Reorientation dynamics of nanoconfined water: power-law decay, hydrogen-bond jumps, and test of a two-state model

The reorientation dynamics of water confined within nanoscale, hydrophilic silica pores are investigated using molecular dynamics simulations. The effect of surface hydrogen-bonding and electrostatic interactions are examined by comparing with both a silica pore with no charges (representing hydrophobic confinement) and bulk water. The OH reorientation in water is found to slow significantly in hydrophilic confinement compared to bulk water, and is well-described by a power-law decay extending beyond one nanosecond. In contrast, the dynamics of water in the hydrophobic pore are more modestly affected. A two-state model, commonly used to interpret confined liquid properties, is tested by analysis of the position-dependence of the water dynamics. While the two-state model provides a good fit of the orientational decay, our molecular-level analysis evidences that it relies on an over-simplified picture of water dynamics. In contrast with the two-state model assumptions, the interface dynamics is markedly heterogeneous, especially in the hydrophilic pore and there is no single interfacial state with a common dynamics.     

Temperature-dependent infrared spectroscopy of water from a first-principles approach

The structure and dynamics of the hydrogen-bond network in water is investigated as a function of the temperature through the application of a first-principles approach that combines an ab-initio-based water potential with an explicit quantum treatment of the molecular motion. A molecular-level picture of the rearrangement of the hydrogen-bond network is derived from the direct analysis of linear and nonlinear vibrational spectra. The results indicate that good agreement with the available experimental data is obtained when the temperature scale is defined relative to the corresponding melting points. In particular, the theoretically predicted energy barriers and time scales associated with the hydrogen-bond dynamics are closely comparable to the experimental values obtained from two-dimensional and pump-probe infrared spectra. The present analysis will also serve as a guide for future developments of an improved ab-initio-based model capable to reproduce the properties of water in different environments and under different conditions.     

Structure and dynamics of water near the interface with oligo(ethylene oxide) self-assembled monolayers

We performed molecular dynamics simulations of the oligo(ethylene oxide) (OEO) self-assembled monolayers in water to determine the nature of the systems' interfacial structure and dynamics. The density profiles, hydrogen bonding, and water dynamics are calculated as a function of the area per molecule A of OEO. At the highest coverages, the interface is hydrophobic, and a density drop is found at the interface. The interfacial region becomes more like bulk water as A increases. The OEO and water become progressively more mixed, and hydrogen bonding increases within the interfacial region. Water mobility is slower within the interfacial region, but not substantially. The implications of our results on the resistance of OEO SAMs to protein adsorption are discussed. Our principal result is that as A increases the increasingly waterlike interfacial region provides a more protein-resistant surface. This finding supports recent experimental measurements that protein resistance is maximal for less than full coverage on Au.     

Reorientational Dynamics of Water Confined in Zeolites

We present a detailed molecular‐dynamics study of water reorientation and hydrogen‐bond dynamics in a strong confinement situation, within the narrow pores of an all‐silica Linde type A (LTA) zeolite. Two water loadings of the zeolite are compared with the bulk case. Water dynamics are retarded in this extreme hydrophobic confinement and the slowdown is more pronounced at higher water loading. We show that water reorientation proceeds mainly by large‐amplitude angular jumps, whose mechanism is similar to that determined in the bulk. The slowdown upon hydrophobic confinement arises predominantly from an excluded‐volume effect on the large fraction of water molecules lying at the interface with the zeolite matrix, with an additional minor contribution coming from a structuring effect induced by the confinement.     

Libration induced stretching mode excitation for pump-probe spectroscopy in pure liquid water

We developed an experimental approach to study pure liquid water in the infrared and avoid thermal effects. This technique is based on libration induced stretching excitation of water molecules. A direct correspondence between frequencies within the libration and OH stretching bands is demonstrated. Energy diffusion is studied in pure liquid water by measuring wave packet dynamics of OH stretching vibrator with infrared femtosecond spectroscopy. Wave packet dynamics reveals ultrafast energy dynamics and reflects 130 fs intermolecular energy transfer between water vibrators. Energy diffusion is almost two orders of magnitude faster than self diffusion in water.     

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water

Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ～10 ? of a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.     

Mechanism of unassisted ion transport across membrane bilayers

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.     

Molecular dynamics simulations of aqueous solutions of ethanolamines

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.     

Flow-induced deformation of shallow microfluidic channels

We study the elastic deformation of poly(dimethylsiloxane) (PDMS) microchannels under imposed flow rates and the effect of this deformation on the laminar flow profile and pressure distribution within the channels. Deformation is demonstrated to be an important consideration in low aspect ratio (height to width) channels and the effect becomes increasingly pronounced for very shallow channels. Bulging channels are imaged under varying flow conditions by confocal microscopy. The deformation is related to the pressure and is thus non-uniform throughout the channel, with tapering occurring along the stream-wise axis. The measured pressure drop is monitored as a function of the imposed flow rate. For a given pressure drop, the corresponding flow rate in a deforming channel is found to be several times higher than expected in a non-deforming channel. The experimental results are supported by scaling analysis and computational fluid dynamics simulations coupled to materials deformation models.     

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined.     

