Hydrophobic effects on partial molar volume

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.     

Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation

We explain the molecular mechanism of the effect of urea and glycerol cosolvents on the partial molar volume (PMV) change associated with the pressure denaturation of staphylococcal nuclease (SNase) protein recently observed in experiments. Native and denatured conformations of SNase are produced by using molecular dynamics simulations in water, and the PMV is obtained from the integral equation theory of molecular liquids called 3D-RISM, which is based on statistical mechanics. The PMV of the native SNase in water predicted by 3D-RISM theory is in good agreement with experiment. The PMV changes associated with pressure denaturation in water and in water-urea and water-glycerol mixtures are qualitatively reproduced. By analyzing the results obtained, we found two interesting cosolvent effects on the PMV: (1) both urea and glycerol cosolvents increase the PMVs of both native and denatured SNase compared to those in water and (2) both urea and glycerol cosolvents increase the PMV of denatured SNase more than that of native SNase. We also showed that these two observations can be explained in terms of the thermal volume, which is related to the packing effect of solvent molecules.     

Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations

The free energy profiles, ΔG(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6-12 kJ mol(-1) more stable in the SDS micelle than in the water phase, and no ΔG(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to ΔG(r), it is clear that methane in the SDS micelle is about 25 kJ mol(-1) more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5-15 kJ mol(-1) by the contribution from the hydrophobic groups of the SDS micelle because of the repulsive interactions between the methane and the crowded hydrophobic groups of the SDS. The large stabilizing effect of the solvent water is higher than the repulsion by the hydrophobic groups, driving methane to become solubilized into the SDS micelle. A good correlation was found between the distribution of cavities and the distribution of methane molecules in the micelle. The methane may move about in the SDS micelle by diffusing between cavities. In contrast, with respect to the water, ΔG(r) has a large positive value of 24-35 kJ mol(-1), so water is not stabilized in the micelle. Analysis showed that the contributions change in complex ways as a function of r and cancel each other out. Reference calculations of the mean forces on a penetrating water molecule into a dodecane droplet clearly showed the same free energy behavior. The common feature is that water is less stable in the hydrophobic core than in the water phase because of the energetic disadvantage of breaking hydrogen bonds formed in the water phase. The difference between the behaviors of the SDS micelles and the dodecane droplets is found just at the interface; this is caused by the strong surface dipole moment formed by sulfate ions and sodium ions in the SDS micelles.     

The solvent shells of cluster ions produced by direct electric field extraction from glycerol/water mixtures

Electric field extraction of gaseous negative ions directly from water/glycerol solutions by use of a track membrane technique was investigated. The distributions of numbers of solvent molecules in the extracted cluster ions for different compounds were obtained. It is shown that the extraction mechanism is a direct field-stimulated evaporation of cluster ions from liquid, with a subsequent loss of several solvent molecules in the vacuum. For relatively simple ions a good correspondence of results was obtained with a continuous medium model. It was found that the number of solvent molecules in a cluster shell, for more complicated ions such as amino acids, is significantly greater than that for halide ions or ions of simple organic acids. An increase in the number of solvent molecules in the case of amino acid negative ions is rationalized in terms of the existence of several charged groups, each of which gives an additional contribution to the cluster shell.     

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane

Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute–solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN /2 potential for methane–water interactions) and 124 water molecules (using the MCY potential for water–water interactions). Again, the convergence of solute–solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN /2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.     

