Water Density Profiles Research Articles

Water Structure at Solid Surfaces of Varying Hydrophobicity

The structure of liquid water at solid surfaces with tunable hydrophobicity has been examined by molecular dynamics simulation. Methods of analysis include water density profiles, angular distributions, tilt and twist order parameters, and hydrogen-bonding coordination. It was found that interfacial water structures could be classified according to two hydrophobic regimes, a nonwetting structure and a semi-wetting structure. A smooth transition between the two occurs at surfaces with a contact angle around 130°. The nonwetting regime is characterized by water immediately adjacent to the interface oriented such that hydrogens are directed toward the surface. The semiwetting regime has water oriented in the plane of the interface. We propose that the emergence of the wetting-type order is strongly dependent on the density profile across the interfacial region. Regions of low density, flanked by high-density areas, present fewer hydrogen bonding opportunities than are found in more dense regions. Our finding...

Photoelectron spectroscopy of liquid water and aqueous solution: Electron effective attenuation lengths and emission-angle anisotropy

Photoelectron (PE) spectroscopy measurements from liquid water and from a 4 m NaI aqueous solution are performed using a liquid microjet in combination with soft X-ray synchrotron radiation. From the oxygen 1s PE signal intensity from liquid water, measured as a function of photon energy (up to 1500 eV), we quantitatively determine relative electron inelastic effective attenuation lengths (EAL) for (photo)electron kinetic energies in the 70–900 eV range. In order to determine the absolute electron escape depths a calibration point is needed, which is not directly accessible by experiment. This information can instead be indirectly derived by comparing PE experiments and molecular dynamics (MD) simulations of an aqueous solution interface where density profiles of water, anions, and cations are distinctively different. We have chosen sodium iodide in water because iodide has a considerable propensity for the solution surface, whereas the sodium cation is repelled from the surface. By measuring the intensities of photoelectrons emitted from different orbitals of different symmetries from each aqueous ion we also evaluate whether gas-phase ionization cross sections and asymmetry parameters can describe the photoemission from ions at and near the aqueous solution/vapor interface. We show that gas-phase data reproduce surprisingly well the experimental observations for hydrated ions as long as the photon energy is sufficiently far above the ionization threshold. Electrons detected at the higher photon energies originate predominantly from deeper layers, suggesting that bulk-solution electron elastic scattering is relatively weak.

Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A.

Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modeled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, head group orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties.

Asymmetric Hydrogen Bonding and Orientational Ordering of Water at Hydrophobic and Hydrophilic Surfaces: A Comparison of Water/Vapor, Water/Talc, and Water/Mica Interfaces

Interfaces involving aqueous fluid phases play critical roles in natural and technologically important systems, and the atomic scale differences between interfaces involving hydrophobic and hydrophilic substrates are essential to understanding and manipulating their chemical and physical properties. This paper compares computational molecular dynamics results for the atomic density profiles, H-bonding configurations, and orientational ordering of water molecules at three different and illustrative interfaces. These are the free liquid water surface, which can be considered hydrophobic, and the interfaces of liquid water with talc (001) and muscovite (001) surfaces, which are prototypical hydrophobic and hydrophilic inorganic oxide surfaces, respectively. The results clearly demonstrate the importance of substrate structure and composition in controlling interfacial behavior and illustrate the differences between the vapor interface and those involving solids. The atomic density profiles of water at the so...

Continuously stratified flow dynamics over a hollow

To study the effects of bathymetric depressions (hollows) on continuously stratified flows, measurements of current velocity and water density profiles were obtained over two hollows in the lower Chesapeake Bay. Measurements showed an acceleration of the middepth flow as it moved toward the deepest part of the hollow, in contrast to the deceleration expected from two‐dimensional Bernoulli‐type dynamics. The acceleration was attributed to lateral water intrusions that were most apparent during floods, as corroborated by observations in a transverse section that crossed the deepest part of one of the hollows. The flow acceleration toward the deepest part of the hollows during flood, favored by lateral water intrusions, was deflected toward the right (looking landward) owing to Coriolis accelerations. In general, during ebb and flood, the dynamics over the hollows could be explained with three‐dimensional Bernoulli‐type dynamics (pressure gradient balanced by advection) modified by Coriolis acceleration. Outside the hollows, the dynamics were between pressure gradient and friction (stress divergence). The transition from frictionally dominated dynamics (outside the hollow) to advection‐dominated dynamics (inside the hollow) appears at the region where the bathymetric slope equals the bottom drag coefficient.

