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Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

We report herein on the use of all-atom molecular dynamics simulations to investigate the solvation environment of C60 and four C60-derived fullerenes immersed in a variety of aromatic solvents. Utilizing a recently developed solvation shell analysis technique that quantifies the spatial relationships between fullerenes and solvent on a molecular level, we show that the number of fullerene substituents and solvent chemistry are crucial determinants of the solvation shell structure and thus fullerene solvation behavior. Specifically, it is shown for the derivatives investigated that the number of fullerene substituents is more critical to solvation behavior than the substituent chemistry.

The formation of hemicucurbit[6]uril (hCB[6]) from ethyleneurea with formaldehyde in acidic aqueous solution was explored using density functional methods and the implicit solvation model in water. The oligomerization and cyclization barriers were approximately half lower than that of the iminium formation. Thus, the initial iminium formation is the rate-determining step, and the formation of hCB[6] is kinetically and thermodynamically favored in acidic aqueous solution. In particular, the ‘alternate’ conformation of hCB[6] is enthalpically and entropically preferred over the ‘cone’ conformation, which is consistent with the crystal structure of hCB[6].

Relativistic density functional theory was used to explore the structural and redox properties of 18 prototypical actinyl silylamides including a variation of metals (U, Np and Pu), metal oxidation states (VI and V) and equatorial ligands. A theoretical approach associated with implicit solvation and spin–orbit/multiplet corrections was proved to be reliable. A marked shift of reduction potentials of actinyl silylamides caused by changes of equatorial coordination ligands and implicit solvation was elucidated by analyses of electronic structures and single-electron reduction mechanism.

The present letter reports results from a comprehensive theoretical analysis of the inclusion process involving 2,4-dichlorophenoxyacetic acid (2,4-D) and β-cyclodextrin (β-CD) for which the experimental data of formation is available. Spatial arrangement and stabilization energies were evaluated in gas phase and aqueous solution through density functional theory (DFT) and through the use of SMD implicit solvation approach. The discussed methodology was applied to predict the stability and identify the most favorable form (deprotonated or neutral) as well as the most probable spatial arrangement of the studied inclusion compound.

State-specific solvation for constructing excited-state free energy surfaces in solution is discussed within the framework of reference interaction site model/time-dependent density functional theory. The self-consistency between the solute electron density and solvation structure is achieved using the linear-response free energy approach. The proposed method is applied to the intramolecular charge-transfer (ICT) state formation of 4-(N-pyrrolo)benzonitrile. The linear-response solvation method underestimates the ICT state severely, and the calculation predicts erroneously that the reaction is endergonic. Therefore, it is essential to apply the state-specific method when the transition density fails in describing the solute–solvent interaction upon excitation.

We describe and present results of the implementation of the surface and volume polarization for electrostatics (SVPE) solvation model. Unlike most other implementations of the solvation model where the solute and the solvent are described with multiple numerical representations, our implementation uses a multiresolution, adaptive multiwavelet basis to describe both the solute and the solvent. This requires reformulation to use integral equations throughout as well as a conscious management of numerical properties of the basis.

Discretization of the integral equations that define widely-used ‘polarizable continuum’ solvation models fails to preserve certain properties of the integral operators. Consequently, the appropriate form of the finite-dimensional matrix equations is ambiguous, with two different asymmetric versions and also a symmetrized version as obvious possibilities. We demonstrate cases where solvation energies differ by as much as 24 kcal/mol amongst these variants. These differences are sometimes exacerbated by new discretization procedures that guarantee smooth potential energy surfaces. Formal and numerical arguments favor one particular formulation of the matrix equations.

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

The solvation properties of a solute in a molecular solvent can be obtained by minimization of a position and orientation-dependent free-energy density functional, with the unknown excess term approximated by the angular-dependent direct correlation function of the pure solvent. We show how this function can be extracted from MD simulations of the pure solvent by computing the pair distribution function and solving subsequently the Molecular Ornstein–Zernike equation using angular grids. The corresponding functional can be minimized in the presence of an arbitrary solute on a three-dimensional cubic grid for positions and Gauss–Legendre angular grid for orientations to provide the solvation structure and free-energy. Applications are presented for solvation in acetonitrile.

