Search

Water fluctuates in a hydrophobic confinement, forming multiple dry and wet hydration states through evaporation and condensation. Transitions between such states are critical to both thermodynamics and kinetics of solute molecular processes, such as protein folding and protein–ligand binding and unbinding. To efficiently predict such dry–wet transition paths, we develop a hybrid approach that combines a variational implicit solvation model, a generalized string method for minimum free-energy paths, and the level-set numerical implementation. This approach is applied to three molecular systems: two hydrophobic plates, a carbon nanotube, and a synthetic host molecule Cucurbit[7]uril. Without an explicit description of individual water molecules, our mesoscale approach effectively captures multiple dry and wet hydration states, multiple dry–wet transition paths, such as those geometrically symmetric and asymmetric paths, and transition states, providing activation energy barriers between different states. Further analysis shows that energy barriers depend on mesoscopic lengths, such as the separation distance between the two plates and the cross section diameter of the nanotube, and that the electrostatic interactions strongly influence the dry–wet transitions. With the inclusion of solute atomic motion, general collective variables as reaction coordinates, and the finite-temperature string method, together with an improved treatment of continuum electrostatics, our approach can be further developed to sample an ensemble of transition paths, providing more accurate predictions of the transition kinetics.

We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of solvation for these approximate models. The parameters of the model are then either fit directly to experimental observables, e.g. the finite ion size, or optimized for agreement with experimental results. Experimental data for this optimization is available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route towards a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods., 21 pages, 5 figures, 3 tables

This study has examined the relative energetics of nine stationary points associated with the three different radical isomers generated by removing a H atom from ethanol at the O atom (ethoxy, CH3CH2O), the α C atom (CH3CHOH), and the β C atom (CH2CH2OH). For the first time, CCSD(T) geometry optimizations and harmonic vibrational frequency computations with the cc-pVTZ and aug-cc-pVTZ basis sets have been carried out to characterize two unique minima for each isomer along with three transition state structures with Cs symmetry. Explicitly correlated CCSD(T) computations were also performed to estimate the relative energetics of these nine stationary points near the complete basis set limit. These benchmark results were used to assess the performance of various density functional theory (DFT) and wave function theory methods, and they will help guide method selection for future studies of alcohols and their radicals. The structures generated by abstracting H from the α C atom have significantly lower electronic energies (by at least 7 kcal mol−1) than the CH3CH2O and CH2CH2OH radicals. Although previously reported as a minimum on the ground-state surface, the 2A″ Cs structure of the ethoxy radical was found to be a transition state in this study with MP2, CCSD(T), and a number of DFT methods. An implicit solvation model used in conjunction with DFT and MP2 methods did not qualitatively change the relative energies of the isomers, but the results suggest that the local minima for the CH3CHOH and CH2CH2OH radicals could become more energetically competitive in condensed phase environments, such as liquid water and ethanol.

Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent in a mean-field fashion with implicit solvent models. However, a challenge with existing implicit solvent models is that they often lack accuracy or certain physical properties compared to explicit solvent models, as the many-body effects of the neglected solvent molecules is difficult to model as a mean field. Here, we leverage machine learning (ML) and multi-scale coarse graining (CG) in order to learn implicit solvent models that can approximate the energetic and thermodynamic properties of a given explicit solvent model with arbitrary accuracy, given enough training data. Following the previous ML--CG models CGnet and CGSchnet, we introduce ISSNet, a graph neural network, to model the implicit solvent potential of mean force. ISSNet can learn from explicit solvent simulation data and be readily applied to MD simulations. We compare the solute conformational distributions under different solvation treatments for two peptide systems. The results indicate that ISSNet models can outperform widely-used generalized Born and surface area models in reproducing the thermodynamics of small protein systems with respect to explicit solvent. The success of this novel method demonstrates the potential benefit of applying machine learning methods in accurate modeling of solvent effects for in silico research and biomedical applications., 16 pages, 6 figures

Bismuth containing compounds are of particular interest for optical or photo-luminescent applications in sensing, bio-imaging, telecommunications, and opto-electronics and as components in non-toxic extremely dense liquids. Bismuth(III) halometallates form highly colored novel ionic liquid based solvents for which experimental characterization and fundamental understanding are limited. In this work, Bismuth(III) halometallates incorporating chloride, bromide, and iodide have been studied via density functional theory employing B3LYP-D3BJ/aug-cc-pVDZ. Lone anions, and anions in clusters with sufficient 1-ethyl-3-methyl-imidazolium [C2C1Im]+ counter-cations to balance the charge, have been investigated in the gas- phase, and with polarizable continuum solvation. Evaluation of speciation profiles indicates that dimeric or trimeric anions are prevalent. In contrast to analogous Al systems, anions of higher charge (−2, −3) are present. Speciation profiles are similar, but not identical with respect to the halide. The Bi based anions [BimXn]x− in the gas phase and generalized solvation environment produce multiple low energy conformers; moreover, key structural interaction patterns emerge from an analysis of ion-pair and neutral-cluster structures (BimXn)x−(C2C1Im)x+ for x = 1, 2, and 3. Cation–anion interactions are weak; with Coulombic and dispersion forces predominating, anion–π structures are favored, while significant hydrogen bonding does not occur. Anion to cation charge transfer is minimal, but mutual polarization is significant, leading to local positive regions in the anion electrostatic potential surface. The key features of experimental x-ray photoelectron, UV–Vis spectra, and Raman spectra are reproduced, validating the computational results and facilitating rationalization of key features.

