Molecular Dynamics Simulations Of Water Research Articles

Effect of surface hydrophobicity on the dynamics of water at the nanoscale confinement: A molecular dynamics simulation study

We present detailed molecular dynamics simulations of water in and around a pair of plates immersed in water to investigate the effect of degree of hydrophobicity or hydrophilicity of the plates on dynamics of water confined between the two plates. The nature of the plate has been tuned from hydrophobic to hydrophilic and vice versa by varying plate-water dispersion interaction. Analyses of the translational dynamics as performed by calculating mean squared displacements of the confined water reveal a monotonically decreasing trend of the diffusivity with increasing hydrophilicity of the plates. Orientational dynamics of the confined water also follows the same monotonic trend. Although orientational time constant almost does not change with the increase of plate-water dispersion interaction in the hydrophobic regime corresponding to the smaller plate-water attraction, it changes considerably in the hydrophilic regime corresponding to larger plate-water dispersion interactions.

Effect of Ionic Aqueous Environments on the Structure and Dynamics of the Aβ21–30 Fragment: A Molecular-Dynamics Study

The amyloid β-protein (Aβ) has been implicated in the pathogenesis of Alzheimer's disease. The role of the structure and dynamics of the central Aβ21-30 decapeptide region of the full-length Aβ is considered crucial in the aggregation pathway of Aβ. Here we report results of isobaric-isothermal (NPT) all-atom explicit water molecular dynamics simulations of the monomeric form of the wild-type Aβ21-30 fragment in aqueous salt environments formed by neurobiologically important group IA (NaCl, KCl) and group IIA (CaCl2, MgCl2) salts. Our simulations reveal the existence of salt-specific changes to secondary structure propensities, lifetimes, hydrogen bonding, salt-bridge formation, and decapeptide-ion contacts of this decapeptide. These results suggest that aqueous environments with the CaCl2 salt, and to a much lesser extent the MgCl2 salt, have profound effects by increasing random coil structure propensities and lifetimes and diminishing intrapeptide hydrogen bonding. These effects are rationalized in terms of direct cation-decapeptide contacts and changes to the hydration-shell water molecules. On the other side of the spectrum, environments with the NaCl and KCl salts have little influence on the decapeptide's secondary structure despite increasing hydrogen bonding, salt-bridge formation, and lifetime of turn structures. The observed enhancement of open structures by group IIA may be of importance in the folding and aggregation pathway of the full-length Aβ.

Molecular dynamics simulations of the condensation coefficient of water

Experiments have found the condensation coefficient for water condensing onto pure water to be between 1 and 0.01. This wide variation persists even in the more recent experiments in which values of about 1, 0.77±0.06, and 0.2±0.1 have been reported. However, current molecular dynamics simulations of water consistently result in a condensation coefficient of about 1. These water models may overestimate the condensation coefficient by assigning condensed phase parameters to the bulk, surface, and gas phase water molecules in the simulations. We varied the dipole moment and the Lennard-Jones parameters for a gas phase water molecule in a condensation simulation using the SPC/E model. With modest changes to the dipole moment and the Lennard-Jones parameters, we have obtained a value of 0.77. However, we have concluded that to obtain a simulation condensation coefficient of 0.2, unrealistic parameters must be assigned to the water molecules.

Viscosity of Ultrathin Water Films Confined between Aluminol Surfaces of Kaolinite: Ab Initio Simulations

Ab initio molecular dynamics simulations of water confined between kaolinite walls were conducted in an effort to make contact with experiments implying dramatic viscosity enhancement for water in nanometer-scale, hydrophilic channels. An earlier ground-state structural optimization of a single water layer on a flat kaolinite(001) surface had yielded a molecular arrangement, which, by appearing hydrophobic to subsequent layers, suggested the possibility of very low flow resistance. Well above the freezing point, however, and under shear, the surface became hydrophilic, as a percentage of first-layer water molecules flipped to expose dangling hydroxyls. This led to simulated steady-state velocity fields consistent with a “no-slip” boundary condition and viscous flow. The magnitude of the viscosity derived from the simulations, only a few times that of bulk water, does not lend theoretical weight to the notion of dramatic enhancement under nanoconfinement.