One of the problems in modelling solute–solvent interactions is the difficulty of incorporating the consideration of solute–solvent hydrogen bonding into continuum-type models. The Letter proposes an option utilizing geometry–character considerations to modify the cavity representing the solute, when solute–solvent hydrogen bonding is possible. The computed geometrical characteristics of adducts with explicit water molecules H-bonded to donor–acceptor sites of selected solute molecules suggest the possibility of utilizing these characteristics to design modifications of the solute-cavity contour in correspondence to H-bond donor–acceptor sites, so as to enable the inclusion of at least part of the hydrogen-bonding effects into the overall continuum-type description.

To describe solvation effects in coarse-grained molecular dynamics simulations, a numerically efficient coarse-grained water model is introduced. The solvent is represented by polarizable pseudo-particles embedding three water molecules. The particles carry induced dipoles that are made sensitive to the solute electric field, but not to each other. The solvent model is compatible with a coarse-grained proteins force field involving a reduced number of grains per residue and yields quantitative description of solvation properties, such as hydrophobic forces and electrostatic solvation free-energies. Those later quantities can be estimated ‘on-the-fly’ over short simulation windows.

The pKa for H2CO3 have been calculated using the combination of the extended clusters-continuum model (ECM) with the polarizable continuum solvation model (PCM) and a comparison has been carried on with the pKa prediction of HCOOH. Our results show that the calculated and experimental pKa of HCOOH are in good agreement as two water molecules are added, the best agreement of pKa1 for H2CO3 is for n = 3 (the number of water molecules) and the closest agreement of pKa2 is for n = 4 at B3LYP/6-311++G(d, p) level. On the base of the results, attempts have been made to evaluate the hydration numbers.

The accurate p K a determinations for some organic acids have been investigated using the combination of the clusters-continuum model with the polarizable continuum solvation model (PCM) The formation of molecular clusters by means of the organic acids wrapped up with water molecules leads to the weakness of the mutual function between the polar solvents and the organic acids, and, hence, the accuracy of p K a has been enhanced by using a coherent and well-defined approach without external approximations or experimental data. The calculations are performed at the HF/6-311++G(d, p) level and agreed well with experimental data.

A linearized RISM technique is developed to treat free energies of hydrated ions. The solvent response on the solute is calculated with the introduction of an empirical repulsive bridge function. The solvent electrostatic potential is approximated by a linear dependence on the solute charge. The approximating coefficients are derived by fitting the electrostatic energy of solvent, that is in turns computed by the charging procedure. For a series of monovalent polyatomic cations and anions the method provides free energies deviating by few percent from the experimental data.

Despite the great attention on the factors affecting the radical addition efficiency onto a double bond, the solvent influence remains largely unknown and the subject of discussions. In this Letter, the influence of the solvent is examined both experimentally (by use of a well adapted radical) and by quantum mechanical calculations associated with continuum solvation models. The combination of experimental measurements and theoretical results in this work shows that the solvent polarity represents indeed an important factor affecting the addition reaction. The validity of conclusions obtained by previous calculations carried out in gas phase is also reexamined.

The validity of the linear response theory in solvation dynamics has been investigated by molecular dynamics simulations for a monoatomic solute dissolved in liquid argon. The solvation dynamics for various modifications in the well-depth and size parameters of the solute–solvent interaction potential were described by the response function and the time correlation functions for the mechanical solvation energy in a high density liquid system. The comparison between the two methodologies clearly indicates differences for solvation models involving changes in the solute’s size parameter.

A theoretical study of ion solvation in a polar supercritical solvent is reported. The solute–solvent microstructure is computed from the nonlocal integral equation theory and is shown to be in good agreement with simulation results. The nonlinear behavior of the solvation free energy of the ion in a highly compressible supercritical regime is rationalized in terms of a strong electrostriction effect. It is shown that the accuracy of the Born expression for the solvation energy can be substantially improved by taking into account the local solvent density augmentation around the ionic solute.

