X‐ray and neutron scattering studies of the structure of water at a hydrophobic surface

Intra-protein interacting collective modes in the terahertz frequency region

Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.

Comparison of atomic force microscopy force curve and solvation structure studied by integral equation theory

Atomic force microscopy can observe structures of liquids (solvents) on solid surfaces as oscillating force curves. The oscillation originates from the solvation force, which is affected by the interaction between the probe, substrate, and solvents. To investigate the effects of the interactions on the force curve, we calculated the force curves by integral equation theory with various probe and substrate conditions. The probe solvophilicity affected the force curves more than the substrate solvophilicity in our calculation, and its reason is qualitatively explained by the amount of the desolvated solvents. We evaluated the probes and parameters in terms of the qualitative estimation of the number density distribution of the solvent on the wall. The negative of the force curve's derivative with respect to the surface separation reflected the number density distribution better than the force curve. This parameter is based on the method that is proposed previously by Amano et al. [Phys. Chem. Chem. Phys. 18, 15534 (2016)]. The normalized frequency shift can also be used for the qualitative estimation of the number density distribution if the cantilever amplitude is small. Solvophobic probes reflected the number density distribution better than the solvophilic probes. Solvophilic probes resulted in larger oscillation amplitudes than solvophobic probes and are suitable for measurements with a high S/N ratio.

X-ray scattering study of water confined in bioactive glasses: experimental and simulated pair distribution function

Temperature-dependent total X-ray scattering measurements for water confined in bioactive glass samples with 5.9 nm pore diameter have been performed. Based on these experimental data, simulations were carried out using the Empirical Potential Structure Refinement (EPSR) code, in order to study the structural organization of the confined water in detail. The results indicate a non-homogeneous structure for water inside the pore, with three different structural organizations of water, depending on the distance from the pore surface: (i) a first layer (4 Å) of interfacial pore water that forms a strong chemical bond with the substrate, (ii) intermediate pore water forming a second layer (4-11 Å) on top of the interfacial pore water, (iii) bulk-like pore water in the centre of the pores. Analysis of the simulated site-site partial pair distribution function shows that the water-silica (O_w-Si) pair correlations occur at ∼3.75 Å. The tetrahedral network of bulk water with oxygen-oxygen (O_w-O_w) hydrogen-bonded pair correlations at ∼2.8, ∼4.1 and ∼4.5 Å is strongly distorted for the interfacial pore water while the second neighbour pair correlations are observed at ∼4.0 and ∼4.9 Å. For the interfacial pore water, an additional O_w-O_w pair correlation appears at ∼3.3 Å, which is likely caused by distortions due to the interactions of the water molecules with the silica at the pore surface.

Forces between zinc sulphide surfaces; amplification of the hydrophobic attraction by surface charge

Smooth Zinc Sulphide (ZnS) surfaces were prepared by magnetron sputtering and the interaction forces were measured between them as a function of pH. At the isoelectric point (iep) of pH 7.1 the attractive force was well described by the van der Waals interaction calculated using Lifshitz theory for a layered system. Away from the iep, the forces were fitted using DLVO theory extended to account for surface roughness. At pH 9.8 the surfaces acquire a negative charge and an electrostatic repulsion is evident. Below the iep the surfaces acquire a positive charge leading to electrostatic repulsion. The forces in the range 3.8 < pH < 4.8 show an additional attraction on approach and much greater adhesion than at other pH values. This is attributed to the hydrophobic attraction being amplified by a small degree of charge on the surface as has previously been reported for adhesion measurements. The range of the measured forces is attributed to the long-range orientational order of water (>5 nm).

Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy

Atomic force microscopy (AFM) in liquids can measure a force curve between a probe and a buried substrate. The shape of the measured force curve is related to hydration structure on the substrate. However, until now, there has been no practical theory that can transform the force curve into the hydration structure, because treatment of the liquid confined between the probe and the substrate is a difficult problem. Here, we propose a robust and practical transform theory, which can generate the number density distribution of solvent molecules on a substrate from the force curve. As an example, we analyzed a force curve measured by using our high-resolution AFM with a newly fabricated ultrashort cantilever. It is demonstrated that the hydration structure on muscovite mica (001) surface can be reproduced from the force curve by using the transform theory. The transform theory will enhance AFM's ability and support structural analyses of solid/liquid interfaces. By using the transform theory, the effective diameter of a real probe apex is also obtained. This result will be important for designing a model probe of molecular scale simulations.

Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity

We perform molecular dynamics simulations to observe the structure and dynamics of water using different water models (TIP3P, TIP4P, TIP5P) at ambient conditions, constrained by planar walls, which are either modeled by smooth potentials or regular atomic lattices, imitating the honeycomb-structure of graphene. We implement walls of different hydroaffinity, different lattice constant, and different types of interaction with the water molecules. We find that in the hydrophobic regime the smooth wall generally represents a good abstraction of the atomically rough walls, while in the hydrophilic regime there are noticeable differences in structure and dynamics between all stages of wall roughness. For a small lattice constant however the smooth and the atomically rough wall still share a number of structural and dynamical similarities. Out of the three water models, TIP5P water shows the largest degree of tetrahedral ordering and is often the one that is least perturbed by the presence of the wall.

The relationship between local liquid density and force applied on a tip of atomic force microscope: a theoretical analysis for simple liquids

The density of a liquid is not uniform when placed on a solid. The structured liquid pushes or pulls a probe employed in atomic force microscopy, as demonstrated in a number of experimental studies. In the present study, the relation between the force on a probe and the local density of a liquid is derived based on the statistical mechanics of simple liquids. When the probe is identical to a solvent molecule, the strength of the force is shown to be proportional to the vertical gradient of ln(ρDS) with the local liquid's density on a solid surface being ρDS. The intrinsic liquid's density on a solid is numerically calculated and compared with the density reconstructed from the force on a probe that is identical or not identical to the solvent molecule.

Photoacoustic contrast imaging of biological tissues with nanodiamonds fabricated for high near-infrared absorbance

Radiation-damaged nanodiamonds (DNDs) are potentially ideal optical contrast agents for photoacoustic (PA) imaging in biological tissues due to their low toxicity and high optical absorbance. PA imaging contrast agents have been limited to quantum dots and gold particles, since most existing carbon-based nanoparticles, including fluorescent nanodiamonds, do not have sufficient optical absorption in the near-infrared (NIR) range. A new DND by He+ ion beam irradiation with very high NIR absorption was synthesized. These DNDs produced a 71-fold higher PA signal on a molar basis than similarly dimensioned gold nanorods, and 7.1 fmol of DNDs injected into rodents could be clearly imaged 3 mm below the skin surface with PA signal enhancement of 567% using an 820-nm laser wavelength.

Rapid water transportation through narrow one-dimensional channels by restricted hydrogen bonds

Water plays an important role in controlling chemical reactions and bioactivities. For example, water transportation through water channels in a biomembrane is a key factor in bioactivities. However, molecular-level mechanisms of water transportation are as yet unknown. Here, we investigate water transportation through narrow and wide one-dimensional (1D) channels on the basis of water-vapor adsorption rates and those determined by molecular dynamics simulations. We observed that water in narrow 1D channels was transported 3-5 times faster than that in wide 1D channels, although the narrow 1D channels provide fewer free nanospaces for water transportation. This rapid transportation is attributed to the formation of fewer hydrogen bonds between water molecules adsorbed in narrow 1D channels. The water-transportation mechanism provides the possibility of rapid communication through 1D channels and will be useful in controlling reactions and activities in water systems.

