Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Monolayer of aerosol-OT surfactants adsorbed at the air/water interface: an atomistic computer simulation study

An atomistic molecular dynamics (MD) simulation has been carried out to investigate the structural and dynamical properties of a monolayer of the anionic surfactant sodium bis(2-ethyl-1-hexyl) sulfosuccinate (aerosol-OT or AOT) adsorbed at the air/water interface. The simulation is performed at room temperature and at a surface coverage corresponding to that at its critical micelle concentration (78 A(2)/molecule). The estimated thickness of the adsorbed layer is in good agreement with neutron reflection data. The study shows that the surfactants exhibit diffusive motion in the plane of the interface. It is observed that the surfactant monolayer has a strong influence in restricting both the translational and reorientational motions of the water molecules close to the interface. A drastic difference in the dipolar reorientational motion of water molecules in the aqueous layer is observed with a small variation of the distance from the surfactant headgroups. It has been observed that the water molecules in the first hydration layer (region 1) form strong hydrogen bonds with surfactant headgoups. This results in the slower structural relaxation of water-water hydrogen bonds in the first hydration layer compared to that in the pure bulk water. Most interestingly, we notice that the water molecules present in the layer immediately after the first hydration layer form weaker hydrogen bonds and thus relax faster than even pure bulk water.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

High-resolution neutron-scattering study of slow dynamics of surface water molecules in zirconium oxide

We have performed a quasielastic neutron-scattering experiment on backscattering spectrometer with sub-mueV resolution to investigate the slow dynamics of surface water in zirconium oxide using the sample studied previously with a time-of-flight neutron spectrometer [E. Mamontov, J. Chem. Phys. 121, 9087 (2004)]. The backscattering measurements in the temperature range of 240-300 K have revealed a translational dynamics slower by another order of magnitude compared to the translational dynamics of the outer hydration layer observed in the time-of-flight experiment. The relaxation function of this slow motion is described by a stretched exponential with the stretch factors between 0.8 and 0.9, indicating a distribution of the relaxation times. The temperature dependence of the average residence time is non-Arrhenius, suggesting that the translational motion studied in this work is more complex than surface jump diffusion previously observed for the molecules of the outer hydration layer. The observed slow dynamics is ascribed to the molecules of the inner hydration layer that form more hydrogen bonds compared to the molecules of the outer hydration layer. Despite being slower by two orders of magnitude, the translational motion of the molecules of the inner hydration layer may have more in common with bulk water compared to the outer hydration layer, the dynamics of which is slower than that of bulk water by just one order of magnitude.     

Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.     

Hydration of the Calcium Dication: Direct Evidence for Second Shell Formation from Infrared Spectroscopy

Infrared laser action spectroscopy in a Fourier‐transform ion cyclotron resonance mass spectrometer is used in conjunction with ab initio calculations to investigate doubly charged, hydrated clusters of calcium formed by electrospray ionization. Six water molecules coordinate directly to the calcium dication, whereas the seventh water molecule is incorporated into a second solvation shell. Spectral features indicate the presence of multiple structures of Ca(H₂O)₇²⁺ in which outer‐shell water molecules accept either one (single acceptor) or two (double acceptor) hydrogen bonds from inner‐shell water molecules. Double‐acceptor water molecules are predominately observed in the second solvent shells of clusters containing eight or nine water molecules. Increased hydration results in spectroscopic signatures consistent with additional second‐shell water molecules, particularly the appearance of inner‐shell water molecules that donate two hydrogen bonds (double donor) to the second solvent shell. This is the first reported use of infrared spectroscopy to investigate shell structure of a hydrated multiply charged cation in the gas phase and illustrates the effectiveness of this method to probe the structures of hydrated ions.     

Long-range influence of carbohydrates on the solvation dynamics of water--answers from terahertz absorption measurements and molecular modeling simulations

We present new terahertz (THz) spectroscopic measurements of solvated sugars and compare the effect of two disaccharides (trehalose and lactose) and one monosaccharide (glucose) with respect to the solute-induced changes in the sub-picosecond network dynamics of the hydration water. We found that the solute affects the fast collective network motions of the solvent, even beyond the first solvation layer. For all three carbohydrates, we find an increase of 2-4% in the THz absorption coefficient of the hydration water in comparison to bulk water. Concentration-dependent changes in the THz absorption between 2.1 and 2.8 THz of the solute-water mixture were measured with a precision better than 1% and were used to deduce a dynamical hydration shell, which extends from the surface up to 5.7 +/- 0.4 and 6.5 +/- 0.9 A for the disaccharides lactose and trehalose, respectively, and 3.7 +/- 0.9 A for the glucose. This exceeds the values for the static hydration shell as determined, for example, by scattering, where the long-range structure was found to be not significantly affected by the solute beyond the first hydration shell. When comparing all three carbohydrates, we found that the solute-induced change in the THz absorption depends on the product of molar concentration of the solute and the number of hydrogen bonds between the carbohydrate and water molecules. We can conclude that the long-range influence on the sub-picosecond collective water network motions of the hydration water is directly correlated with the average number of hydrogen bonds between the molecule and adjacent water molecules for carbohydrates. This implies that monosaccharides have a smaller influence on the surrounding water molecules than disaccharides. This could explain the bioprotection mechanism of sugar-water mixtures, which has been found to be more effective for disaccharides than for monosaccharides.     

Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations

We have analyzed a set of molecular dynamics (MD) trajectories of maltose in vacuum and water for solute imposed structuring on the solvent. To do this, we used a novel technique to calculate water probability densities to locate the areas in which the solvent is most populated in the maltose solution. We found that only the layer of water within the first maltose hydration shell has a probability density 50% and greater than that of bulk water. On investigating this water layer using Voronoi polyhedra (VP) analysis it was seen that only the waters adjacent to the hydrophobic (CH and CH₂) groups are more structured than bulk water. We found that in a maltose solution of approximately 1.0 g/cm³ the solute does not disrupt the structure of the surrounding water beyond the first hydration shell. Next we performed a 700‐ps MD simulation of a maltohexaose strand in a box of 4096 SPC/E waters. The water probability density calculations and the VP analysis of the maltohexaose solution show that the larger amylose repeat unit decreases the solvent configurational entropy of the water beyond the first hydration shell. Analysis of this trajectory reveals that the helical conformation of the maltohexaose strand is preserved via bridging intermolecular water hydrogen bonds, indicating that a single amylose helical turn in water is preserved by hydrophilic and not hydrophobic interactions. Using VP analysis we present a method to accurately determine the number of water molecules in the first hydration shell of dissolved solutes. In the case of maltose, there are 40 water molecules in this shell, while for maltohexaose the number is 98. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 445–456, 2001     

Structure and dynamics of the hydration shells of the Al3+ ion

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.     

Equatorial and apical solvent shells of the UO2 2+ ion

First principles molecular dynamics simulations of the hydration shells surrounding UO(2)(2+) ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average U=O bond length was found to be 1.77 A. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 A (2.46 A, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59 A. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO(2)(2+) ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO(2)(2+), oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.     

Relaxation and jump dynamics of water at the mica interface

The orientational relaxation dynamics of water confined between mica surfaces is investigated using molecular dynamics simulations. The study illustrates the wide heterogeneity that exists in the dynamics of water adjacent to a strongly hydrophilic surface such as mica. Analysis of the survival probabilities in different layers is carried out by normalizing the corresponding relaxation times with bulk water layers of similar thickness. A 10-fold increase in the survival times is observed for water directly in contact with the mica surface and a non-monotonic variation in the survival times is observed moving away from the mica surface to the bulk-like interior. The orientational relaxation time is highest for water in the contact layer, decreasing monotonically away from the surface. In all cases the ratio of the relaxation times of the 1st and 2nd rank Legendre polynomials of the HH bond vector is found to lie between 1.5 and 1.9 indicating that the reorientational relaxation in the different water layers is governed by jump dynamics. The orientational dynamics of water in the contact layer is particularly novel and is found to undergo distinct two-dimensional hydrogen bond jump reorientational dynamics with an average waiting time of 4.97 ps. The waiting time distribution is found to possess a long tail extending beyond 15 ps. Unlike previously observed jump dynamics in bulk water and other surfaces, jump events in the mica contact layer occur between hydrogen bonds formed by the water molecule and acceptor oxygens on the mica surface. Despite slowing down of the water orientational relaxation near the surface, life-times of water in the hydration shell of the K(+) ion are comparable to that observed in bulk salt solutions.     

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.     

Comparative Analysis of Hydration Layer Reorientation Dynamics of Antifreeze Protein and Protein Cytochrome P450

Antifreeze proteins (AFPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFPs' hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.     

An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree‐Fock level in conjunction with Dunning double‐ζ plus polarization function basis sets. The simulation predicts an average H? Cl bond distance of 1.28 Å, which is in good agreement with the experimental value. The H_HCl···O_w and Cl_HCl···H_w distances of 1.84 and 3.51 Å were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure‐making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Vibrational and orientational dynamics of water in aqueous hydroxide solutions

We report the vibrational and orientational dynamics of water molecules in isotopically diluted NaOH and NaOD solutions using polarization-resolved femtosecond vibrational spectroscopy and terahertz time-domain dielectric relaxation measurements. We observe a speed-up of the vibrational relaxation of the O-D stretching vibration of HDO molecules outside the first hydration shell of OH(-) from 1.7 ± 0.2 ps for neat water to 1.0 ± 0.2 ps for a solution of 5 M NaOH in HDO:H(2)O. For the O-H vibration of HDO molecules outside the first hydration shell of OD(-), we observe a similar speed-up from 750 ± 50 fs to 600 ± 50 fs for a solution of 6 M NaOD in HDO:D(2)O. The acceleration of the decay is assigned to fluctuations in the energy levels of the HDO molecules due to charge transfer events and charge fluctuations. The reorientation dynamics of water molecules outside the first hydration shell are observed to show the same time constant of 2.5 ± 0.2 ps as in bulk liquid water, indicating that there is no long range effect of the hydroxide ion on the hydrogen-bond structure of liquid water. The terahertz dielectric relaxation experiments show that the transfer of the hydroxide ion through liquid water involves the simultaneous motion of ~7 surrounding water molecules, considerably less than previously reported for the proton.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Molecular simulation study of temperature effect on ionic hydration in carbon nanotubes