The present Letter describes a systematic analysis of the solvent effect on the hydrolysis process of an important cisplatin analogue ( cis -DEP). Self-consistent reaction field continuum models were used to include the solvent effect at the HF, DFT and MP2 levels of theory. A disagreement between the gas phase calculated ( k 2 =1.92×10 −11 M −1 s −1 ) and experimental ( k 2 =4.4×10 −5 M −1 s −1 ) rate constant for the second aquation reaction of cis -DEP was recently reported by us. The value calculated in aqueous solution at the PCM–MP2 level was 2.87 × 10 −5 M −1 s −1 in perfect accordance with experiment. Calculations using spherical cavity SCRF model require inclusion of high order multipole terms (up to octupole).

Solvation dynamics of 4-aminophthalimide (4-AP) in dioxane-water mixtures display a slow component of 350-500 ps. This is attributed to transient dioxane-water clusters and rupture of water-dioxane hydrogen bond. A detailed analysis indicates that there is no preferential solvation of 4-AP in dioxane-water mixture. The solvent shift of the emission maximum of 4-AP in a solution is shown to be controlled by hydrogen bond parameters of the solvent.

First principles molecular dynamics has been used to investigate the solvation of Mg2+ in water. In agreement with experiment, we find that the first solvation shell around Mg2+ contains six water molecules in an octahedral arrangement. The electronic structure of first solvation shell water molecules has been examined with a localized orbital analysis. We find that water molecules tend to asymmetrically coordinate Mg2+ through one of the oxygen lone pair orbitals and that the first solvation shell dipole moments increase by 0.2 Debye relative to pure liquid water.

The absolute solvation free energy of 30 univalent ions, mainly organic species, has been calculated from experimental and theoretical data on proton affinities, aqueous acidity constants, solvation free energy of neutral species, and the new value for the absolute solvation free energy of the proton determined by Tissandier et al. [J. Phys. Chem. A 102 (1998) 7787]. Our new values reveal considerable differences with previous compilations, and should be taken into consideration for comparison with liquid simulation results and in the development of implicit solvation models.

A study of Monte Carlo simulations (MCS) with statistical perturbation theory has been carried out to investigate the solvent effects on the relative free energies of solvation and the difference in partition coefficients (log P) for two solutes mutated to each other. It is proved that three or five MCS using doublewide sampling are necessary for obtaining results with enough precision and fluid simulations are required in which pyrazine is mutated to pyridine in several solvents. The computed results are compared with the previous published relative free energies of solvation and Δ log P data. For the present solute pairs, the solvent permittivity and the differences of solvation dominate the differences in the relative free energies of solvation and partition coefficients.

A modified generalized Born equation is incorporated with a semiempirical molecular orbital method to calculate electrostatic solvation energies for solute ions. A parameter corresponding to the atomic radius is introduced as a function of size of the solute ion and the position of the atom with respect to the solute surface. This method is applied to benzene and 17 polycyclic aromatic hydrocarbon mono-cations with various sizes and shapes in acetonitrile. The results are compared with experimental values obtained from the data of oxidation and ionization potentials. The present calculations based on the simple dielectric continuum model can predict the solvation energies with an average error of 0.07 eV.

The dependence of configurational entropy change in the fused hard-sphere reference system upon solvation on the solute's volume, surface, and curvature is investigated by using the thermodynamical perturbation theory of the fused hard spheres based on a rigorous treatment of the PV term. It is shown that no volume-proportional terms exist in the solvation free energy for spherical solutes, except for the PV term which is usually negligible in liquids. The effect of solute's and solvent's chain length on the configurational entropy is also presented.

A solvation model is described which utilises a hybrid quantum mechanical/molecular mechanical potential incorporating solvent polarization via a classical fluctuating charge method. The model is implemented within a molecular dynamics scheme which treats the fluctuating charges as dynamical variables and is validated using a number of dimers involving water.

Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.