Anomalies of water and hydrogen bond dynamics in hydrophobic nanoconfinement

Using molecular dynamic (MD) simulations of the TIP5P model of water, we investigate the effect of hydrophobic confinement on the anomalies of liquid water. For confinement length Lz = 1.1 nm, such that there are 2-3 molecular layers of water, we find the presence of the bulk-like density and diffusion anomaly in the lateral directions. However, the lines of these anomalies in the P-T plane are shifted to lower temperatures (ΔT≈40 K) and pressures compared to bulk water. Furthermore, we introduce a method to calculate the effective diffusion constant along the confinement direction and find that the diffusion anomaly is absent. Moreover, we investigate the hydrogen bond dynamics of confined water and find that the hydrogen bond dynamics preserves the characteristics of HB dynamics in bulk water, such as a non-exponential behavior followed by an exponential tail of HB lifetime probability distributions and an Arrhenius temperature dependence of the average HB lifetime. The average number and lifetime of HBs decrease in confined water compared to bulk water at the same temperature. This reduction may be the origin of the reasons for the different physical properties of confined water from bulk water, such as the 40 K temperature shift.

Structural characterization of water/ice formation in SBA-15 silicas: III. The triplet profile for 86 Å pore diameter

The diffraction results for the formation of ice in 86 Å diameter pores of a SBA-15 silica sample are analysed to provide information on the characteristics of the ice created in the pores. The asymmetric triplet at ∼1.7 Å(-1), which involves several overlapping peaks, is particularly relevant to the different ice phases and contains a number of components that can be individually identified. The use of a set of three peaks with an asymmetric profile to represent the possibility of facetted growth in the pores was found to give an unsatisfactory fit to the data. The alternative method involving the introduction of additional peaks with a normal symmetric profile was found to give excellent fits with five components and was the preferred analytic procedure. Three peaks could be directly linked to the positions for the triplet of hexagonal ice, I(h), and one of the other two broad peaks could be associated with a form of amorphous ice. The variation of the peak intensity (and position) was systematic with temperature for both cooling and heating runs. The results indicate that a disordered state of ice is formed as a component with the defective crystalline ices. The position of a broad diffraction peak is intermediate between that of high-density and low-density amorphous ice. The remaining component peak is less broad but does not relate directly to any of the known ice phases and cannot be assigned to any specific structural feature at the present time.

Effect of water-wall interaction potential on the properties of nanoconfined water

Much of the understanding of bulk liquids has progressed through study of the limiting case in which molecules interact via purely repulsive forces, such as a hard-core or "repulsive ramp" potential. In the same spirit, we report progress on the understanding of confined water by examining the behavior of waterlike molecules interacting with planar walls via purely repulsive forces and compare our results with those obtained for Lennard-Jones (LJ) interactions between the molecules and the walls. Specifically, we perform molecular dynamics simulations of 512 waterlike molecules interacting via the TIP5P potential and confined between two smooth planar walls that are separated by 1.1nm . At this separation, there are either two or three molecular layers of water, depending on density. We study two different forms of repulsive confinement, when the water-wall interaction potential is either (i) 1r;{9} or (ii) a WCA-like repulsive potential. We find that the thermodynamic, dynamic, and structural properties of the liquid in purely repulsive confinements qualitatively match those for a system with a pure LJ attraction to the wall. In previous studies that include attractions, freezing into monolayer or trilayer ice was seen for this wall separation. Using the same separation as these previous studies, we find that the crystal state is not stable with 1r;{9} repulsive walls but is stable with WCA-like repulsive confinement. However, by carefully adjusting the separation of the plates with 1r;{9} repulsive interactions so that the effective space available to the molecules is the same as that for LJ confinement, we find that the same crystal phases are stable. This result emphasizes the importance of comparing systems only using the same effective confinement, which may differ from the geometric separation of the confining surfaces.