We consider the factors that affect the photoactivity of silicon electrodes for the water-splitting reaction using a self-consistent continuum solvation (SCCS) model of the solid-liquid interface. This model allows us to calculate the charge-voltage response, Schottky barriers, and surface stability of different terminations while accounting for the interactions between the charge-pinning centers at the surface and the depletion region of the semiconductor. We predict that the most stable oxidized surface does not have a favorable Schottky barrier, which further explains the low solar-to-hydrogen performance of passivated silicon electrodes., Comment: 20 pages, 5 figures, plus supporting information

In computer simulations of solvation effects on chemical reactions, continuum modeling techniques regain popularity as a way to efficiently circumvent an otherwise costly sampling of solvent degrees of freedom. As effective techniques, such implicit solvation models always depend on a number of parameters that need to be determined earlier. In the past, the focus lay mostly on an accurate parametrization of water models. Yet, non-aqueous solvents have recently attracted increasing atten- tion, in particular, for the design of battery materials. To this end, we present a systematic parametrization protocol for the Self-Consistent Continuum Solvation (SCCS) model resulting in optimized parameters for 67 non-aqueous solvents. Our parametrization is based on a collection of ≈6000 experimentally measured partition coefficients, which we collected in the Solv@TUM database presented here. The accuracy of our optimized SCCS model is comparable to the well-known universal continuum solvation model (SMx) family of methods, while relying on only a single fit parameter and thereby largely reducing sta- tistical noise. Furthermore, slightly modifying the non-electrostatic terms of the model, we present the SCCS-P solvation model as a more accurate alternative, in particular, for aromatic solutes. Finally, we show that SCCS parameters can, to a good degree of accuracy, also be predicted for solvents outside the database using merely the dielectric bulk permittivity of the solvent of choice.

Confinement plays an important role in determining ion transport in porous materials, which, in turn, may influence the performance of many energy storage and desalination devices. In this work, we combined density functional theory (DFT) with an implicit solvation model and ab initio molecular dynamics (AIMD) to investigate the effects of nanoconfinement on several solvated alkaline metal cations in a single-digit 1T-MoS2 nanochannel. Our DFT calculations with a solvation model indicated that cations with stronger hydration energy introduce a higher number of co-intercalated water molecules into the channel, consistent with early experimental observation obtained for MXene (2D transition metal carbide) channels. The predicted optimal water numbers for the cations were then used for AIMD simulations that explicitly include the effects of the solvent. When compared with the cations in bulk solution, our simulations showed that the hydration structure and coordination number (CN) of the solvated cations confined in the MoS2 channel can be significantly altered. We found that larger cations with weaker hydration energy (K+, Rb+, and Cs+) exhibited a distinctive CN decrease under confinement, while smaller cations (Li+ and Na+) retained a similar hydration shell as in the bulk solution. More specifically, the hydration shell of large cations (K+, Rb+, and Cs+) in MoS2 showed similar features of the coordination angle to the bulk, which suggests the partially broken hydration shell with no geometry change under confinement. Our simulations provided insights into the change of the hydration structure of alkaline metal cations under confinement, which may have important implications on their transport in the 1T-MoS2 channel.

The concept of the formation of a solute-sized cavity in a solvent is widely used in the theories of solvation processes; however, most of the studies of cavity formation using atomistic simulations were limited to water and hydrocarbon models. We calculated the Gibbs free energy of cavity formation ΔcavG for a structurally diverse set of 23 common organic solvents. For the calculation, molecular dynamics simulations of solvent boxes were conducted, and the Widom particle insertion method was applied. The results obtained with two different force fields for the same solvent were in good agreement with each other in most cases. The obtained cavity size dependences of ΔcavG allowed ranking the solvents by the free energy cost of creation of a cavity with a certain size. Surprisingly, this cost was somewhat higher in glycerol, formamide, and ethylene glycol than in water. In general, higher values of ΔcavG are observed for the solvents with a branched network of intermolecular hydrogen bonds and strongly polar aprotic solvents. The numerical results can be used to improve the accuracy of the calculation of the cavity term in non-aqueous continuum solvation models.