Molecular dynamics simulations have been performed to investigate the hydration of Li(+), Na(+), K(+), F(-), and Cl(-) inside the carbon nanotubes at temperatures ranging from 298 to 683 K. The structural characteristics of the coordination shells of ions are studied, including the ion-oxygen radial distribution functions, the coordination numbers, and the orientation distributions of the water molecules. Simulation results show that the first coordination shells of the five ions still exist in the nanoscale confinement. Nevertheless, the first coordination shell structures of cations change more significantly than those of anions because of the preferential orientation of the water molecules induced by the carbon nanotube. The first coordination shells of cations are considerably less ordered in the nanotube than in the bulk solution, whereas the change of the first coordination shell structures of the anions is minor. Furthermore, the confinement induces the anomalous behavior of the coordination shells of the ions with temperature. The first coordination shell of K(+) are found to be more ordered as the temperature increases only in the carbon nanotube with the effective diameter of 1.0 nm, implying the enhancement of the ionic hydration with temperature. This is contrary to that in the bulk solution. The coordination shells of the other four ions do not have such behavior in the carbon nanotube with the effective diameter ranging from 0.73 to 1.00 nm. The easier distortion of the coordination shell of K(+) and the match of the shell size and the nanotube size may play roles in this phenomenon. The exchange of water molecules in the first coordination shells of the ions with the solution and the ion diffusion along the axial direction of the nanotube are also investigated. The mobility of the ions and the stability of the coordination shells are greatly affected by the temperature in the nanotube as in the bulk solutions. These results help to understand the biological and chemical processes at the high temperature.     

Hydration layer of a cationic micelle, C(10)TAB: structure, rigidity, slow reorientation, hydrogen bond lifetime, and solvation dynamics

We report a theoretical study of the structure and dynamics of the water layer (the hydration layer) present at the surface of the cationic micelle decyltrimethylammonium bromide (DeTAB) by using atomistic molecular dynamics simulations. The simulated micelle consisted of 47 surfactant molecules (and an equal number of bromide ions), in good agreement with the pioneering light scattering experiments by Debye which found an aggregation number of 50. In this micelle, three partially positively charged methyl groups of each surfactant headgroup face the surrounding water. The nature of the cationic micellar surface is found to play an important role in determining the arrangement of water which is quite different from that in the bulk or on the surface of an anionic micelle, like cesium perfluorooctanoate. Water molecules present in the hydration layer are found to be preferentially distributed in the region between the three partially charged methyl headgroups. It is found that both the translational and rotational motions of water exhibit appreciably slower dynamics in the layer than those in the bulk. The solvation time correlation function (TCF) of bromide ions exhibits a long time component which is found to originate primarily from the interaction of the probe with the micellar headgroups. Thus, the decay of the solvation TCF is controlled largely by the residence time of the probe in the surface. The residence time distribution of the water molecules also exhibits a slow time component. We also calculate the collective number density fluctuation in the layer and find a prominent slow component compared to the similar quantity in the bulk. This slow component demonstrates that water structure in the hydration layer is more rigid than that in the bulk. These results demonstrate that the slow dynamics of hydration layer water is generic to macromolecular surfaces of either polarity.     

Structure and dynamics of Au+ ion in aqueous solution: ab initio QM/MM MD simulations

Structure and dynamics of hydrated Au(+) have been investigated by means of molecular dynamics simulations based on ab initio quantum mechanical molecular mechanical forces at Hartree-Fock level for the treatment of the first hydration shell. The outer region of the system was described using a newly constructed classical three-body corrected potential. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells and bulk indicate a very labile structure of the first hydration shell whose average coordination number of 4.7 is a mixture of 3-, 4-, 5-, 6-, and 7-coordinated species. Fast water exchange reactions between first and second hydration shell occur, and the second hydration shell is exceptionally large. Therefore, the mean residence time of water molecules in the first hydration shell (5.6 ps/7.5 ps for t*= 0.5 ps/2.0 ps) is shorter than that in the second shell (9.4 ps/21.2 ps for t*= 0.5 ps/2.0 ps), leading to a quite specific picture of a "structure-breaking" effect.     

Molecular dynamics simulations of hydration shell on montmorillonite (001) in water

Molecular dynamics simulations (MDS) of montmorillonite (001)/water interface system were used for studying the hydration shell on the montmorillonite surface in this work. The study was performed on the simulation of concentration profile and self‐diffusion coefficients. The results have shown that there was a hydration shell on the surface with the thickness of approximately 1.74 nm, which was composed of six ordered water molecule layers, including ordered layers and transition layers. The water molecules in the shell were closely and orderly arranged than those in bulk water, leading to a higher concentration of water molecules. Copyright © 2016 John Wiley & Sons, Ltd.