Solvation of coumarin 314 at water/air interfaces containing anionic surfactants. I. Low coverage

Through the use of molecular dynamics techniques, we analyze equilibrium and dynamical aspects of the solvation of Coumarin 314 adsorbed at water/air interfaces in the presence of sodium dodecyl sulfate surfactant molecules. Three different coverages in the submonolayer regime were considered, 500, 250, and 100 A(2)/SDS molecule. The surfactant promotes two well-differentiated solvation environments, which can be clearly distinguished in terms of their structures for the largest surfactant coverage considered. The first one is characterized by the probe lying adjacent or exterior to two-dimensional spatial domains formed by clustered surfactant molecules. A second type of solvation environment is found in which the coumarin appears embedded within compact surfactant domains. Equilibrium and dynamical aspects of the interfacial orientation of the probe are investigated. Our results show a gradual transition from parallel to perpendicular dipolar alignment of the probe with respect to the interface as the concentration of surfactant rho(s) increases. The presence of the surfactant leads to an increase in the roughness and in the characteristic width of the water/air interface. These modifications are also manifested by the decorrelation times for the probe reorientational dynamics, which become progressively slower with rho(s) in both solvation states, although much more pronounced for the embedded ones. The dynamical characteristics of the solvation responses of the charged interfaces are also analyzed, and the implications of our findings to the interpretation of available experimental measurements are discussed.     

Collapse mechanisms and extreme deformation of particle-laden interfaces

Particle-laden interfaces are at the basis of many advanced materials, such as bijels and dry water. While the final properties of these materials can generally be controlled, their response to deformation during processing and use is still poorly understood. In particular, the dynamics of particle-laden interfaces in relevant flow conditions is receiving increasing attention. These conditions are typically highly dynamic and can involve unsteady flow or large deformations. This article gives an overview of the remarkable phenomena of particle-laden interfaces undergoing deformations of large amplitude and at high strain rate, in other words extreme deformation. Upon large-amplitude compression, a monolayer of particles can collapse by buckling or by expelling particles in the liquid. The criteria for buckling or expulsions, as well as recent experiments in highly dynamic conditions, are discussed, showing that these criteria can depend also on the rate of deformation. The emerging use of ultrasound-driven bubbles as an experimental platform for controlled deformation of particle-laden interfaces at high strain rate is also discussed. The ability to control the fate of particles at interfaces during dynamic deformation of droplets or bubbles ultimately underpins a variety of applications from controlled release to catalysis.     

Forward-backward semiclassical and quantum trajectory methods for time correlation functions

Forward-backward trajectory formulations of time correlation functions are reviewed. Combination of the forward and reverse time evolution operators within the time-dependent semiclassical approximation minimizes phase cancellation, giving rise to an efficient methodology for simulating the dynamics of low-temperature fluids. A quantum mechanical version of the forward-backward formulation, based on the hydrodynamic formulation of time-dependent quantum mechanics, is also available but is practical only for small systems.     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

The dynamics of a bubble ensemble in a cavitation field

A system of equations was obtained to describe the dynamics of bubbles in a cavitation cloud taking into account the interaction of pulsating bubbles involved in translational motion. The kinetics of cavitation bubble concentration changes, changes in the compressibility of the liquid, and phase transitions within a cavitation bubble and in the neighboring volume of the liquid were taken into account. The role played by bubble deformation in a cavitation cloud was considered. The Bernoulli pressure effect was shown to be negligible. The interaction of cavitation bubbles was a substantial factor that strongly influenced the dynamics of bubbles. It was suggested that there was at least one more mechanism that reduced sonoluminescence intensity from the multiple-bubble cavitation field, namely, a fairly high efficiency of sonoluminescence quenching could additionally be related to the arrival of a cumulative liquid stream at the central cavitation bubble region, where the concentration of active species was high. The dynamics of bubbles in the cavitation field is not only related to the expansion and compression of cavitation bubbles in the acoustic field, but also governed to a great extent by their interaction, translational motion, deformation, and the influence of cumulative streams penetrating the bubbles.     

Hydrogen-bond dynamics in the air-water interface

Hydrogen-bond (H-bond) dynamics in the air-water interface is studied by molecular dynamics simulations. The analysis reveals that the dynamics of breaking and forming hydrogen bonds in the air-water interface is faster than that in bulk water for the polarizable water models. This is in contrast to the results found on a protein surface. We show that the difference stems from more rapid translational diffusion in the interface. When the effect of pair diffusion is eliminated, the hydrogen-bond dynamics in the interface is observed to be slower than that in the bulk. This occurs because the number of water molecules adjacent to a hydrogen-bonded pair and available to accept or donate a hydrogen bond is smaller in the interface than in the bulk. The comparison between polarizable water models and fixed-charge models highlights the potential importance of the polarization effect in the water-vapor interface.     

An accurate and simple quantum model for liquid water

The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics simulations. The present results suggest that the inclusion of nuclear quantum effects into an empirical model for water enhances the ability of such model to faithfully represent experimental data, presumably through an increased ability of the model itself to capture realistic physical effects.     

A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease

Structural water molecules are crucial for the stability and function of proteins. Recently, we presented a molecular dynamics (MD) study on blood coagulation factor Xa (fXa) to investigate the effect of water molecules on the flexibility of the protein structure. We showed that neglecting important water positions at the outset of the simulation leads to severe structural distortions during the MD simulations: A stable trajectory was obtained with a water set that was derived from all 73 X-ray structures of the protein. However, for many proteins of interest, only limited structural data is available, which precludes the merging of information from many X-ray structures. Here, we show that an in silico assembled water network, derived from molecular interaction fields generated with the GRID program, is a viable alternative to X-ray data. MD simulations with the GRID water set show a significantly improved stability over alternative setups without water or the X-ray resolved water molecules in the starting structure. The performance is comparable to a water setup derived from a recently presented clustering approach.     

Carbohydrate clustering in aqueous solutions and the dynamics of confined water

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.