We study the site-dependent dissolution of platinum nanoparticles under electrochemical conditions to assess their thermodynamic stability as a function of shape and size using empirical molecular dynamics and electronic-structure models. The third-generation charge optimized many-body potential is employed to determine the validity of uniform spherical representations of the nanoparticles in predicting dissolution potentials (the Kelvin model). To understand the early stages of catalyst dissolution, implicit solvation techniques based on the self-consistent continuum solvation method are applied. It is demonstrated that interfacial charge and polarization can shift the dissolution energies by amounts on the order of 0.74 eV depending on the surface site and nanoparticle shape, leading to the unexpected preferential removal of platinum cations from highly coordinated sites in some cases.

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

The cluster expansion method has been used in the imperfect gas theory for several decades. This paper proposes a cluster expansion of the solvation free energy difference. This difference, which results from a change in the solute-solvent potential energy, can be written as the logarithm of a finite series. Similar to the Mayer function, the terms in the series are related to configurational integrals, which makes the integrand relevant only for configurations of the solvent molecules close to the solute. In addition, the terms involve interaction of solute with one, two, and so on solvent molecules. The approach could be used for hybrid quantum mechanical and molecular mechanics methods or mixed cluster-continuum approximation. A simple form of the theory was applied for prediction of pKa in methanol; the results indicated that three explicit methanol molecules and the dielectric continuum lead to a root of mean squared error (RMSE) of only 1.3 pKa units, whereas the pure continuum solvation model based on density method leads to a RMSE of 6.6 pKa units.

Implicit solvation calculations based on a Stern-layer corrected size-modified Poisson-Boltzmann (SMPB) model are an effective approach to capture electrolytic effects in first-principles electronic structure calculations. For a given salt solution, they require a range of ion-specific parameters, which describe the size of the dissolved ions as well as thickness and shape of the Stern layer. Out of this defined parameter space, we show that the Stern layer thickness expressed in terms of the solute’s electron density and the resulting ionic cavity volume completely determine ion effects on the stability of neutral solutes. Using the efficient SMPB functionality of the full-potential density-functional theory package FHI-aims, we derive optimized such Stern layer parameters for neutral solutes in various aqueous monovalent electrolytes. The parametrization protocol relies on fitting to reference Setschenow coefficients that describe solvation free energy changes with ionic strength at low to medium concentrations. The availability of such data for NaCl solutions yields a highly predictive SMPB model that allows to recover the measured Setschenow coefficients with an accuracy that is comparable to prevalent quantitative regression models. Correspondingly derived SMPB parameters for other salts suffer from a much scarcer experimental data base but lead to Stern layer properties that follow a physically reasonable trend with ionic hydration numbers.

Influence of the excitation energy of a probe solute molecule on its solvation dynamics and emission spectrum in 1-ethyl-3-methylimidazolium hexafluorophosphate (EMI(+)PF6 (-)) is studied via molecular dynamics simulations using a coarse-grained model description. By exciting the probe at different energies, each with an extremely narrow distribution, ensuing solvent relaxation and its dynamic variance are monitored using the isoconfigurational ensemble method. Resulting Stokes shift function, S(t), indicates that long-time solvent relaxation becomes slower with the decreasing excitation energy and approaches the equilibrium correlation function, C(t), of solvent fluctuations. This suggests that the system excited at the red-edge of the spectrum observes linear response better than that at the blue-edge. A detailed analysis of nonequilibrium trajectories shows that the effect of initial configurations on variance of relaxation dynamics is mainly confined to short times; it reaches a maximum around 0.1 ≲ t ≲ 1 ps and diminishes as time further increases. The influence of the initial velocity distribution, on the other hand, tends to grow with time and dominates the long-time variations of dynamics. The emission spectrum shows the red-edge effect in accord with previous studies.

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into "fast" versus "slow" polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are

The conformation of a polymer chain in solution is coupled to the local structure of the surrounding solvent and can undergo large changes in response to variations in solvent density and temperature. The many-body effects of solvent on the structure of an n-mer polymer chain can be formally mapped to an exact n-body solvation potential. Here, we use a pair decomposition of this n-body potential to construct a set of two-body potentials for a Lennard-Jones (LJ) polymer chain in explicit LJ solvent. The solvation potentials are built from numerically exact results for 5-mer chains in solvent combined with an approximate asymptotic expression for the solvation potential between sites that are distant along the chain backbone. These potentials map the many-body chain-in-solvent problem to a few-body single-chain problem and can be used to study a chain of arbitrary length, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have constructed solvation potentials at a large number of state points across the LJ solvent phase diagram including the vapor, liquid, and super-critical regions. We use these solvation potentials in single-chain Monte Carlo (MC) simulations with n ≤ 800 to determine the size, intramolecular structure, and scaling behavior of chains in solvent. To assess our results, we have carried out full chain-in-solvent MC simulations (with n ≤ 100) and find that our solvation potential approach is quantitatively accurate for a wide range of solvent conditions for these chain lengths.

