Collective solvent flows around a protein investigated by molecular dynamics simulation

Translational motions of water molecules in various systems equilibrated at room temperature are thought to be diffusive and nondirectional. We performed molecular dynamics simulations of a protein system and showed that the water molecules collectively move around the protein. The motions of two water molecules, which were about 12 A away from each other, are correlated to each other. Such collective motions of water can be regarded as flows around the protein, and the flows exhibited various coherent patterns: fair currents, vortices, and divergent flows. The patterns were highly fluctuating: a set of patterns changed to a different set of patterns within a time scale of 10 ps. Thus, the water motions observed in a scale of length smaller than 12 A and a time scale shorter than 10 ps were nondiffusive, and the motions above these scales were diffusive, where the flows disappeared. The flows near the protein surface had an orientational propensity to be highly parallel to the protein surface, and this propensity gradually vanished with an increment of distance from the protein surface. The divergent patterns of flows, which frequently emerge during the fluctuations of flows, may temporarily cause solvent drying in the vicinity of solutes. The current simulation is supportive of a molecular interaction mechanism that the fluctuations of hydration structure induce attractive interactions between solutes.     

How hydrophobic buckminsterfullerene affects surrounding water structure

The hydrophobic hydration of fullerenes in water is of significant interest as the most common Buckminsterfullerene (C60) is a mesoscale sphere; C60 also has potential in pharmaceutical and nanomaterial applications. We use an all-atom molecular dynamics simulation lasting hundreds of nanoseconds to determine the behavior of a single molecule of C60 in a periodic box of water, and compare this to methane. A C60 molecule does not induce drying at the surface; however, unlike a hard sphere methane, a hard sphere C60 solute does. This is due to a larger number of attractive Lennard-Jones interactions between the carbon atom centers in C60 and the surrounding waters. In these simulations, water is not uniformly arranged but rather adopts a range of orientations in the first hydration shell despite the spherical symmetry of both solutes. There is a clear effect of solute size on the orientation of the first hydration shell waters. There is a large increase in hydrogen-bonding contacts between waters in the C60 first hydration shell. There is also a disruption of hydrogen bonds between waters in the first and second hydration shells. Water molecules in the first hydration shell preferentially create triangular structures that minimize the net water dipole near the surface near both the methane and C60 surface, reducing the total energy of the system. Additionally, in the first and second hydration shells, the water dipoles are ordered to a distance of 8 A from the solute surface. We conclude that, with a diameter of approximately 1 nm, C60 behaves as a large hydrophobic solute.     

Monte Carlo study of three-dimensional organization of water molecules around DNA fragments

Interactions with water molecules are important for the stabilization of three-dimensional structures of nucleic acids and for their functioning. The first hydration shells of macromolecules can be considered as structural parts of nucleic acid. We performed a Monte Carlo study of systems containing a nucleic acid base or base pair with water molecules using improved potential functions. These potential functions enable experimental data on both single base–single water interaction energies and enthalpies of base hydration to be reproduced. Hydration shell structures of base pairs are dependent on the pair geometry. Structural elements of hydration shells can contribute to the pair stability and hence to the probability of mispair formation during nucleic acid biosynthesis. The distribution of water molecules around bases and base pairs is essentially nonhomogeneous.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002).     

Effect of solute size and solute-water attractive interactions on hydration water structure around hydrophobic solutes.

Using Monte Carlo simulations, we investigated the influence of solute size and solute-water attractive interactions on hydration water structure around spherical clusters of 1, 13, 57, 135, and 305 hexagonally close-packed methanes and the single hard-sphere (HS) solute analogues of these clusters. We obtain quantitative results on the density of water molecules in contact with the HS solutes as a function of solute size for HS radii between 3.25 and 16.45 A. Analysis of these results based on scaled-particle theory yields a hydration free energy/surface area coefficient equal to 139 cal/(mol A2), independent of solute size, when this coefficient is defined with respect to the van der Waals surface of the solute. The same coefficient defined with respect to the solvent-accessible surface decreases with decreasing solute size for HS radii less than approximately 10 A. We also find that solute-water attractive interactions play an important role in the hydration of the methane clusters. Water densities in the first hydration shell of the three largest clusters are greater than bulk water density and are insensitive to the cluster size. In contrast, contact water densities for the HS analogues of these clusters decrease with solute size, falling below the bulk density of water for the two largest solutes. Thus, the large HS solutes dewet, while methane clusters of the same size do not.     

Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: a MD study at various temperatures

The temperature dehydration of a C(12)E(6) spherical micelle is characterized through the study of the structure and dynamics of the hydrogen bonds formed by water within the micellar interface. Water molecules in proximity of the hydrophilic fragment of the C(12)E(6) surfactants form strong H-bonds with the oxyethilene units E and with the polar alcoholic heads. The activation energies of such H-bonds fall in the range 2-3 Kcal mol(-1). On the exposed oil core, the number of water-water H-bonds decreases as an effect of dehydration. The dynamics of such bonds exhibits a slow relaxation with respect to the bulk, and two time scales can be discerned: the first one, tau approximately 3-6 ps, is typical of water-water H-bonds around small hydrophobic molecules, whereas the second one, tau approximately 40-80 ps, is probably due to the confining effect of the long hydrophilic fragments which reduces the probability of a water molecule to leave the hydration layer of the exposed oil core. Water molecules around the core form H-bond clusters whose size and distribution change with temperature. From a cluster analysis, the system appears to be below the percolation threshold, suggesting that the exposed oily surface is formed by disconnected patches of size around 1 nm(2), close to the estimate of the solvated hydrophobic patches on protein surfaces. The network connectivity is also considered for concentric hydration shells along the interface: it turns out that near the oil core, the cluster size is larger than elsewhere in the interface demonstrating a strong structural effect induced by the exposed hydrocarbon tails. Temperature affects the cluster size only in the innermost shell.     

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     

Thermal signature of hydrophobic hydration dynamics

Hydrophobic hydration, the perturbation of the aqueous solvent near an apolar solute or interface, is a fundamental ingredient in many chemical and biological processes. Both bulk water and aqueous solutions of apolar solutes behave anomalously at low temperatures for reasons that are not fully understood. Here, we use (2)H NMR relaxation to characterize the rotational dynamics in hydrophobic hydration shells over a wide temperature range, extending down to 243 K. We examine four partly hydrophobic solutes: the peptides N-acetyl-glycine-N'-methylamide and N-acetyl-leucine-N'-methylamide, and the osmolytes trimethylamine N-oxide and tetramethylurea. For all four solutes, we find that water rotates with lower activation energy in the hydration shell than in bulk water below 255 +/- 2 K. At still lower temperatures, water rotation is predicted to be faster in the shell than in bulk. We rationalize this behavior in terms of the geometric constraints imposed by the solute. These findings reverse the classical "iceberg" view of hydrophobic hydration by indicating that hydrophobic hydration water is less ice-like than bulk water. Our results also challenge the "structural temperature" concept. The two investigated osmolytes have opposite effects on protein stability but have virtually the same effect on water dynamics, suggesting that they do not act indirectly via solvent perturbations. The NMR-derived picture of hydrophobic hydration dynamics differs substantially from views emerging from recent quasielastic neutron scattering and pump-probe infrared spectroscopy studies of the same solutes. We discuss the possible reasons for these discrepancies.     

A salt-free zero-charged aqueous onion-phase enhances the solubility of fullerene C60 in water

An onion-phase (multilamellar vesicular phase or Lalpha-phase) was prepared from salt-free zero-charged cationic and anionic (catanionic) surfactant mixtures of tetradecyltrimethylammonium hydroxide (TTAOH)/lauric acid (LA)/H2O. The H+ and OH- counterions form water (TTAOH + LA --> TTAL + H2O), leaving the solution salt free. The onion-phase solution has novel properties including low conductivity, low osmotic pressure and unscreened electrostatic repulsions between cationic and anionic surfactants because of the absence of salt. The spherical multilamellar vesicles have an average 250 nm radius as measured by freeze-fracture transmission electron microscopy (FF-TEM) and the maximum interlayer distance, i.e., the thickness of the hydrophobic bilayer and the water layer, was calculated to be around 52 nm by small-angle X-ray scattering (SAXS). Extremely hydrophobic C60 fullerene can be solubilized in this salt-free zero-charged aqueous onion-phase. As a typical result, 0.588 mg.mL(-1) (approximately 0.82 mmol.L(-1)) C60 has been successfully solubilized into a 50 mmol.L(-1) catanionic surfactant onion-phase aqueous solution. The weight ratio of fullerene to TTAL is calculated to be around 1:40. Solubilization of C60 in the salt-free catanionic onion-phase solution was investigated by using different sample preparation routes, and a variety of techniques were used to characterize these vesicular systems with or without encapsulated C60. The onion-phase solution changed color from slightly bluish to yellow or brown after C60 was solubilized. 1H and 13C NMR measurements indicated that the C60 molecules are located in the hydrophobic layers, i.e., in the central positions [omega-CH3 and delta-(CH2)x] of the hydrophobic layers of the TTAL onion-phase. Salt-free zero-charged catanionic vesicular aqueous solutions are good candidates for enhancing the solubility of C60 in aqueous solutions and may broaden the functionality of fullerenes to new potential applications in biology, medicine, and materials. Hopefully, our method can also be extended to solubilize functionalized carbon nanotubes in aqueous solutions.     