Structure, Dynamics, and Phase Behavior of Water in TiO2 Nanopores

Mesoporous titania is a highly studied material due to its energy and environment-related applications, which depend on its tailored surface and electronic properties. Understanding the behavior of water in titania pores is a central issue for practical purposes in photocatalysis, solar cells, bone implants, or optical sensors. In particular, the mechanisms of capillary condensation of water in titania mesopores and the organization and mobility of water as a function of pore filling fraction are not yet known. In this work, molecular dynamics simulations of water confined in TiO2-rutile pores of diameters 1.3, 2.8, and 5.1 nm were carried out at various water contents. Water density and diffusion coefficients were obtained as a function of the distance from the surface. The proximity to the interface affects density and diffusivity within a distance of around 10 A from the walls, beyond which all properties tend to converge. The densities of the confined liquid in the 2.8 and the 5.1 nm pores decrease, r...

Interaction of the model alkyltrimethylammonium ions with alkali halide salts: an explicit water molecular dynamics study

We present an explicit water molecular dynamics simulation of dilute solutions of model alkyltrimethylammonium surfactant ions (number of methylene groups in the tail is 3, 5, 8, 10, and 12) in mixture with NaF, NaCl, NaBr, and NaI salts, respectively. The SPC/E model is used to describe water molecules. Results of the simulation at 298 K are presented in the form of radial distribution functions between nitrogen and carbon atoms of CH$_2$ groups on the alkyltrimethylammonium ion, and the counterion species in the solution. The running coordination numbers between carbon atoms of surfactants and counterions are also calculated. We show that I$^-$ counterion exhibits the highest, and F$^-$ the lowest affinity to "bind" to the model surfactants. The results are discussed in view of the available experimental and simulation data for this and similar solutions.

The Differences in Dynamics and Stability of the Wild Type Beta-Amyloid Aβ1-40, and ΔE22-Aβ1-39 (Japanese) Mutant, a Molecular Dynamics Study

Alzheimer's disease (AD) has been identified as a progressive, neurodegenerative disorder associated with protein misfolding due to the aggregation of monomeric β-amyloid proteins (Aβ) to form fibrillar plaques. Experimental attempts to purify and chemically analyze the structure of Aβ protofibrils and to elucidate the mechanism of fibril formation have yet to reveal much about the molecular etiology of AD, due to the low solubility and non-crystalline nature of Aβ. It has been shown experimentally that the ΔE22-Aβ1-39 (Japanese) mutation of the β-amyloid leads to production of typical Aβ fibrils essentially instantaneously, much faster than the fibril formation in wild-type (WT) Aβ1-40. To better understand the fibril-forming mechanism of the Japanese mutant peptide we have ran several long (μs) all atom explicit water molecular dynamics simulations of the mutant and WT peptide starting from the random-coil structure at two different temperatures (310 and 350 K). Our simulations showed that the ΔE22-Aβ1-39 mutant formed a stable semi-helical hairpin structure about 5 times faster than the WT. The helical hairpin conformation was less evident in WT trajectory and was quickly unfolded (particularly at 310K). The RMSF plots showed similar patterns of fluctuations in both the WT and mutant backbone atoms. However, the deletion of the E22 lowered the fluctuations of the mutant structure by about 2A at 310K. This fast and stable conformational change in ΔE22-Aβ1-39 can be used as a seed for the rapid fibril formation as observed in the experimental studies.