Hydrophobic and ionic interactions in nanosized water droplets

A number of situations such as protein folding in confined spaces, lubrication in tight spaces, and chemical reactions in confined spaces require an understanding of water-mediated interactions. As an illustration of the profound effects of confinement on hydrophobic and ionic interactions, we investigate the solvation of methane and methane decorated with charges in spherically confined water droplets. Free energy profiles for a single methane molecule in droplets, ranging in diameter (D) from 1 to 4 nm, show that the droplet surfaces are strongly favorable as compared to the interior. From the temperature dependence of the free energy in D = 3 nm, we show that this effect is entropically driven. The potentials of mean force (PMFs) between two methane molecules show that the solvent separated minimum in the bulk is completely absent in confined water, independent of the droplet size since the solute particles are primarily associated with the droplet surface. The tendency of methanes with charges (M(q+) and M(q-) with q(+) = |q(-)| = 0.4e, where e is the electronic charge) to be pinned at the surface depends dramatically on the size of the water droplet. When D = 4 nm, the ions prefer the interior whereas for D < 4 nm the ions are localized at the surface, but with much less tendency than for methanes. Increasing the ion charge to e makes the surface strongly unfavorable. Reflecting the charge asymmetry of the water molecule, negative ions have a stronger preference for the surface compared to positive ions of the same charge magnitude. With increasing droplet size, the PMFs between M(q+) and M(q-) show decreasing influence of the boundary owing to the reduced tendency for surface solvation. We also show that as the solute charge density decreases the surface becomes less unfavorable. The implications of our results for the folding of proteins in confined spaces are outlined.     

Confusing cause and effect: energy-entropy compensation in the preferential solvation of a nonpolar solute in dimethyl sulfoxide/water mixtures

We performed molecular simulations to analyze the thermodynamics of methane solvation in dimethyl sulfoxide (DMSO)/water mixtures (298 K, 1 atm). Two contributions to the interaction thermodynamics are studied separately: (i) the introduction of solute-solvent interactions (primary contribution) and (ii) the solute-induced disruption of cohesive solvent-solvent interactions (secondary contribution). The energy and entropy changes of the secondary contribution always exactly cancel in the free energy (energy-entropy compensation), hence only the primary contribution is important for understanding changes of the free energy. We analyze the physical significance of the solute-solvent energy and solute-solvent entropy associated with the primary contribution and discuss how to obtain these quantities from experiments combining solvation thermodynamic and solvent equation of state data. We show that the secondary contribution dominates changes in the methane solvation entropy and enthalpy: below 30 mol % DMSO in the mixture, methane, because of more favorable dispersion interactions with DMSO molecules, preferentially attracts DMSO molecules, which, in response, release water molecules into the bulk, causing an increase in the entropy. This large energy-entropy compensating process easily causes a confusion in the cause for and the effect of preferred methane-DMSO interactions. Methane-DMSO dispersion interactions are the cause, and the entropy change is the effect. Procedures that infer thermodynamic driving forces from analyses of the solvation entropies and enthalpies should therefore be used with caution.     

Stepwise and concerted electron-transfer/bond breaking reactions. solvent control of the existence of unstable pi ion radicals and of the activation barriers of their heterolytic cleavage

Available data from various sources seem to indicate an important role of solvation in the cleavage rates of intermediate pi ion radicals, in the passage from concerted to stepwise electron-transfer/bond breaking reaction pathways and even in the very existence of pi ion radicals. After preliminary computations treating the solvent as dielectric continuum, these expectations are examined with the help of a simple model system involving the anion radical of ONCH(2)Cl and two molecules of water, which allows the application of advanced computational techniques and a treatment of these solvent effects that emphasizes the role of solvent molecules that sit close to the charge centers of the molecule. A pi ion radical minimum indeed appears upon introduction of the two water molecules, and cleavage is accompanied by their displacement toward the leaving anion, thus offering a qualitative mimicry of the experimental observations.     

Pressure Effect on Conformational Equilibria of Analog Peptides in Aqueous Solution by Raman Spectroscopy

We investigated the pressure effect on the conformational equilibria of glycinamide (GA) and 2-chloroacetamide (MCA) in aqueous solution by Raman spectroscopy. Scattering intensities in the CH₂ scissoring mode of GA and the NH₂ rocking mode of MCA in aqueous solution were decomposed into two component bands by ab initio MO calculations at the HF/6-31G(d,p) level. From the pressure dependence of the Raman band intensities, we determined the difference in the partial molar volume (PMV) between the cis and trans conformers of each for GA and MCA. The volume changes for the isomerization of the cis to trans conformer are ?(1.9 ± 0.3) and ?(1.5 ± 0.3) cm³-mol^?1 for GA and MCA, respectively. The volume difference between the cis and trans conformers is due to the hydration effect, which seems to be mainly the result of local effects of solute–solvent interactions in both cases. This contribution is due to the influence of the solute–solvent interaction with water molecules on the PMV of the cis conformer being less than that of the trans conformer.     