Heat capacity effects associated with the hydrophobic hydration and interaction of simple solutes: a detailed structural and energetical analysis based on molecular dynamics simulations

We examine the SPCE [H. J. C. Berendsen et al., J. Chem. Phys. 91, 6269 (1987)] and TIP5P [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys 112, 8910 (2000)] water models using a temperature series of molecular-dynamics simulations in order to study heat-capacity effects associated with the hydrophobic hydration and interaction of xenon particles. The temperature interval between 275 and 375 K along the 0.1-MPa isobar is studied. For all investigated models and state points we calculate the excess chemical potential for xenon employing the Widom particle insertion technique. The solvation enthalpy and excess heat capacity is obtained from the temperature dependence of the chemical potentials and, alternatively, directly by Ewald summation, as well as a reaction field based method. All three methods provide consistent results. In addition, the reaction field technique allows a separation of the solvation enthalpy into solute/solvent and solvent/solvent parts. We find that the solvent/solvent contribution to the excess heat capacity is dominating, being about one order of magnitude larger than the solute/solvent part. This observation is attributed to the enlarged heat capacity of the water molecules in the hydration shell. A detailed spatial analysis of the heat capacity of the water molecules around a pair of xenon particles at different separations reveals that even more enhanced heat capacity of the water located in the bisector plane between two adjacent xenon atoms is responsible for the maximum of the heat capacity found for the desolvation barrier distance, recently reported by Shimizu and Chan [J. Am. Chem. Soc. 123, 2083 (2001)]. The about 60% enlarged heat capacity of water in the concave part of the joint xenon-xenon hydration shell is the result of a counterplay of strengthened hydrogen bonds and an enhanced breaking of hydrogen bonds with increasing temperature. Differences between the two models with respect to the heat capacity in the xenon-xenon contact state are attributed to the different water model bulk heat capacities, and to the different spatial extension of the structure effect introduced by the hydrophobic particles. Similarities between the different states of water in the joint xenon-xenon hydration shell and the properties of stretched water are discussed.     

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model

A physics-based model is proposed to derive approximate analytical expressions for the cavity component of the free energy of hydrophobic association of spherical and spheroidal solutes in water. The model is based on the difference between the number and context of the water molecules in the hydration sphere of a hydrophobic dimer and of two isolated hydrophobic solutes. It is assumed that the water molecules touching the convex part of the molecular surface of the dimer and those in the hydration spheres of the monomers contribute equally to the free energy of solvation, and those touching the saddle part of the molecular surface of the dimer result in a more pronounced increase in free energy because of their more restricted mobility (entropy loss) and fewer favorable electrostatic interactions with other water molecules. The density of water in the hydration sphere around a single solute particle is approximated by the derivative of a Gaussian centered on the solute molecule with respect to its standard deviation. On the basis of this approximation, the number of water molecules in different parts of the hydration sphere of the dimer is expressed in terms of the first and the second mixed derivatives of the two Gaussians centered on the first and second solute molecules, respectively, with respect to the standard deviations of these Gaussians, and plausible analytical expressions for the cavity component of the hydrophobic-association energy of spherical and spheroidal solutes are introduced. As opposed to earlier hydration-shell models, our expressions reproduce the desolvation maxima in the potentials of mean force of pairs of nonpolar solutes in water, and their advantage over the models based on molecular-surface area is that they have continuous gradients in the coordinates of solute centers.     