A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates

Thin films of water under nanoscopic confinement are prevalent in natural and manufactured materials. To investigate the equilibrium and dynamic behavior of water in such environments, we perform molecular dynamics simulations of water confined between atomistically detailed hydrophobic plates at T = 298 K for pressures (-0.1) ≤ P ≤ 1.0 GPa and plate separations of 0.40 ≤ d ≤ 0.80 nm. From these simulations, we construct an expanded P-d phase diagram for confined water, and identify and characterize a previously unreported confined monolayer ice morphology. We also study the decompression-induced sublimation of bilayer ice in a d = 0.6 nm slit, employing principal component analysis to synthesize low-dimensional embeddings of the drying trajectories and develop insight into the sublimation mechanism. Drying is observed to proceed by the nucleation of a bridging vapor cavity at one corner of the crystalline slab, followed by expansion of the cavity along two edges of the plates, and the subsequent recession of the remaining promontory of bilayer crystal into the bulk fluid. Our findings have implications for the understanding of diverse phenomena in materials science, nanofluidics, and protein folding and aggregation.

Explicit water molecular dynamics study of the mobility of halide ions in presence of ionene oligocations

We present explicit water molecular dynamics simulations of solutions of aliphatic 3,3- and 6,6-ionene oligocations neutralized with (i) fluoride, chloride, bromide, or iodide counterions, respectively, or (ii) with a 1:1 mixture of chloride and bromide anions in presence of a low molecular weight salt at 298 K. The SPC/E model was used to describe water molecules. Results of the simulation are presented in form of the pair distribution functions between various atoms on the ionene oligoion and counterions in solution. In addition, we were interested in the dynamics of counterions around model ionenes. We showed that counterions residing in the vicinity of the oligoion exchange rapidly with those in the bulk solution, with the frequency depending on the nature of the counterion and on the charge density of the oligoion. We calculated the average residence times of the various counterion species to the oligoions and proposed the model which divides the counterions into "free" and "bound" and calculated the fraction of "free" counterions. In the second part of the study, we investigated interaction of the sodium chloride and sodium bromide, being simultaneously present in the solution, with differently charged ionenes in water. The selectivity effect was clearly observed: bromide ions tend to replace chloride ions in the immediate vicinity of the ionene oligoions. Simulation results are discussed in light of our recent measurements of thermodynamic and transport properties of aqueous ionene solutions.

Inhibition of interdomain motion in g‐actin by the natural product latrunculin: A molecular dynamics study

As part of the cytoskeleton, actin is essential for the morphology, motility, and division of eukaryotic cells. Recent X-ray fiber diffraction studies have shown that the conformation of monomeric actin is flattened upon incorporation into the filament by a relative rotation of its two major domains. The antiproliferative activity of latrunculin, a macrolide toxin produced by sponges, seems to be related to its binding to monomeric actin and inhibition of polymerization. Yet, the mechanism of inhibition is not known in detail. Here, multiple explicit water molecular dynamics simulations show that latrunculin binding hinders the conformational transition related to actin polymerization. In particular, the presence of latrunculin at the interface of the two major domains of monomeric actin reduces the correlated displacement of Domain 2 with respect to Domain 1. Moreover, higher rotational flexibility between the two major domains is observed in the absence of ATP as compared to ATP-bound actin, offering a possible explanation as to why actin polymerizes more favorably in the absence of nucleotides.

Tunable transmembrane chloride transport by bis-indolylureas

A series of bis-indolylureas have been found to mediate chloride transport across vesicle bilayers. The anion transport activity of these receptors may be readily modulated by small structural changes to the receptor scaffold as shown by the combination of experimental chloride efflux studies and molecular dynamics simulations in water and POPC bilayers.

Effects of thermodynamic ensembles and mineral surfaces on interfacial water structure

While performing molecular dynamics simulations of water or aqueous solutions in a slab geometry, such as at mineral surfaces, it is important to match bulk water density in the diffuse region of the model system with that expected for the appropriate experimental conditions. Typically, a slab geometry represents parallel surfaces with a variable region of confined water (this region can range in size from a few Ångstroms to many tens of Ångstroms). While constant-pressure simulations usually result in appropriate density values in the bulk diffuse region removed from either surface, constant-volume simulations have also been widely used, sometimes without careful consideration of the method for determining water content. Simulations using two thermodynamic ensembles as well as two methods for calculating the water-accessible volume have been investigated for two distinct silicate surfaces-hydrophilic cristobalite (111) and hydrophobic pyrophyllite (001). In cases where NPT simulations are not feasible, a simple geometry-based treatment of the accessible volume can be sufficient to replicate bulk water density far from the surface. However, the use of the Connolly method can be more appropriate in cases where a surface is less well-defined. Specific water-surface interactions (e.g., hydrophobic repulsion) also play a role in determining water content in a confined water simulation. While reported here for planar surfaces, these results can be extended to an interface with any solvent, or to other types of surfaces and geometries.