Beyond the Poisson-Boltzmann Model: Modeling Biomolecule-Water and Water-Water Interactions

We present an extension to the Poisson-Boltzmann model in which the solvent is modeled as an assembly of self-orienting dipoles of variable densities. Interactions between these dipoles are included implicitly using a Yukawa potential field. This model leads to a set of equations whose solutions give the dipole densities; we use the latter to study the organization of water around biomolecules. The computed water density profiles resemble those derived from molecular dynamics simulations. We also derive an excess free energy that discriminates correct from incorrect conformations of proteins.

Water and ice in contact with octadecyl-trichlorosilane functionalized surfaces: A high resolution x-ray reflectivity study

We present a high energy x-ray reflectivity study of the density profiles of water and ice at hydrophobic and hydrophilic substrates. At the hydrophobic water/octadecyl-trichlorosilane (water-OTS) interface, we find clear evidence for a thin density depletion layer with an integrated density deficit corresponding to approximately 40% of a monolayer of water molecules. We discuss the experimental results in terms of a simple model of hydrophobic/hydrophilic solid-liquid interfaces. Our results also exclude the presence of nanobubbles. A detailed study of possible radiation damage induced by the intense x-ray beam at the dry OTS surface and at the ice-OTS, as well as at water-OTS interfaces, discloses that noticeable damage is only induced at the water-OTS interface, and thus points to the dominant role of highly mobile radicals formed in bulk water close to the interface.

DISPERSED OIL TRANSPORT MODELING CALIBRATED BY FIELD-COLLECTED DATA MEASURING FLUORESCEIN DYE DISPERSION

ABSTRACT Oil-spill fate and transport modeling may be used to evaluate water column hydrocarbon concentrations, potential exposure to organisms, and impacts of oil spills with and without dispersant use. Important inputs to transport modeling for such analyses are current velocities and turbulent dispersion coefficients. Fluorescein dye studies off San Diego, California, were used to calibrate an oil transport model by hindcasting movement and dispersion of dye. The oil spill model was then used to predict subsurface hydrocarbon concentrations and potential water column impacts if oil were to be dispersed into the water column under similar conditions. Field-collected data included surface currents calculated from high-frequency radar data (HF-Radar), near-surface currents from drifter measurements drogued at several depths (1m, 2m, 4m or 5m), dye concentrations measured by fluorescence, spreading and dye intensity measurements based on aerial photography, and water density profiles from CTD casts. As the dye plume quickly extended throughout an upper mixed layer (7–15m), the horizontal dye movements were better indicated by the drifters drogued to a depth near the middle of that layer than the HF-Radar, which measured surface (∼top 50 cm) currents (including wind drift). Diffusion rates were estimated based on dye spreading measured by aerial photography and fluorescence-depth profiles. The model used these data as inputs, modeling of wind-forced surface water turbulence and drift as a function of wind speed and direction (based on published results of fluid dynamics studies), and Stokes law for droplet rise/sinking rates, to predict oil transport and dispersion rates within the water column. Use of such diffusion rate data in an oil fate model can provide estimates of likely dispersed oil concentrations under similar conditions, which may be used to evaluate potential impacts on water column biota. However, other conditions with different patterns of current shear (due to background currents, tidal currents, and wind stress) should be examined before these results can be generalized.

Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

Comparison of the Solvation Structure of Polarizable and Nonpolarizable Ions in Bulk Water and Near the Aqueous Liquid−Vapor Interface

All-atom molecular dynamics simulations are performed on bulk and aqueous liquid−vapor interfacial systems for neat water and 1 M solutions of NaCl, CsCl, and NaI to more quantitatively characterize ion solvation in these environments and to more fully elucidate trends accompanying the introduction of ion polarizability in the context of a polarizable water potential. In the bulk systems, computed densities, hydration free energies, compressibilities, coordination numbers, and a variety of two- and three-atom distribution functions show that the polarizable ions exhibit smaller effective radii, a slightly increased propensity for bulk hydration (particularly for the anions), and no biased preference for contact ion or solvent-separated ion pairing relative to the corresponding nonpolarizable cases. For the interfacial systems employing long (>40 ns) sampling times, we obtain good convergence for a variety of interfacial characteristics such as slab thicknesses and interfacial widths, depth-dependent water and ion density profiles, surface excesses, and depth-dependent transverse distribution functions. We compare interface characteristics derived from fits to both a hyperbolic tangent and error function form and find negligible differences in the resulting parameters. For all three salt solutions, we observe that ion polarizability leads to a slight contraction of the liquid slab and simultaneous expansion of the interfacial thickness arising from the strong surface enhancement of polarizable anions. Computed values of the surface excess show that for the present Drude ion models and polarizable fluctuating charge water model the introduction of ion polarizability consistently leads to a slightly less-negative surface excess, implying a significant but incomplete cancellation of the surface enhancement by the corresponding subsurface anion depletion. Depth-dependent, transverse correlation functions for the oxygen−oxygen separation indicate slight water relaxation at the interface of both neat TIP4P-FQ water and the corresponding salt solutions.

833 肺サーファクタントの分子シミュレーション : 肺のマルチシミュレータ開発にむけて(J05-3 生命体統合シミュレーション(3),ジョイントセッション,21世紀地球環境革命の機械工学:人・マイクロナノ・エネルギー・環境)

Molecular dynamics simulation of pulmonary surfactant on a water layer is conducted to investigate the effect of the surfactant on gaseous exchange in alveolus. The pulmonary surfactant is modeled by a monolayer comprised by dipalmitoylphosphatidylcholine (DPPC) molecules, which are the major component of human pulmonary surfactant. The constant temperature and volume MD calculation is performed in 10 ns. From the result of density profile of water across the system calculated it is found that the reduction of the water density in the liquid-vapor interface is more gradually than that calculated in the system without surfactant. In addition, the vapor water density is locally decreased in the hydrophobic region of the surfactant monolayer. The results of this water density profile and snapshots obtained here suggest that water exchange across the pulmonary surfactant hardly occurs in the time scale calculated here.

Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop Family

Understanding the mechanisms of gating and ion permeation in biological channels and receptors has been a long-standing challenge in biophysics. Recent advances in structural biology have revealed the architecture of a number of transmembrane channels and allowed detailed, molecular-level insight into these systems. Herein, we have examined the barriers to ion conductance and origins of ion selectivity in models of the cationic human alpha7 nicotinic acetylcholine receptor (nAChR) and the anionic alpha1 glycine receptor (GlyR), based on the structure of Torpedo nAChR. Molecular dynamics simulations were used to determine water density profiles along the channel length, and they established that both receptor pores were fully hydrated. The very low water density in the middle of the nAChR pore indicated the existence of a hydrophobic constriction. By contrast, the pore of GlyR was lined with hydrophilic residues and remained well-hydrated throughout. Adaptive biasing force simulations allowed us to reconstruct potentials of mean force (PMFs) for chloride and sodium ions in the two receptors. For the nicotinic receptor we observed barriers to ion translocation associated with rings of hydrophobic residues-Val13' and Leu9'-in the middle of the transmembrane domain. This finding further substantiates the hydrophobic gating hypothesis for nAChR. The PMF revealed no significant hydrophobic barrier for chloride translocation in GlyR. For both receptors nonpermeant ions displayed considerable barriers. Thus, the overall electrostatics and the presence of rings of charged residues at the entrance and exit of the channels were sufficient to explain the experimentally observed anion and cation selectivity.