A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints

If the rotational motion of a single macromolecule is constrained during a molecular dynamics simulation with periodic boundary conditions it is possible to perform such simulations in a computational box with a minimal amount of solvent. In this article we describe a method to construct such a box, and test the approach on a number of macromolecules, randomly chosen from the protein databank. The essence of the method is that the molecule is first dilated with a layer of at least half the cut-off radius. For the enlarged molecule a near-densest lattice packing is calculated. From this packing the simulation box is derived. On average, the volume of the resulting box proves to be about 50% of the volume of standard boxes. In test simulations this yields on average a factor of about two in simulation speed.     

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald (PME) method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects.     

Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations

We consider model systems consisting of a methane molecule and hemispherical pockets of subnanometer radii whose walls are made of hydrophobic material. The potential of mean force for process of translocation of the methane molecule from bulk water into the pockets' interior is obtained, based on an explicit solvent molecular dynamics simulations. Accompanying changes in water density around the interacting objects and spatial distribution of solvent's potential energy are analyzed, allowing for interpretation of details of hydrophobic interactions in relation to hydrophobic hydration properties. Applicability of surface area-based models of hydrophobic effect for systems of interest is also investigated. A total work for the translocation process is not dependent on pocket's size, indicating that pocket desolvation has little contribution to free energy changes, which is consistent with the observation that solvent density is significantly reduced inside "unperturbed" pockets. Substantial solvent effects are shown to have a longer range than in case of a well investigated methane pair. A desolvation barrier is present in a smaller pocket system but disappears in the larger one, suggesting that a form of a "hydrophobic collapse" is observed.     

IR and Raman spectra of a water-methane disperse system. Computer experiment

Methane adsorption by water clusters is studied using a flexible molecule model. An increase in the number of methane molecules surrounding a water cluster leads to their structurization in its vicinity. The pattern of the frequency spectrum of complex permittivity strongly changes after methane molecules are captured by the disperse water system. The integral intensity of IR absorption grows with methane adsorption, whereas the Raman spectrum of the system is considerably depleted. Methane absorption markedly enhances the reflectivity and IR emission ability of the disperse system.     

Energy contribution of the solvent to the charge migration in DNA

The authors have investigated the interactions of the reaction centers, participating in the charge transfer reaction within the DNA molecule with the phosphate backbones and the solvent molecules, and have estimated the contribution of these interactions into the charge migration in DNA. They have determined the unequal shift of the energy surfaces of the initial and final transition states of the transfer reaction along the energy axis and the dependence of the magnitude of the energy shift on the nature of the reaction centers and the surrounding environment. The nonuniform distribution of the negative charge in the DNA phosphate backbones results in an increase of the positive shift of the energy surface of the DNA base pairs in the center of the structure, where the maximum density of the negative charge is concentrated. Localization of the positive charge on the guanine and the adenine in the DNA base pairs in the oxidized state results in a dependence of the free energy of reaction in the solvent on the pair sequences and their arrangement in the DNA chain. As an example, for the G-C/A-T configuration the positive charges are localized on the same strand that results in a decrease of the free energy of reaction in the solvent for charge migration from G-C to A-T pair by 0.125 eV.     

Negative Hydration of Ions

The negative hydration, that is the increase in the mobility of water molecules near sufficiently large single-charged ions, is studied by modeling, cold-neutron scattering, and computer modeling. Special attention is paid to the mechanism of negative hydration and the boundary of transition from positive to negative and from negative to hydrophobic hydration. Hypothetical ions with radii of approximately 1.1 and 3.3 Å correspond to these boundaries. Dynamic characteristics of hydration water in these ions are identical to those of water molecules in bulk water.     