The Relationship Between the Number of Residues in the Dynamics and Stability of the A-Beta Amyloid, a Molecular Dynamics Study

Alzheimer's disease has been identified as a progressive, neurodegenerative disorder associated with protein misfolding due to the aggregation of monomeric beta-amyloid proteins (A-beta) to form fibrillar plaques. Experimental attempts to purify and chemically analyze the structure of A-beta protofibrils and to elucidate the mechanism of fibril formation have yet to reveal much about the molecular etiology of AD, due to the low solubility and non-crystalline nature of A-beta. Experimentally, it is shown that the 43-residue strand of A-beta has higher cytotoxicity than the 40 or 42 strands. To better understand the relationship between the number of residue and the fibril-forming propensity of the peptide we have ran several all atom explicit water molecular dynamics simulations of A-beta strands of 40, 42, and 43 residues starting from their NMR structures. Overall, our simulations shows a transition of existing alpha helices to 3(10)- or pi-helices in agreement with experimental data. Our simulation of A-beta 40 and 42 residue strands confirms the substantial shift of secondary structure formation due to the additional two residues. However, it is interesting that the addition of the 43rd residue (threonine) only cause a small secondary structure change in the A-beta strand of 42 residues. Therefore it seems that the residues 41 and 42 are more important in secondary structure formation than the residue 43.

Isothermal titration calorimetry and molecular dynamics study of ion-selectivity in mixtures of hydrophobic polyelectrolytes with sodium halides in water

Aliphatic x,y-ionenes are polyelectrolytes in which x and y denote the numbers of methylene groups separating quaternary ammonium ions. They represent useful model substances for studying hydrophobic and charge effects in aqueous solutions. We used isothermal titration calorimetry to measure the enthalpies of mixing, ΔH(mix), of 3,3- and 6,6-ionene fluorides and bromides with low molecular weight salts (NaF, NaCl, NaBr, and NaI) at 298 K in water. The signs and magnitudes of the measured enthalpies depend on the hydrophobicity of the ionene and on the nature of the added salt. For example, addition of sodium fluoride to solutions of 3,3- and 6,6-ionene fluorides produced endothermic effects, while addition of sodium bromide to 3,3-ionene bromide resulted in a strong exothermic effect. Interestingly, mixing of 6,6-ionene bromide and NaBr solutions in water gave a small exothermic heat effect. Polyelectrolyte theories, based on continuum-solvent models, predict enthalpies of mixing to be positive (endothermic) for all the solutions examined in this work. The ion-specific effect is more strongly expressed in ionene solutions with higher charge density (3,3-ionene). The most important result of this work is the finding that the enthalpy of mixing of 3,3- (and of 6,6-ionene) fluorides with sodium halides can be expressed as a linear function of the enthalpy of hydration of the halide counterions. The experimental results were complemented with an explicit water molecular dynamics simulation of solutions of oligoions modelling 3,3- and 6,6-ionenes. The computer simulation results for various nitrogen-counterion pair distribution functions were in most cases consistent with the enthalpy measurements.

Dielectric Profile of Interfacial Water and its Effect on Double-Layer Capacitance

The framework for deriving tensorial interfacial dielectric profiles from bound charge distributions is established and applied to molecular dynamics simulations of water at hydrophobic and hydrophilic surfaces. In conjunction with a modified Poisson-Boltzmann equation, the trend of experimental double-layer capacitances is well reproduced. We show that the apparent Stern layer can be understood in terms of the dielectric profile of pure water.