Molecular dynamics simulation of methane in potassium montmorillonite clay hydrates

We present molecular dynamics simulation results for molecular structure, density profile and radial distribution functions of water, cation and methane in hydrated potassium montmorillonite clays. The systems we have studied consist of eight Otay Montmorillonite unit cells forming a clay patch of 21.12 × 18.28 Å2 with a thickness of 6.56 Å, eight potassium interlayer cations, with 0.5, 1.0 and 2.25 CH4 per unit cell, corresponding to 11.5, 11.0 and 9.75 H2O per unit cell. The calculations are conducted in constant (N, V, T) ensembles at T = 300 K and with a layer spacing of 18 Å. Visualization of simulation results in the 1.0 CH4 per unit cell system indicated that the methane molecule is nested inside the hexagonal cavities of the clay surface oxygen due to the fact that the clay surfaces include neutral regions that are hydrophobic. The calculated CH4–O coordination number of around 20 for 0.5 and 1.0 CH4 per unit cell systems is consistent with previous simulations. Our simulations show that water in potassium montmorillonite formed stretched hydrogen bonds with either the clay surface or other water molecules.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson–Boltzmann–Langevin equation (GPBLE). We have implemented a web server () that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Hydrogen bond dynamics and microscopic structure of confined water inside carbon nanotubes

We have investigated the density and temperature dependences of microscopic structure and hydrogen bond dynamics of water inside carbon nanotubes (CNTs) using molecular dynamics simulation. The CNTs are treated as rigid, and smoothly truncated extended simple point charge water model is adopted. The results show that as the overall density increases, the atomic density profiles of water inside CNTs become sharper, the peaks shift closer to the wall, and a new peak of hydrogen atomic density appears between the first (outermost) and second layer. The intermittent hydrogen bond correlation function C(HB)(t) of water inside CNTs decays slower than that of bulk water, and the rate of decay decreases as the tube diameter decreases. C(HB)(t) clearly decays more slowly for the first layer of water than for other regions inside CNTs. The C(HB)(t) of the interlayer hydrogen bonds decays faster than those of the other regions and even faster than that of the bulk water. On the other hand, the hydrogen bond lifetimes of the first layer are shorter than those of the inner layer(s). Interlayer hydrogen bond lifetimes are clearly shorter than those of the constituent layers. As a whole, the hydrogen bond lifetimes of water inside CNTs are shorter than those of bulk water, while the relaxation of C(HB)(t) is slower for the confined water than for bulk water. In other words, hydrogen bonds of water inside CNTs break more easily than those of bulk water, but the water molecules remain in each other's vicinity and can easily reform the bonds.

New multi‐fluid MHD model of comet 26P/Grigg‐Skjellerup: Extrapolation to comet 67P/Churyumov‐Gerasimenko

The Multi‐fluid MHD simulator CASIM3D models the atmosphere of comet 26P/Grigg‐Skjellerup as it was seen by the Giotto spacecraft during its flyby of the comet in July 1992. CASIM3D integrates the major chemical reactions and physical interactions to compute self‐consistently over an adaptive Cartesian mesh the dynamics of ions, electrons, and neutrals within the coma. Using this model, we derived water ion velocity and density profiles and magnetic field strength along the Giotto path that are in good agreement with the recorded observations. This model is also extrapolated to the case of 67P/Churyumov‐Gerasimenko for its perihelion passage of 2015 to provide a preliminary assessment of the structure of the coma of this comet. We show that the inner boundary layers are just few dozen kilometers large. This could provide an additional constraint to the orbit of the spacecraft Rosetta to maximize the science return of the mission.

Observations of bipolar residual circulation in two equatorward-facing semiarid bays

Two equatorward-facing semiarid bays in Chile (around 30°S) were sampled between March 23 and 27, 1997 with the purpose of determining whether the similar coastline morphology of the bays caused residual circulation patterns that were alike. A towed acoustic Doppler current profiler and a conductivity-temperature-depth recorder were used to measure water current and density profiles along a triangular trajectory during two semidiurnal tidal cycles at each of the bays. The bays were influenced by semidiurnal tides. The bay to the north, Coquimbo Bay, featured a bipolar residual circulation consisting of a well-defined surface counter-clockwise gyre that occupied the northern two-thirds of the bay. The southern third of the bay was not completely resolved by the sampling but measurements suggested the presence of a clockwise circulation. The bay to the south, Guanaquero Bay, showed a well-defined clockwise gyre that occupied the southern half of the bay. Counter-clockwise circulation was apparent over the northern half. Near-surface circulations changed little with depth in both bays. The similarity in surface residual circulation patterns between bays, namely the presence of two counter-rotating gyres, was attributed to flow separation at the upstream headland of the embayment. In this context, “upstream” was relative to the direction of wind forcing and prevalent coastal currents. This direction was different during sampling of Coquimbo Bay (northerly winds and coastal currents) than in Guanaquero Bay (southwesterly winds and coastal currents). It was proposed that, in general, two counter-rotating gyres will appear in bays where the entrance width exceeds twice the radius of curvature of the headlands that limit them.