Widely used continuum solvation models for electronic structure calculations, including popular polarizable continuum models (PCMs), usually assume that the continuum environment is isotropic and characterized by a scalar dielectric constant, e. This assumption is invalid at a liquid/vapor interface or any other anisotropic solvation environment. To address such scenarios, we introduce a more general formalism based on solution of Poisson's equation for a spatially varying dielectric function, e(r). Inspired by nonequilibrium versions of PCMs, we develop a similar formalism within the context of Poisson's equation that includes the out-of-equilibrium dielectric response that accompanies a sudden change in the electron density of the solute, such as that which occurs in a vertical ionization process. A multigrid solver for Poisson's equation is developed to accommodate the large spatial grids necessary to discretize the three-dimensional electron density. We apply this methodology to compute vertical ionization energies (VIEs) of various solutes at the air/water interface and compare them to VIEs computed in bulk water, finding only very small differences between the two environments. VIEs computed using approximately two solvation shells of explicit water molecules are in excellent agreement with experiment for F-(aq), Cl-(aq), neat liquid water, and the hydrated electron, although errors for Li+(aq) and Na+(aq) are somewhat larger. Nonequilibrium corrections modify VIEs by up to 1.2 eV, relative to models based only on the static dielectric constant, and are therefore essential to obtain agreement with experiment. Given that the experiments (liquid microjet photoelectron spectroscopy) may be more sensitive to solutes situated at the air/water interface as compared to those in bulk water, our calculations provide some confidence that these experiments can indeed be interpreted as measurements of VIEs in bulk water.

Reliable first-principles calculations of electrochemical processes require accurate prediction of the interfacial capacitance, a challenge for current computationally-efficient continuum solvation methodologies. We develop a model for the double layer of a metallic electrode that reproduces the features of the experimental capacitance of Ag(100) in a non-adsorbing, aqueous electrolyte, including a broad hump in the capacitance near the Potential of Zero Charge (PZC), and a dip in the capacitance under conditions of low ionic strength. Using this model, we identify the necessary characteristics of a solvation model suitable for first-principles electrochemistry of metal surfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectric-only region at the interface. The dielectric nonlinearity, caused by the saturation of dipole rotational response in water, creates the capacitance hump, while ionic nonlinearity, caused by the compactness of the diffuse layer, generates the capacitance dip seen at low ionic strength. We show that none of the previously developed solvation models simultaneously meet all these criteria. We design the Nonlinear Electrochemical Soft-Sphere solvation model (NESS) which both captures the capacitance features observed experimentally, and serves as a general-purpose continuum solvation model., 7 pages, 4 figures, 2 tables; supplementary information (SI.pdf) in source archive

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that-from the three analyzed solvation shells of CfAFP-the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.

Free energy of solvation of a spherical ion in a force-field water is studied by numerical simulations. The focus is on the linear solvation susceptibility connecting the linear response solvation free energy to the squared ion charge. Spherical hard-sphere solutes, hard-sphere ions, and Kihara solutes (Lennard-Jones modified hard-sphere core) are studied here. The scaling of the solvation susceptibility with the solute size significantly deviates from the Born equation. Using empirical offset corrections of the solute size (or the position of the first peak of the solute-solvent distribution function) do not improve the agreement with simulations. We advance a new perspective on the problem by deriving an exact relation for the radial susceptibility function of the interface. This function yields an effective cavity radius in the Born equation calculated from the solute-solvent radial distribution function. We find that the perspective of the local response, assuming significant alteration of the solvent structure by the solute, is preferable compared to the homogeneous approximation assuming intact solvent structure around the solute. The model finds a simple explanation of the asymmetry of hydration between anions and cations in denser water shells around anions and smaller cavity radii arising from the solute-solvent density profiles.

We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation 〈Nsolv〉, and second osmotic virial coefficient B2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

We present a theoretical study of solvation dynamics in supercritical fluids. Molecular dynamics simulations show a significant difference between equilibrium and nonequilibrium solvent response functions, especially pronounced at medium and low solvent densities. We propose an analytical theory for the nonequilibrium solvation function based on the generalized nonlinear Smoluchowski-Vlasov equation. The theory is shown to be in good agreement with simulation, providing an accurate description of the nonequilibrium time-dependent solvent density profile around the solute over a wide range of supercritical solvent densities. The nonequilibrium solvent response function is shown to reflect gradual solvent clustering around the excited solute.