Molecular origin of anticooperativity in hydrophobic association

The structuring of water molecules in the vicinity of nonpolar solutes is responsible for hydrophobic hydration and association thermodynamics in aqueous solutions. Here, we studied the potential of mean force (PMF) for the formation of a dimer and trimers of methane molecules in three specific configurations in explicit water to explain multibody effects in hydrophobic association on a molecular level. We analyzed the packing and orientation of water molecules in the vicinity of the solute to explain the effect of ordering of the water around nonpolar solutes on many-body interactions. Consistent with previous theoretical studies, we observed cooperativity, manifested as a reduction of the height of the desolvation barrier for the trimer in an isosceles triangle geometry, but for linear trimers, we observed only anticooperativity. A simple mechanistic picture of hydrophobic association is drawn. The free energy of hydrophobic association depends primarily on the difference in the number of water molecules in the first solvation shell of a cluster and that in the monomers of a cluster; this can be approximated by the molecular surface area. However, there are unfavorable electrostatic interactions between the water molecules from different parts of the solvation shell of a trimer because of their increased orientation induced by the nonpolar solute. These electrostatic interactions make an anticooperative contribution to the PMF, which is clearly manifested for the linear trimer where the multibody contribution due to changes in the molecular surface area is equal to zero. The information theory model of hydrophobic interactions of Hummer et al. also explains the anticooperativity of hydrophobic association of the linear trimers; however, it predicts anticooperativity with a qualitatively identical distance dependence for nonlinear trimers, which disagrees with the results of simulations.     

Temperature and length scale dependence of tetraalkylammonium ion-amide interaction

We have studied the temperature and length scale dependence of the energetics of the pair interaction of well-established hydrophobic solutes tetraalkylammonium bromides with hydrophilic formamide (FA) and hydrophobic hexamethylphosphoric triamide (HMPT). Our results do indicate the anomalous length scale dependence of the tetraalkylammonium cation-amide interaction in water. As the cation size is increased, the unfavorable enthalpy of interaction is increased rather linearly until the maximum is reached, after which there appears to be a reversal of the trend. We believe that this phenomenon arises from the impossibility of water to maintain its H-bond network near large tetraalkylammonium cations that leads to the formation of a somewhat disordered solute hydration shell. The energetic cost for overlapping this shell with the amide hydration shell in water is noticeably smaller than that for tetraalkylammonium cations of a moderated size.     

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.     

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.     

Global potential energy minima of C60(H2O)n clusters

Likely candidates for the global potential energy minima of C60(H2O)n clusters with n < or = 21 are found using basin-hopping global optimization. The potential energy surfaces are constructed using the TIP4P intermolecular potential for the water molecules, a Lennard-Jones water-fullerene potential, and a water-fullerene polarization potential, which depends on the first few nonvanishing C60 multipole polarizabilities. This combination produces a rather hydrophobic water-fullerene interaction. As a consequence, the water component of the lowest C60(H2O)n minima is quite closely related to low-lying minima of the corresponding TIP4P (H2O)n clusters. In most cases, the geometrical substructure of the water molecules in the C60(H2O)n global minimum coincides with that of the corresponding free water cluster. Exceptions occur when the interaction with C60 induces a change in geometry. This qualitative picture does not change significantly if we use the TIP3P model for the water-water interaction. Structures such as C60@(H2O)60, in which the water molecules surround the C60 fullerene, correspond to local minima with much higher potential energies. For such a structure to become the global minimum, the magnitude of the water-fullerene interaction must be increased to an unphysical value.     

Atomistic simulation of nafion membrane. 2. Dynamics of water molecules and hydronium ions

We have performed a detailed and comprehensive analysis of the dynamics of water molecules and hydronium ions in hydrated Nafion using classical molecular dynamics simulations with the DREIDING force field. In addition to calculating diffusion coefficients as a function of hydration level, we have also determined mean residence time of H(2)O molecules and H(3)O(+) ions in the first solvation shell of SO(3)(-) groups. The diffusion coefficient of H(2)O molecules increases with increasing hydration level and is in good agreement with experiment. The mean residence time of H(2)O molecules decreases with increasing membrane hydration from 1 ns at a low hydration level to 75 ps at the highest hydration level studied. These dynamical changes are related to the changes in membrane nanostructure reported in the first part of this work. Our results provide insights into slow proton dynamics observed in neutron scattering experiments and are consistent with the Gebel model of Nafion structure.     

Effects of simple model solutes on water dynamics: residence time analysis

The water residence time around pairs of simple hydrophilic and hydrophobic solutes, kept immobilized to model groups on slowly diffusing macromolecules, has been investigated along 400 ps molecular dynamics simulations. Results show that the water mobility around one solute strongly depends on the polarity characteristics of the other solute of the pair.     

Ions in water: the microscopic structure of concentrated hydroxide solutions

Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45 degrees from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.