Peculiar Properties of Water as Solute

Water has been investigated for a long time as the most important solvent; the peculiar behavior of water as solute has been studied in binary mixtures with organic solvents, mainly exploring the whole phase diagram. In this Article, we studied the behavior of water in binary mixtures with propylene carbonate in the phase diagram region where water acts as a solute as a function of the water molar fraction X(water). Surface tension measurements, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) have been used to investigate the state of water molecules and hydrogen bonds when water is to be considered a solute instead of a solvent, and peculiar and interesting properties were discovered. The interaction of water molecules among themselves and between water and propylene carbonate has been shown to be dependent on the water concentration in the mixtures. All of the measured properties showed a break at X(water) approximately 0.15-0.20 similar to the break due to the critical micellar concentration in surfactant solutions. In particular, from the FTIR spectra, it was possible to deduce that at this concentration water has a transition from pure solute ("multimers" solvated by PC) to cosolvent ("intermediate" and "network" water).

Confined Water: A Mercedes-Benz Model Study

We study water that is confined within small geometric spaces. We use the Mercedes-Benz (MB) model of water, in NVT and muVT Monte Carlo computer simulations. For MB water molecules between two planes separated by a distance d, we explore the structures, hydrogen bond networks, and thermodynamics as a function of d, temperature T, and water chemical potential mu. We find that squeezing the planes close enough together leads to a vaporization of waters out of the cavity. This vaporization transition has a corresponding peak in the heat capacity of the water. We also find that, in small pores, hydrogen bonding is not isotropic but, rather, it preferentially forms chains along the axis of the cavity. This may be relevant for fast proton transport in pores. Our simulations show oscillations in the forces between the inert plates, due to water structure, even for plate separations of 5-10 water diameters, consistent with experiments by Israelachvili et al. [Nature 1983, 306, 249]. Finally, we find that confinement affects water's heat capacity, consistent with recent experiments of Tombari et al. on Vycor nanopores [J. Chem. Phys. 2005, 122, 104712].

Thermodynamics, structure, and dynamics of water confined between hydrophobic plates

We perform molecular dynamics simulations of 512 waterlike molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic properties of water are shifted to lower temperatures relative to the bulk by approximately 40 K. The dynamics and structure of the confined water resemble bulk water at higher temperatures, consistent with the shift of thermodynamic anomalies to lower temperature. Because of this T shift, our confined water simulations (down to T=220 K) do not reach sufficiently low temperature to observe a liquid-liquid phase transition found for bulk water at T approximately 215 K using the TIP5P potential, but we see inflections in isotherms at lower temperatures presumably due to the presence of a liquid-liquid critical point. We find that the different crystalline structures that can form for two different separations of the plates, 0.7 and 1.10 nm, have no counterparts in the bulk system, and we discuss the relevance to experiments on confined water.

Electrofreezing of confined water

We report results from molecular dynamics simulations of the freezing transition of TIP5P water molecules confined between two parallel plates under the influence of a homogeneous external electric field, with magnitude of 5 V/nm, along the lateral direction. For water confined to a thickness of a trilayer we find two different phases of ice at a temperature of T=280 K. The transformation between the two, proton-ordered, ice phases is found to be a strong first-order transition. The low-density ice phase is built from hexagonal rings parallel to the confining walls and corresponds to the structure of cubic ice. The high-density ice phase has an in-plane rhombic symmetry of the oxygen atoms and larger distortion of hydrogen bond angles. The short-range order of the two ice phases is the same as the local structure of the two bilayer phases of liquid water found recently in the absence of an electric field [J. Chem. Phys. 119, 1694 (2003)]. These high- and low-density phases of water differ in local ordering at the level of the second shell of nearest neighbors. The results reported in this paper, show a close similarity between the local structure of the liquid phase and the short-range order of the corresponding solid phase. This similarity might be enhanced in water due to the deep attractive well characterizing hydrogen bond interactions. We also investigate the low-density ice phase confined to a thickness of 4, 5, and 8 molecular layers under the influence of an electric field at T=300 K. In general, we find that the degree of ordering decreases as the distance between the two confining walls increases.