The hybrid molecular–continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic (inertialess) polarization effects and a molecular dynamics (MD) simulation for the slow (inertial) polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced (electronic) components. MD simulations are performed in a manner consistent with the choice of solvent and solute charges such that all electrostatic interactions are scaled by the factor 1/e∞, where e∞ is the optical dielectric permittivity. This approach yields an ensemble of equilibrium solvent configurations adjusted to the electric field created by a charged or strongly polar solute. The electrostatic solvent response field is found as the solution of the Poisson equation including both solute and explicit solvent charges, with accurate acco...

Solvation in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate is studied via molecular dynamics simulations by employing a diatomic solute as a probe. It is found that solvent fluctuations are chacterized by at least two distinct dynamics occurring on vastly different time scales—rapid subpicosecond dynamics arising mainly from anion translations and slow relaxation ascribed to anion and cation diffusions. Fast subpicosecond dynamics are responsible for more than 50% of the entire relaxation of solvent fluctuations in the temperature range 350 K⩽T⩽500 K. It is also found that solvent spectral shifts and reorganization free energies in these liquids are comparable to those in ambient water.

Molecular exclusion surfaces [J. Bentley, J. Phys. Chem. A 104, 9630 (2000)] have been determined for a number of molecules and molecular ions interacting with argon or helium atoms. These surfaces represent the boundaries between the molecules and their environment and have application, for instance, to continuum solvation models. To make these surfaces useful for such applications, we present some simple models for exclusion surfaces which depend only on properties of the electron densities of the isolated molecules.

A mode-coupling treatment of nonpolar solvation dynamics in supercritical fluids is presented. Both neat fluids and dilute attractive supercritical solutions are considered. The equilibrium solvation time correlation function for the solute fluctuating transition frequency is obtained from the mode-coupling theory method and from molecular dynamics simulations. Theory is shown to be in good agreement with simulation for all solvent thermodynamic conditions studied. The microscopic origins of the density dependence of the time correlation function are discussed.

The challenging task of reproducing solvent effects on computed nuclear shieldings requires a careful analysis of different solvation models: We have compared the performances of continuum, cluster, and molecular dynamics approaches for sp(3) and sp(2) O-17 in aqueous solution. The various solvation models have to be combined to reproduce the experimental results satisfactorily; a different behavior is found for the two hybridization states of the oxygen atom. The proposed procedure allows the accurate calculation of solvent effects on the nuclear shielding, and the separation of the main effects contributing to this quantity.

We present results of molecular dynamics simulations of solvation dynamics of coumarin 153 in dimethylsulfoxide (DMSO)–water mixtures of different compositions (xD=0.00, 0.25, 0.32, 0.50, 0.75, and 1.00) using an all-atom model for the solute probe. Results are reported for the global solvation responses of the simulated systems, as well as for the separate contributions from each cosolvent and the individual solute–site couplings to water and DMSO. The solvation dynamics is predominantly given by DMSO’s contribution, even at low (25%) DMSO content, because of the preferential solvation of the probe. We find that the water molecules are only mildly coupled to the charge transfer in the coumarin, resulting in a small, largely diffusive, water relaxation component. Simulation results, including solvation responses, characteristic times, and Stokes shifts are compared with recent fluorescence upconversion experimental measurements showing good agreement for the relaxation but significant differences for the ...

The density dependence of time correlation functions for the solvation energy in a simple Lennard-Jones liquid has been investigated by molecular dynamics computer simulations. Considering argon dissolved in liquid argon, mechanical solvation dynamics has been studied treating interactions between excited solute states and the solvent by changes in the Lennard-Jones well-depth parameter, the Lennard-Jones size parameter, and a combination of the two. Densities have been varied from supercritical to triple point densities at a constant temperature of 151 K. In addition, a thermodynamic state close to the argon triple point has been considered. All the solvation energy time correlation functions have been broken down into their partial two- and three-body contributions giving an insight into the cancellation effect of solvation dynamics. It is found that the well-depth solvation process produces slowly decaying time correlation functions for the solvation dynamics at lower densities. In this case, the solva...

We present an implementation of the conductor-like screening model (COSMO) within the framework of Car–Parrinello ab initio molecular dynamics. In order to obtain the accurate forces needed for energy-conserving dynamics, analytic derivatives with respect to the atomic positions are required for all energy terms. We use a steep, but continuous surface function that effectively switches the surface charges off when they are not exposed on the molecular surface. This allows us to construct the cavity surface in such a way that the required analytic derivatives of the surface charges and surface segments are always available. Furthermore, we treat the surface charges as fictitious dynamic variables within the extended Lagrangian approach, solving the electrostatic problem determining the charges “on the fly” as the system evolves in time. Our implementation makes it possible to perform energy-conserving ab initio molecular dynamics simulations in which continuum solvation is included. It provides solvation e...

The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water–Na + system. The distinctively different statistical complexity of water molecules in the bulk and in the first solvation shell of the ion is demonstrated. It is shown that the molecules undergo more complex orientational motion when surrounded by other water molecules compared to those constrained by the electric field of the ion. However the spatial coordinates of the oxygen atom shows the opposite complexity behavior in that complexity is higher for the solvation shell molecules. New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site–site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion–solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain ...