Kinetic energy of protons in ice Ih and water: A path integral study

The kinetic energy of H and O nuclei has been studied by path integral molecular-dynamics simulations of ice Ih and water at ambient pressure. The simulations were performed by using the q-TIP4P/F model, a point-charge empirical potential that includes molecular flexibility and anharmonicity in the OH stretch of the water molecule. Ice Ih was studied in a temperature range between 210 and 290 K, and water between 230 and 320 K. Simulations of an isolated water molecule were performed in the range 210--320 K to estimate the contribution of the intramolecular vibrational modes to the kinetic energy. Our results for the proton kinetic energy ${K}_{H}$ in water and ice Ih show both agreement and discrepancies with different published data based on deep inelastic neutron-scattering experiments. Agreement is found for water at the experimental melting point and in the range 290--300 K. Discrepancies arise because data derived from the scattering experiments predict in water two maxima of ${K}_{H}$ around 270 and 277 K, and that ${K}_{H}$ is lower in ice than in water at 269 K. As a check of the validity of the employed water potential, we show that our simulations are consistent with other experimental thermodynamic properties related to ${K}_{H}$, such as the temperature dependence of the liquid density, the heat capacity of water and ice at constant pressure, and the isotopic shift in the melting temperature of ice upon isotopic substitution of either H or O atoms. Moreover, the temperature dependence of ${K}_{H}$ predicted by the q-TIP4P/F model for ice Ih is found to be in good agreement with results of path integral simulations using ab initiodensity-functional theory.

Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice.

Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.

WHY WATER FILLS NANOTUBES

POSSIBLE APPLICATIONS of carbon nanotubes (CNTs) for nanofluidics and nanofiltration depend on an important but perplexing phenomenon: Water spontaneously enters CNTs, despite the fact that such nanotubes are made from hydrophobic graphene sheets. Two recent papers explore the effect. One finds that the answer to the mystery lies in water’s unique hydrogen-bonding interactions, while the other shows that at low temperatures CNTs containing water also unexpectedly empty. In the first paper, researchers report molecular dynamics simulations of water confined to single-walled CNTs of various sizes to compare their entropy, enthalpy, and free energy and pin down the driving force behind spontaneous filling at 300 K ( Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.1108073108). Postdoctoral researcher Tod A. Pascal and professor Yousung Jung of Korea Advanced Institute of Science & Technology ’s (KAIST’s) Graduate School of Energy, Environment, Water & Sustainability, along with California Institute of Technolog...

Entropy and the driving force for the filling of carbon nanotubes with water

The spontaneous filling of hydrophobic carbon nanotubes (CNTs) by water observed both experimentally and from simulations is counterintuitive because confinement is generally expected to decrease both entropy and bonding, and remains largely unexplained. Here we report the entropy, enthalpy, and free energy extracted from molecular dynamics simulations of water confined in CNTs from 0.8 to 2.7-nm diameters. We find for all sizes that water inside the CNTs is more stable than in the bulk, but the nature of the favorable confinement of water changes dramatically with CNT diameter. Thus we find (i) an entropy (both rotational and translational) stabilized, vapor-like phase of water for small CNTs (0.8-1.0 nm), (ii) an enthalpy stabilized, ice-like phase for medium-sized CNTs (1.1-1.2 nm), and (iii) a bulk-like liquid phase for tubes larger than 1.4 nm, stabilized by the increased translational entropy as the waters sample a larger configurational space. Simulations with structureless coarse-grained water models further reveal that the observed free energies and sequence of transitions arise from the tetrahedral structure of liquid water. These results offer a broad theoretical basis for understanding water transport through CNTs and other nanostructures important in nanofluidics, nanofiltrations, and desalination.

Phase Transitions of Water in Graphite and Mica Pores

We report all-atom molecular dynamics simulations of water confined in graphite and mica slit pores of variable size ranging from 10 to 60 A. For each pore size, we demonstrate that the confinement...