Structure and dynamics of water at the interface with phospholipid bilayers

We have performed two molecular-dynamics simulations to study the structural and dynamical properties of water at the interface with phospholipid bilayers. In one of the simulations the bilayer contained neutral phospholipid molecules, dioleoylphosphatidylcholine (DOPC); in the second simulation the bilayer contained charged lipid molecules, dioleoylphosphatidylserine (DOPS). From the density profile of water we observe that water next to the DOPS bilayer is more perturbed as compared to water near the DOPC bilayer. Using an energetic criterion for the determination of hydrogen bonding we find that water molecules create strong hydrogen bonds with the headgroups of the phospholipid molecules. Due to the presence of these bonds and also due to the confinement of water, the translational and orientational dynamics of water at the interface are slowed down. The degree of slowing down of the dynamics depends upon the location of water molecules near a lipid headgroup.

Gas Solubility in Hydrophobic Confinement

Measured forces between apolar surfaces in water have often been found to be sensitive to exposure to atmospheric gases despite low gas solubilities in bulk water. This raises questions as to how significant gas adsorption is in hydrophobic confinement, whether it is conducive to water depletion at such surfaces, and ultimately if it can facilitate the liquid-to-gas phase transition in the confinement. Open Ensemble molecular simulations have been used here to determine saturated concentrations of atmospheric gases in water-filled apolar confinements as a function of pore width at varied gas fugacities. For paraffin-like confinements of widths barely exceeding the mechanical instability threshold (spinodal) of the liquid-to-vapor transition of confined water (aqueous film thickness between three and four molecular diameters), mean gas concentrations in the pore were found to exceed the bulk values by a factor of approximately 30 or approximately 15 in cases of N2 and CO2, respectively. At ambient conditions, this does not result in visible changes in the water density profile next to the surfaces. Whereas the barrier to capillary evaporation has been found to decrease in the presence of dissolved gas (Leung, K.; Luzar, A.; and Bratko, D. Phys. Rev. Lett. 2003, 90, 065502), gas concentrations much higher than those observed at normal atmospheric conditions would be needed to produce noticeable changes in the kinetics of capillary evaporation. In simulations, dissolved gas concentrations corresponding to fugacities above approximately 40 bar for N2, or approximately 2 bar for CO2, were required to trigger expulsion of water from a hydrocarbon slit as narrow as 1.4 nm. For nanosized pore widths corresponding to the mechanical instability threshold or above, no significant coupling between adsorption layers at opposing confinement walls was observed. This finding explains the approximately linear increase in gas solubility with inverse confinement width and the apparent validity of Henry's law in the pores over a broad fugacity range.

Dynamics and Density Profile of Water in Nanotubes as One-Dimensional Fluid

The transport and structural properties of water confined in nanotubes with different diameters were studied by molecular dynamics (MD) simulation. The effects of pore size, molecule-wall interaction, and the helicity of CNT on the diffusivity, thermal conductivity, and shear viscosity as well as density profile were analyzed. For diffusivity, in model NT > in armchair CNT > in zigzag CNT at similar conditions. However in contrast to the diffusivity, the thermal conductivity and the shear viscosity increase as the pore size decreases, in zigzag CNT > in armchair CNT > (or approximately ) in model NT. The ordered layer distribution of water molecules in nanotubes is clear. It suggests the structure of fluid in the zigzag CNTs is more ordered, and more solidlike. In the nanotubes, where the molecule and the pore dimensions are of similar order of magnitude, the nature of water-water and water-wall interactions, the confinement effect of space, and the helicity of CNT become more significant.