A hydrodynamic model of electron solvation in polar liquids is suggested. The electron is assumed to be localized within a spherical cavity in an ideal incompressible liquid. The solvation process is modelled by the contraction of the cavity size to its equilibrium value. The contraction dynamics are determined by the competition between the gain in electron-solvent interaction energy and increase in kinetic energy of the electron. An explicit expression for the timescale of the process is derived. Its dependence on the solvent density and polarity, external pressure and initial radius of the cavity is explored. The calculated timescale of the electron solvation in water is in agreement with experimental data. The theory predicts a small isotope effect (∼5%) on the electron solvation process in heavy water.

We present an optimized set of atomic radii for H, C, N, O, F, P, S and Cl, which can be used in quantum dielectric continuum calculations. These atomic radii yield differences in hydration energies with experimental data of about 1 kcal/mol for neutral molecules, 2 kcal/mol for cations and 2–5 kcal/mol for anions at the Hartree-Fock, second order Moller-Plesset perturbation, and various non-local density functional theories within the framework of the generalized conductor-like screening model. Almost the same accuracy was also found when these radii were used with the polarizable continuum model (PCM). The accuracy of the recently proposed self-consistent isodensity PCM model is also discussed.

The effect on solvation dynamics and energetics of the length and charge distribution of a model linear solvent has been determined. Solvent clustering around the ion is independent of the solvent molecule length if the solvent dipole terminus is attracted to the charged solute. In contrast, if they repel, the structure around the solute ion depends on the length of the solvent molecules and on the solute charge. The calculated solvation dynamics has two components and depends on solvent structure. The fraction of the fast relaxation component decreases with the length of the solvent molecules.

The electron transfer and ground-state solvation dynamics of betaine-30 (B-30) in n-butanol at low temperatures are investigated by femtosecond pump-probe spectroscopy. Two separate components of the solvent response to solute excitation are observed. At higher temperatures (292-273 K), spectral evolution corresponding to diffusional solvation is evident. However, low-temperature studies (273-193 K) show the presence of a second process characterized by a ≈ 100 ps decay time and weak temperature dependence demonstrating that specific intermolecular hydrogen-bond dynamics are involved in the solvation of B-30 in protic solvents.

A general expression for the dispersion energy contribution to the solvation free energy is derived by exploiting the analogy between certain aspects of the theory of intermolecular forces and of the theory of solvation in the polarizable continuum model. The proposed method of calculation requires a knowledge of the solvent dielectric constant at imaginary frequencies, often efficiently approximated in terms of simple experimental data such as refractive index and ionization potential, and molecular transition densities and energies obtained by standard ab initio methods. By way of examples, the dispersion contribution is calculated for the systems CH 4 , NH 3 , H 2 O, HF and Ne in water as solvent.

The solvation of the benzophenone anion is studied in alcohols by observing the shift of the absorption spectrum of the anion. The anion is formed by pulse-radiolysis techniques. The solvation process is faster for smaller alcohols. Because the rate of change of the absorption is different at different wavelengths, the solvation process does not seem to be well described by the two-state model of solvation. The two-state model of solvation has been successful in describing the solvation of the electron in water or in alcohols at room temperature.

We study the non-linear effects on the dynamical process of the solvation in a polar solvent. On the basis of the non-linear generalized Smoluchowski equation with the linear-responce free energy, we calculate the time dependence of the solvent-solute interaction. It is shown that the solvation process becomes slow in the long-time region where the non-linear coupling between the dynamics of the solvent number density and the orientational relaxation is significant.

A simple model of solvation within the molecular orbital method is proposed whereby the effect of solvent molecules is simulated by the inclusion of fractional point charges at the solvent atomic centers. The method is applied to three solvation problems: the hydration of Li+ and F− and the solvation effect on the interaction between NH3 and HF. The results of the first two calculations indicate that the point charge model is capable of reliably predicting solvation energies. The calculations for H3N···HF demonstrate that the hydration has a profound effect on the potential energy surface favoring a proton transfer structure H3NH+···F−.

Experimental and theoretical evidence for the dominance of first solvation shell orientation on the spectral changes observed during electron solvation is evaluated.