A combined approach to study reactions in solution in which the solute and a number of solvent molecules are described with a hybrid quantum mechanical/molecular mechanical (QM/MM) method, and the bulk solvent is represented by a polarizable continuum model (PCM) has been implemented. In this way, both short-range effects of the first-solvation shell and long-range electrostatics due to the bulk solvent can be taken into account. By carefully choosing the size of the solute–solvent cluster and the QM/MM partition, the current QM/MM/PCM approach can offer both computational efficiency and accuracy. The approach has been illustrated by two simple systems: water-dimer and glycine in water. The results demonstrated that the current approach offers a satisfactory description of solvation effects on the geometry and energetics of neutral and charged hydrogen-bonding systems. The method correctly produced the relative stability of the zwitterionic and neutral forms of glycine in solution, which was found to be a subtle issue in previous studies. The approach can be extended to study reactions in biomolecules in which part of the system is treated with QM/MM, and the bulk solvent plus part of the protein or nucleic acids are described with either a continuum or approximate microscopic representation.

While dynamics of polar solvation have been tabulated for a wide range of pure polar solvents, substantially less is known about the dynamic response of solvent mixtures. Here, results for polar solvation dynamics are presented for the nonassociating mixture of a dipolar solvent, acetonitrile, and a quadrupolar solvent, benzene. The solvation response observed is sensitive to the mixing of the pure solvents, affecting both the inertial and diffusive components of the solvation response function. Addition of acetonitrile to benzene increases the amplitude of the inertial response. At high benzene mole fractions, the diffusive relaxation reveals a slow component attributed to translational diffusion of the acetonitrile.

The accurate modeling of the environment response is a fundamental challenge for accurately describing the photophysics and photochemistry of molecules both in solution and in more complex embeddings. When large rearrangements of the electron density occur after an electronic transition, state-specific formulations, such as the vertical excitation model, are necessary to achieve a proper modeling of the processes. Such a state-specific model is fundamental not only to obtain accurate energies, but also to follow the geometrical relaxation accompanying the evolution of the excitedstates. This study presents the analytical expression of the gradients of the vertical excitation model approach by a Lagrangian formulation in the time dependent density functional theory framework. Representative organic chromophores in solution are used to test the reliability of the implementation and provide comparisons with the linear response description. Published by AIP Publishing.

Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ωPBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

The alignment of electrostatic potential between different atomic configurations is necessary for first-principles calculations of band offsets across interfaces and formation energies of charged defects. However, strong oscillations of this potential at the atomic scale make alignment challenging, especially when atomic geometries change considerably from bulk to the vicinity of defects and interfaces. We introduce a method to suppress these strong oscillations by eliminating the deep wells in the potential at each atom. We demonstrate that this method considerably improves the system-size convergence of a wide range of first-principles predictions that depend on the alignment of electrostatic potentials, including band offsets at solid-liquid interfaces, and formation energies of charged vacancies in solids and at solid surfaces in vacuum. Finally, we use this method in conjunction with continuum solvation theories to investigate energetics of charged vacancies at solid-liquid interfaces. We find that for the example of an NaCl (001) surface in water, solvation reduces the formation energy of charged vacancies by 0.5 eV: calculation of this important effect was previously impractical due to the computational cost in molecular-dynamics methods.

Charge transfer excitations play a prominent role in the fields of molecular electronics and light harvesting. At the same time they have developed a reputation for being hard to predict with time-dependent density functional theory, which is the otherwise predominant method for calculating molecular structure and excitations. Recently, it has been demonstrated that range-separated hybrid functionals, in particular with an “optimally tuned” range separation parameter, describe charge-transfer excitations reliably for different molecules. Many of these studies focused on molecules in vacuum. Here we investigate the influence of solvation on the electronic excitations of thiophene oligomers, i.e., paradigm low gap systems. We take into account bulk solvation using a continuum solvation model and geometrical distortions from molecular dynamics. From our study, three main findings emerge. First, geometrical distortions increase absorption energies by about 0.5 eV for the longer thiophene oligomers. Second, combining optimal tuning of the range separation parameter with a continuum solvation method is not straightforward and has to be approached with great care. Third, optimally tuned range-separated hybrids without a short-range exchange component tend to inherit undesirable characteristics of semi-local functionals: with increasing system size the range separation parameter takes a smaller value, leading to a functional of effectively more semi-local nature and thus not accurately capturing, e.g., the saturation of the optical gap with increasing system size.