Water coordination structures and the excess free energy of the liquid

We assess the contribution of each coordination state to the hydration free energy of a distinguished water molecule, the solute water. We define a coordination sphere, the inner-shell, and separate the hydration free energy into packing, outer-shell, and local, solute-specific (chemical) contributions. The coordination state is defined by the number of solvent water molecules within the coordination sphere. The packing term accounts for the free energy of creating a solute-free coordination sphere in the liquid. The outer-shell contribution accounts for the interaction of the solute with the fluid outside the coordination sphere and it is accurately described by a Gaussian model of hydration for coordination radii greater than the minimum of the oxygen-oxygen pair-correlation function: theory helps identify the length scale to parse chemical contributions from bulk, nonspecific contributions. The chemical contribution is recast as a sum over coordination states. The nth term in this sum is given by the probability p(n) of observing n water molecules inside the coordination sphere in the absence of the solute water times a factor accounting for the free energy, W(n), of forming an n-water cluster around the solute. The p(n) factors thus reflect the intrinsic properties of the solvent while W(n) accounts for the interaction between the solute and inner-shell solvent ligands. We monitor the chemical contribution to the hydration free energy by progressively adding solvent ligands to the inner-shell and find that four-water molecules are needed to fully account for the chemical term. For a chemically meaningful coordination radius, we find that W(4) ≈ W(1) and thus the interaction contribution is principally accounted for by the free energy for forming a one-water cluster, and intrinsic occupancy factors alone account for over half of the chemical contribution. Our study emphasizes the need to acknowledge the intrinsic solvent properties in interpreting the hydration structure of any solute, with particular care in cases where the solute-solvent interaction strength is similar to that between the solvent molecules.     

溶剂极性控制下的煤抽余物吸附甲烷能力研究

基于原煤和有机溶剂抽余物的等温吸附实验结果,对比分析溶剂极性与其煤抽余物吸附甲烷能力变化关系,探讨抽提溶剂极性差异对煤抽余物吸附甲烷能力控制的地球化学机理。结果表明,煤溶剂抽余物等温吸附甲烷曲线都遵循Langmuir方程,且二硫化碳(CS₂)和苯(C₆H₆)溶剂抽提作用增大了煤吸附甲烷量,四氢呋喃(THF)和丙酮溶剂抽提作用减小了煤吸附甲烷量。实验发现,煤抽余物吸附甲烷能力变化与抽提溶剂极性成负相关关系,该现象可用相似相容原理解释:CS₂和C₆H₆溶剂极性较弱,抽提出较多具有非极性结构(-CH₃和-CH₂-)的烷烃和芳烃,为甲烷在煤表面吸附增多了吸附位而增强了抽余物吸附甲烷能力,THF和丙酮溶剂极性较强,抽提出较多具有极性结构(-CHO、-OH、和-COOH)的非烃和沥青质,减少了吸附位而降低煤抽余物的甲烷吸附能力。     

An empirical boundary potential for water droplet simulations

An empirical modified boundary potential has been derived to correct the structural perturbations arising from the presence of the vacuum boundary in the simulation of spherical TIP4P water systems. The potential is parameterized for a 12.0-Å sphere of TIP4P water and gives improved number density and orientational sampling behavior. It is also transferable to both larger and smaller simulation systems with only a moderate degradation in performance. Free-energy calculations have been conducted for the perturbation of a TIP4P water molecule to methane under aqueous conditions, and the modified boundary potential gives results consistent with those from simulations using periodic boundary conditions. However, simple half-harmonic boundary potentials give unsatisfactory number density, orientational sampling, and free-energy results. Moreover, use of the modified boundary potential results in a negligible increase in simulation time. It is envisaged that the modified boundary potential will find use in free-energy perturbation calculations on proteins with a solvent sphere centered on the active site. © 1995 by John Wiley & Sons, Inc.     

On the molecular origin of cold denaturation of globular proteins

A polypeptide chain can adopt very different conformations, a fundamental distinguishing feature of which is the water accessible surface area, WASA, that is a measure of the layer around the polypeptide chain where the center of water molecules cannot physically enter, generating a solvent-excluded volume effect. The large WASA decrease associated with the folding of a globular protein leads to a large decrease in the solvent-excluded volume, and so to a large increase in the configurational/translational freedom of water molecules. The latter is a quantity that depends upon temperature. Simple calculations over the -30 to 150 °C temperature range, where liquid water can exist at 1 atm, show that such a gain decreases significantly on lowering the temperature below 0 °C, paralleling the decrease in liquid water density. There will be a temperature where the destabilizing contribution of the polypeptide chain conformational entropy exactly matches the stabilizing contribution of the water configurational/translational entropy, leading to cold denaturation.