Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described.

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We investigate local phase transitions of the solvent in the neighborhood of a solvophobic polymer chain which is induced by a change of the polymer-solvent repulsion and the solvent pressure in the bulk solution. We describe the polymer in solution by the Edwards model, where the conditional partition function of the polymer chain at a fixed radius of gyration is described by a mean-field theory. The contributions of the polymer-solvent and the solvent-solvent interactions to the total free energy are described within the mean-field approximation. We obtain the total free energy of the solution as a function of the radius of gyration and the average solvent number density within the gyration volume. The resulting system of coupled equations is solved varying the polymer-solvent repulsion strength at high solvent pressure in the bulk. We show that the coil-globule (globule-coil) transition occurs accompanied by a local solvent evaporation (condensation) within the gyration volume.

We report results of molecular dynamics simulations and detailed analysis of the local structure of sub- and supercritical ammonia in the range of temperature between 250 and 500 K along the 135 bar isobar. This analysis is based on the behavior of distributions of metric and topological properties of the Voronoi polyhedra (VP). We show that by increasing the temperature, the volume, surface, and face area distributions of the Voronoi polyhedra as well as the vacancy radius distribution broaden, particularly near the temperature T(α), where the calculated thermal expansion coefficient has its maximum. Furthermore, the rate of increase of the corresponding mean values and fluctuations increases drastically when approaching T(α). This behavior clearly indicates that the local structure, as described by the VP, becomes increasingly heterogeneous upon approaching this temperature. This heterogeneous distribution of ammonia molecules is traced back to the increase of the large voids with increasing temperature, and is also clearly seen in the behavior of the fluctuation of the local density, as measured by the VP. More interestingly, the maximum in the heterogeneity coincides with the maximum of the fluctuation in the density of the VP.

Binary mixtures of CO(2) with ethanol and with acetone are studied by computer simulation, including extensive free energy calculations done by the method of thermodynamic integration, at 313 K, i.e., above the critical point of CO(2) in the entire composition range. The calculations are repeated with three different models of acetone and ethanol, and two models of CO(2). Comparisons of the molar volume of the different systems as well as of the change of their molar volume accompanying the mixing of the two components with experimental data reveal that, among the model pairs tested, the best results are obtained if both components are described by the Transferable Potentials for Phase Equilibria (TraPPE) force field. Around the ethanol/acetone mole fraction of 0.05 all ethanol/CO(2) and almost all acetone/CO(2) model pairs considered predict the existence of a sharp maximum of the molar volume. Due to the lack of experimental data in this composition range, however, these predictions cannot be verified/falsified yet. Most of the model pairs considered also predict limited miscibility of these compounds, as seen from the positive values of the free energy change accompanying their mixing, and the miscibility gap is located at the same composition range as the aforementioned molar volume maximum.

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The nearest neighbor approach was used to characterize the local structure of CO(2) fluid along its coexistence curve (CC) and along the critical isochore (CI). The distributions of the distances, orientations, and interaction energies between a reference CO(2) molecule and its subsequent nearest neighbors were calculated. Our results show that the local structure may be resolved into two components or subshells: one is characterized by small radial fluctuations, the parallel orientation and a dominance of the attractive part of both the electrostatic (EL) and Lennard-Jones (LJ) to the total interaction energy. Conversely, the second subshell is characterized by large radial fluctuations, a perpendicular orientation, and a concomitant increase of the repulsive contribution of the EL interaction and a shift to less attractive character of the LJ contribution. When the temperature increases along the liquid-gas CC, the first subshell undergoes large changes which are characterized by an obvious increase of the radial fluctuations, by an increase of the random character of the orientation distribution except for the first nearest neighbor which maintains its parallel orientation, and by a drastic decrease of the EL interaction contribution to the total interaction energy. When the temperature is close to the critical isochore, the local structure is no longer resolved into two subshells. Starting from the idea that the profile of vibration modes is sensitive to the local structure as revealed from the nearest neighbor approach, the hypothesis that the CO(2) vibration profile may be deconvoluted into two contributions is discussed in a qualitative manner.

Combining infrared spectroscopy and molecular dynamics simulations, we have investigated the structural and dynamical properties of ammonia from liquid state (T = 220 and 303 K) up to the supercritical domain along the isotherm T = 423 K. Infrared spectra show that the N-H stretching and bending modes are significantly perturbed which is interpreted as a signature of the change of the local environment. In order to compare the experimental spectra with those obtained using molecular dynamics simulation, we have used a flexible four sites model which allows to take into account the anharmonicity in all the vibration modes particularly that of the inversion mode of the molecule. A good agreement between our experimental and calculated spectra has been obtained hence validating the intermolecular potential used in this study to simulate supercritical ammonia. The detailed analysis of the molecular dynamics simulation results provides a quantitative insight of the relative importance of hydrogen bonding versus nonhydrogen bonded interactions that governs the structure of fluid ammonia.