By considering the influence of volume exclusion on the solvent dielectric, a variable dielectric Poisson-Boltzmann (VDPB) model is explored for molecular solvation studies by using a dielectric as an explicit function of ionic sizes and concentrations. A finite element method is adopted and an iterative strategy is introduced to numerically solve the VDPB equation. According to our computations, the current dielectric model can result in considerable differences compared with the traditional Poisson-Boltzmann (PB) solutions, especially for those systems with highly charged biomolecule and/or under high salt concentration condition. The model to certain extent captures the fact of dielectric decrement of electrolyte solutions, which is especially remarkable in the vicinity of molecules. Counter-ion concentration very near the molecular surface in VDPB calculation is found higher than that in PB. The new dielectric model may also influence the charge compensation behavior near biomolecular surface. For a spherical cavity solvated in a concentrated ionic solution, charge inversion is observed in VDPB, which does not occur with the traditional PB model. Besides, the solvation energy predicted by VDPB will always be greater than that by PB. Moreover, differing from PB, the VDPB also allows non-monotonous dependencies of solvation energy on ionic strength.

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Moller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Variational transition state theory (VTST) is used to calculate rate constants for a model proton transfer reaction in a polar solvent. We start from an explicit description of the reacting solute in a solvent, and we model the effects of solvation on the reaction dynamics by a generalized Langevin equation (GLE) for the solute. In this description, the effects of solvation on the reaction energetics are included in the potential of mean force, and dynamical, or nonequilibrium, solvation is included by solvent friction. The GLE solvation dynamics are approximated by a collection of harmonic oscillators that are linearly coupled to the coordinates of the reacting system. This approach is applied to a model developed by Azzouz and Borgis [J. Chem. Phys. 98, 7361 (1993)] to represent proton transfer in a phenol-amine complex in liquid methyl chloride. In particular, semiclassical VTST, including multidimensional tunneling contributions, is applied to this model with three explicit solute coordinates and a mu...

Results on single-wavelength transient hole burning (SW-THB) developed in paper II [J. Chem. Phys. 115, 4223 (2001)] are applied to the dichroism experiments on anthracene in benzyl alcohol reported in paper I [J. Chem. Phys. 115, 4212 (2001)]. The intermediate component of the dichroism decay is assigned to a SW-THB effect caused by nonpolar electronic solvation. The presence of a solvation component in dichroism experiments has not been demonstrated previously. The sparseness of anthracene’s electronic spectrum eliminates vibrational dynamics from the solvation measurement. Because data collection is focused on a single dimension, the viscosity dependence of the nonpolar solvation is determined with greater accuracy than in our previous two-dimensional transient hole-burning studies. The solvation time is obtained as a function of viscosity/temperature from 14.4 to 2.7 cP (1–56 °C). The times show good agreement with a viscoelastic theory of the diffusive component of nonpolar solvation. Combining the results of this paper with those of paper I allows for comparison of solvation and rotation dynamics within a single system. A correlation between the ratio of diffusive solvation and rotation times and the magnitude of the inertial rotation is suggested.

An approximate method, recently proposed to include in continuum solvation models the effects of electronic charge lying outside the solute cavity, has been adapted and implemented in the framework of the polarizable continuum model (PCM). This formulation exploits all the features already developed for the other PCM versions; it provides molecular free energies, gradients and second derivatives with respect to nuclear coordinates. The performances of this method have been tested in comparison with other PCM versions, in particular, we examined the reliability of this technique to reproduce actual volume charge distribution effects, compared to traditional procedures based on Gauss’ Law.

The recently developed self-consistent continuum solvation model (SCCS) [O. Andreussi, I. Dabo, and N. Marzari, J. Chem. Phys. 136, 064102 (2012)] is applied here to charged species in aqueous solutions. Describing ions in solution represents a great challenge because of the large electrostatic interactions between the solute and the solvent. The SCCS model is tested over 106 monocharged species, both cations and anions, and we demonstrate its flexibility, notwithstanding its much reduced set of parameters, to describe charged species in solution. Remarkably low mean absolute errors are obtained with values of 2.27 and 5.54 kcal/mol for cations and anions, respectively. These results are comparable or better than the state of the art to describe solvation of charged species in water. Finally, differences of behavior between cations and anions are discussed. (C) 2013 AIP Publishing LLC.

A modified conductorlike screening continuum solvation model, implemented in the quantum chemistry program GAMESS, has been extended to second order perturbation theory (MP2). Two possible schemes have been considered: (a) the calculation of the MP2 energy using the solvated Hartree–Fock (HF) orbitals, and (b) the implementation of a double-iterative procedure where the HF density is updated with respect to the MP2 surface charges. The influence of the self-consistency of the surface charge distribution with respect to the MP2 density has been analyzed for a small dataset of 21 neutral molecules and 13 ions. In addition, the details of the distribution of surface charge density (σ profiles) and the effects of electron correlation on the accuracy of such distributions is analyzed in terms of the overall concept of deviation of continuum models from dielectric theory, leading to insights into higher order models.

