Molecular dynamics study on hydrophobic effects in aqueous urea solutions.

Hydrophobic effects in aqueous urea were analyzed by molecular dynamics simulations. The contribution of solvents to the potential of mean force between two methane molecules was calculated by using molecular dynamics simulations and was compared with the solubility data of hydrocarbons in aqueous urea. Both the simulation results and the solubility data indicated that urea stabilizes methane-methane association. The stabilization was due to increasing the solvation free energies of small hydrocarbons such as methane by addition of urea. The solvation free energies of larger hydrocarbons, on the other hand, are decreased by addition of urea. This effect of the solute size on hydrophobic free energies in aqueous urea was also analyzed by using molecular dynamics simulations by means of division of the solvation process into two parts: the cavity formation and the introduction of the solute-solvent attractive interactions. In the cavity formation, urea increased hydrophobic free energies, and in the introduction of the solute-solvent attractive interactions, urea decreased hydrophobic free energies. The influence of urea on hydrophobic free energies was determined by the balance of effects of the two parts of the solvation process.     

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.     

Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach

Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.     

Strong solute-solute dispersive interactions in a protein-ligand complex

The contributions of solute-solute dispersion interactions to binding thermodynamics have generally been thought to be small, due to the surmised equality between solute-solvent dispersion interactions prior to the interaction versus solute-solute dispersion interactions following the interaction. The thermodynamics of binding of primary alcohols to the major urinary protein (MUP-I) indicate that this general assumption is not justified. The enthalpy of binding becomes more favorable with increasing chain length, whereas the entropy of binding becomes less favorable, both parameters showing a linear dependence. Despite the hydrophobicity of the interacting species, these data show that binding is not dominated by the classical hydrophobic effect, but can be attributed to favorable ligand-protein dispersion interactions.     

Benchmarking the thermodynamic analysis of water molecules around a model beta sheet

Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P‐2005 and TIP5P‐Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the water–water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application. © 2012 Wiley Periodicals, Inc.     

New approach to free energy of solvation applying continuum models to molecular dynamics simulation

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.     

Excess enthalpies of solution of some primary and secondary alcohols in sodium dodecylsulfate micellar solutions

The exces enthalpies of solution of some primary and secondary alcohols in aqueous sodium dodecylsulfate micellar solutions were measured and the results were explained by considering the distribution of alcohols between aqueous and micellar phases. The distribution constant and the enthalpy of transfer (and the standard free energy and entropy of transfer) were obtained. The thermodynamic parameters for the transfer of secondary alcohols from the aqueous to the sodium dodecylsulfate (NaDS) micellar phase differ slightly from those of the corresponding primary alcohols. For both series of alcohols the additivity rule holds for free energies of transfer whereas enthalpies and entropies display convex curves. The present data are compared to those for the transfer of the same solutes from the aqueous to the dodecyldimethylamine oxide (DDAO) and dodecyltrimethylammonium bromide (DTAB) micellar phases. The role of the hydrophilic interactions between the OH group and the micelles' head groups is formulated. The thermodynamics of the branched methyl group were determined. Furthermore, the thermodynamics of solvation of primary alcohols in water, in NaDS micelles, and in octane have been calculated using reference states based on the assumption that the empty space around alcohols in the initial and final states is the same. It is shown that the solvation of alcohols in NaDS micellar phase is enthalpy driven and that the thermodynamic properties of solvation vs. the length of the alcohol tail is the same for water and NaDS micelles whereas it is different for octane. A possible explanation for this difference is that the alkyl chain of alcohols folds in octane.     

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.     

Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: an analysis by solvent exchange model

Folded protein stabilization or destabilization induced by cosolvent in mixed aqueous solutions has been studied by differential scanning microcalorimetry and related to difference in preferential solvation of native and denatured states. In particular, the thermal denaturation of a model system formed by lysozyme dissolved in water in the presence of the stabilizing cosolvent glycerol has been considered. Transition temperatures and enthalpies, heat capacity, and standard free energy changes have been determined when applying a two-state denaturation model to microcalorimetric data. Thermodynamic parameters show an unexpected, not linear, trend as a function of solvent composition; in particular, the lysozyme thermodynamic stability shows a maximum centered at water molar fraction of about 0.6. Using a thermodynamic hydration model based on the exchange equilibrium between glycerol and water molecules from the protein solvation layer to the bulk, the contribution of protein-solvent interactions to the unfolding free energy and the changes of this contribution with solvent composition have been derived. The preferential solvation data indicate that lysozyme unfolding involves an increase in the solvation surface, with a small reduction of the protein-preferential hydration. Moreover, the derived changes in the excess solvation numbers at denaturation show that only few solvent molecules are responsible for the variation of lysozyme stability in relation to the solvent composition.     

Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents

The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale (E(T)) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.     

Solvation of hydrophobes in water and simple liquids

The solvation of nonpolar molecules in water and that in simple liquids are compared and contrasted. First, solvation thermodynamics is reviewed in a way that focuses on how the enthalpy and entropy of solvation depend on the choice of microscopic volume change v in the solvation process--including special choices v being zero (fixed-volume condition) and v being the partial molecular volume of a solute molecule (fixed-pressure condition)--and how the solvation quantities are related with temperature derivatives of the solvation free energy. Second, the solvation free energy and the solvation enthalpy of a Lennard-Jones (LJ) atom in model water are calculated in the parameter space representing the solute size and the strength of the solute-solvent interaction, and the results are compared with those for an LJ atom in the LJ solvent. The solvation diagrams showing domains of different types of solvation in the parameter space are obtained both for the constant-volume condition and for the constant-pressure condition. Similarities between water and the simple liquid are found when the constant-volume solvation is considered while a significant difference manifests itself in the fixed-pressure solvation. The domain of solvation of hydrophobic character in the parameter space is large in the constant-volume solvation both for water and for the simple liquid. When switched to the constant-pressure condition accompanying a microscopic volume change, the hydrophobic domain remains large in water but it becomes significantly small in the simple liquid. The contrasting results are due to the smallness of the thermal pressure coefficient of water at low temperatures.     

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.     

温度对二甲基亚砜水溶液的结构和热力学性质的影响

应用参考作用格位模型理论计算了二甲基亚砜(DMSO)摩尔分数为0.002时不同温度下溶液的微观结构和热力学性质. 计算结果表明, DMSO加入到水中能够增强溶液的分子网络结构. 温度升高, 配位数减小, 溶液中分子排布趋向无序. 平均力势的波动增大表明分子间的诱导力表现为斥力. 计算得到的各种热力学性质显示: 温度升高, 溶液的熵和溶剂化自由能增加, 相互作用能和过剩化学位也增加, 即高温下溶液越来越偏离理想溶液; 空位形成能降低表明溶液分子结构在高温下更容易重组.     

Compensation Between the Entropic and Enthalpic Changes Arising from Changes in Solvent–Solvent Interactions in Mixed Solvents

A theorem presented by Professor Ben-Naim (J Phys Chem 82:874–885, 1978) states that the standard state enthalpy and entropy changes arising from changes in the solvent structure that are induced by solvation of a solute cancel exactly in the standard state Gibbs energy. In this paper this is explored by consideration of the thermodynamics of transfer of electrolytes in mixed solvents, using previously developed models of the solvation process. Two cases are considered. One is random solvation, where curvatures in plots of the transfer enthalpies and entropies, which arise from changes in solvent–solvent interactions, exactly compensate in the transfer Gibbs (free) energies, which are sensibly linear with solvent composition. The second type of system are those with strong preferential solvation where it is found that the transfer Gibbs energies can be accounted for quantitatively in terms of changes in the solute–solvent interactions, with no contribution from changes in solvent–solvent interactions. The results are entirely consistent with the Ben-Naim theorem.     

Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation

We present a simple computational method for the evaluation of solute-solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.     

Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy

Carboxylic acid dimers are useful model systems for understanding the interplay of hydrogen bonding, hydrophobic effects, and entropy in self-association and assembly. Through extensive sampling with a classical force field and careful free energy analysis, it is demonstrated that both hydrogen bonding and hydrophobic interactions are indeed important for dimerization of carboxylic acids (except formic acid). The dimers are only weakly ordered, and the degree of ordering increases with stronger hydrophobic interactions between longer alkyl chains. Comparison of calculated and experimental dimerization constants reveals a systematic tendency for excessive self-aggregation in current classical force fields. Qualitative and quantitative information on the thermodynamics of hydrogen bonding and hydrophobic interactions derived from these simulations is in excellent agreement with existing results from experiment and theory. These results provide a verification from first principles of previous estimations based on two statistical mechanical hydrophobic theories. We also revisit and clarify the fundamental statistical thermodynamics formalism for calculating absolute binding constants, external entropy, and solvation entropy changes upon association from detailed free energy simulations. This analysis is believed to be useful for a wide range of applications including computational studies of protein-ligand and protein-protein binding.     

Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes

Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.