the channel water molecules. The significant reduction of the diffusion coefficient matches well with the experimental results obtained by NMR, QENS and PCFR techniques. With increasing distance from the channel, the structural and dynamical behavior of the water molecules vary and gradually translate into bulk water properties at distances of 10–15Å from the liquid–solid interface. In the respect of the ions and tobermorite interaction, there is Cl− repulsion and Ca2+ adsorption from the surface. In addition, in simulation time longer than 1ns, Cl− can diffuse to the surficial Ca2+ and forms the unstable Ca-Cl cluster, which accelerates the desorption of the surface Ca atoms.

Molecular Dynamics Study of Water and Ions Transported during the Nanopore Calcium Silicate Phase: Case Study of Jennite

AbstractDurability is an important property that determines the long-term behavior of cement-based materials. Water and ions are transported in nanopores of calcium-silicate-hydrate (C-S-H) gels, the main element in cement-based material, which significantly influences the durability of cement. Because of its structural similarity, jennite, an important mineral analog of C-S-H gel, is first taken to investigate the transport behavior at a molecular level. In this paper, structural and dynamical properties of the water/ions and the jennite interface are studied by the molecular dynamics (MD) simulation method. On the (001) surface of jennite, water molecules diffusing in the channel between silicate chains demonstrate the following structural water features: large density, good orientation preference, ordered interfacial organization, and low diffusion rate. The channel water molecules have more H-bonds connected with the neighboring water molecules and solid surface. As the distance from the channel incre...

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.

Effect of hydration layer and surface wettability in enhancing thermal conductivity of nanofluids

In a molecular dynamics study of water based nanofluids, we show that a hydration layer is formed at the particle-fluid interface, where the attraction or cohesive potential between the liquid molecules is dominant. In the hydration layer, the collision mode rather than the kinetic or potential mode is primarily responsible for the enhancement of thermal transport properties in nanofluids, as it results in more interactions. The thermal conductivity for a wetting particle is found to be higher than for a neutral or a nonwetting particle.

Quantum molecular dynamics study of water on TiO2(110) surface

The adsorption of water on perfect TiO(2)(110) surface is studied by quantum molecular dynamics simulation adopting a periodic model formed by five water molecules on a (5 x 1) surface unit cell of a five layer slab of TiO(2). The total simulation time is 3.2 ps. At about 1.3 ps, one water molecule dissociates with the help of other adsorbed waters and surface bridging oxygens. During the remaining 1.9 ps, the waters and OH groups vibrate, but no more dissociation or recombination is observed. By comparing recent experimental O1s photoemission (x-ray photoelectron spectroscopy) spectra of H(2)O/TiO(2)(110) to the computed spectrum of the adsorbate in the configurations supplied by the molecular dynamics simulation, the observed peaks can be attributed to different oxygen species. The proposed assignment of the main spectral features supports the occurrence of partial water dissociation (approximately 20%) also on a perfect TiO(2) surface.

Molecular Dynamics Study of Water−Benzene Interactions at the Liquid/Vapor Interface of Water

The free energy profile of the transport of a benzene molecule across the liquid/vapor interface of water was investigated using molecular dynamics techniques. A large free energy minimum was found near the Gibbs dividing surface. At this free energy minimum, which is an indication of surface activity, the benzene molecule lies parallel to the surface and has an adsorption free energy of about −4 kcal/mol. In addition, there is a free energy barrier to passage from the bulk solution to the surface-adsorbed site. The hydration free energy estimated from the difference between gas-phase and liquid-phase free energies is about −0.1 ± 0.4 kcal/mol, a value that agrees well with the corresponding experimental measurement of −0.767 kcal/mol. The results described in this paper demonstrate the validity of our approach, as well as the quality of our potential energy surfaces.

Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor

The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model.

Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor.

The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model.

Molecular Dynamics Study of Water next to Electrified Ag(111) Surfaces

The aim of this report is to compare the density profiles, orientation, and structure of water near charged and uncharged Ag(111) interfaces obtained using molecular dynamics calculations with those suggested from a recent experiment. In the simulations, water contained between two parallel Ag(111) surfaces with charge densities of 0.0, 8.85, and 26.55 μC/cm2 on the left wall and opposite values on the right wall experiences external electric fields of 0.0, 1.0, and 3.0 V/Å. The predicted orientation and density of water for the zero field case is consistent with previous predictions for water near metal surfaces and indicates that water is present in layers and has an orientational structure similar to that of hexagonal ice. For simulations with charged surfaces, there is a reordering of water throughout the simulation cell in response to the polarization of the water dipoles. We show that the spacing between the peaks in the liquid density profiles obtained from our MD calculations matches the results of the experiment but that, contrary to the experimental results, we have not observed a dramatic increase of water density near the charged metal.

Molecular dynamics study of water adopting a potential function with explicit atomic dipole moments and anisotropic polarizabilities

Liquid water is studied in a molecular dynamics simulation using an intermolecular potential where the electrostatic and induction interactions are described with atomic charges, dipole moments and anisotropic dipole polarizability tensors. Avoiding virtual charge sites drastically decreases the simulation time even though a more complex potential form is adopted. Results are presented concerning energies, structure and dynamics of liquid water. The results are similar to a previous simulation using a NEMO potential with virtual charge sites [J. Phys. Chem. 94 (1990) 1649], but we find a somewhat more ice-like behaviour.

Molecular Dynamics Study of Water in Trans-Critical Region. Analysis of Microscopic Structure.

A molecular dynamics (MD) study was performed on water in wide ranges of temperatures and densities. The vapor-liquid coexistence region and near-critical region are intensively studied. By applying the Carravetta-Clementi (CC) potential model for the intermolecular potential function, the pressure and enthalpy responses to temperature and density were obtained. Microscopic information on the molecular structure and behavior, including the velocity auto-correlation and the formation of dimers and clusters, is also presented.

A molecular dynamics study of water near silicate surfaces

We have conducted a molecular dynamics simulation of water between uncharged silicate surfaces in order to understand, on a molecular basis, the structural and dynamical properties of vicinal water (i.e., the water between the surfaces). The results of our preliminary simulation indicate that the vicinal water differs substantially from pure bulk water in the transient orientation of molecular dipole moments and rate of relaxation of these moments. In contrast, no significant long-range differences between the radial distribution functions or hydrogen bonding patterns of vicinal and bulk water are evident.

A molecular dynamics study of water between Lennard-Jones walls

An MD simulation of 216 ST2 water molecules between 12-6 Lennard-Jones walls has been performed which extend over 20 ps at an average temperature of 287 K. The oxygen atom density profile is reported the influence of the walls on the orientation of the water molecules on the self-diffusion coefficient have been investigated The results are compared with those from MC and MD simulations of similar systems.