The conductorlike continuum solvation model, modified for ab initio in the quantum chemistry program GAMESS, implemented at the Moller–Plesset Order 2 (MP2) level of theory has been applied to a group of push–pull pyrrole systems to illustrate the effects of donor/acceptor and solvation on the stability and energetics of such systems. The most accurate theoretical gas and solution phase data to date has been presented for the parent furan-2-carbaldehyde (furfural) system, and predictions made for three additional analogues, thiophene-2-carbaldehyde, pyrrole2-carbaldehyde, and, cyclopentadiene-1-carbaldehyde. Solvent effects on internal rotational barriers in all systems were evaluated over six different values of dielectric, using the new method. Calculated electrostatic energies are shown to be highly sensitive to level of theory incorporated.

A new solvation model that combines discrete and continuum descriptions of the solvent has been developed. The discrete solvent molecules are represented by effective fragment potentials (EFP), while the continuum is represented by the Onsager model. This (EFP+Onsager) model has been applied to the relative stabilities of the neutral and zwitterionic forms of glycine. Other supermolecule-continuum calculations were also performed, using quantum mechanical discrete waters and the isodensity polarizable continuum model (IPCM) or solvation model 5.42R (SM5.42R) for the continuum. It is shown that the Onsager model provides a poor description of the solvent in the supermolecule-continuum calculations. On the other hand, more sophisticated models can predict the correct energy order of the glycine isomers. Thus, the development of mixed methods that combine sophisticated continuum models with the discrete EFP model appear to be promising.

We applied the three-dimensional reference interaction site model (3D-RISM) integral equation theory with the 3D hypernetted chain (3D-HNC) closure or its partial linearization (3D-PLHNC) to obtain the potentials of mean force (PMFs) and the solvation structure of sodium chloride in ambient water. The bulk solvent correlations are treated by the dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) to provide a proper description of the dielectric properties of solution and to include the case of a finite salt concentration. The PMF is calculated as a difference in the solvation free energy of an ion pair and of individual ions. We obtained and analyzed in detail the PMFs and solvation structure for ion pairs of NaCl at infinite dilution and a concentration of 1 M. The results are in reasonably good agreement with molecular dynamics simulations for the same model of the solution species. Positions and orientations of water molecules in the first solvation shell around the ion pair are deduced. The short-range hydration structure of the ion pairs at infinite dilution and at moderate concentration is very similar. Ionic ordering and clustering is found in 1 M solution.

We adapt the three-dimensional reference interaction site model (3D-RISM) to calculate the potentials of mean force for ion–molecular solution as a difference between the chemical potential of solvation of a cluster of solutes and of individual ones. The method yields the solvation structure around the cluster of solutes in detail. The solvation chemical potential is obtained for the three-dimensional hypernetted chain (3D-HNC) closure as well as for its partial linearization (3D-PLHNC approximation). The solvation chemical potential is obtained in a closed analytical form for both the 3D-HNC and 3D-PLHNC closures. The 3D-RISM integral equations are solved by using the supercell technique. A straightforward supercell treatment of ionic solute in polar molecular solvent leads to a big error in the potential of mean force as well as the solvation chemical potential, which for simple ions in water amounts to about 35 kcal/mol. We elaborated corrections to the 3D-RISM integral equations, alleviating the artifact of the supercell periodicity with an accuracy of 0.05 kcal/mol or better and restoring the long-range asymptotics of the solute–solvent correlation functions. The dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) is employed for the solvent correlations to provide a proper description of the dielectric properties of solution. This allowed us to extend the description to solution at a finite salt concentration. We converge both the 3D-RISM and site–site DRISM integral equations by using the method of modified direct inversion in the iterative subspace. Owing to the proper initial guess of the correlation functions, iteration begins at once for a given temperature and full molecular charge, avoiding a gradual decrease of the temperature and increase of the site charges, which greatly reduces the computation time. We calculate and discuss the potentials of mean force for sodium chloride in ambient water at infinite dilution as well as at a finite concentration.

We present a study on the IR vibrational shifts of the OH stretch mode for water and methanol when passing from gas to liquid phase. Both a purely continuum solvation model (here the polarizable continuum model) and its semicontinuum extensions, obtained explicitly considering small clusters of H-bonded molecules of liquid, have been tested. The definition of such clusters as the new quantum mechanical system to be coupled to a continuum description of the remainder liquid has allowed us to take into account both the "local permanent specific" interaction due to the H-bond and the long-range effects present in all liquids. The analysis mainly focused on harmonic approximations and has been extended to include mechanical anharmonicities in order to have a more reliable comparison with the experiments. Finally, careful attention has been paid to the analysis of the "intrinsic" parameters of continuum models (i.e., the shape and size of the molecular cavity containing the QM system) and to their effects on the vibrations.