When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.     

Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560 ns of simulation time. A finite, positive potential of 13-24 kbTec(-1) (where T=300 K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 A from the solute surface, on average 0.008 ec/A3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.     

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.     

Electrostatic interactions of charged dipolar proteins in reverse micelles

The electrostatic interactions in a reverse micelle containing a small-ionized protein are studied by Monte Carlo simulation. The electrostatic contribution to the potential of mean force of the protein in the reverse micelle is determined for a neutral protein, a uniformly charged protein, and a uniformly charged protein with a dipole moment. The effect of addition of a simple electrolyte is studied. While symmetrically distributed micellar charge exerts no force on enclosed ionic species, the protein is driven to the micellar wall due to interactions with simple ions. Protein binding to the inner wall of the micelle can be regulated by added salt. The presence of a dipole drives the protein further to the wall. These effects are studied for several proteins characterized by different charges and dipole moments. For a weakly charged protein with a strong dipole moment the contribution of dipolar interaction to the free energy can represent a major driving force for protein solubilization in the microemulsion.     

Charge asymmetries in hydration of polar solutes

We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.     

Nature of hydration shells of a polyoxy‐anion with a large cationic centre: The case of iodate ion in water

The structural nature of the solvation shells of an iodate ion, which is known to be a polyoxy‐anion with a large cationic centre, is investigated by means of Born–Oppenheimer molecular dynamics (BOMD) simulations using BLYP and the dispersion corrected BLYP‐D3 functionals. The iodate ion is found to have two distinct solvation regions around the positively charged iodine (iodine solvation shell or ISS) and the negatively charged oxygens (oxygen solvation shell or OSS). We have looked at the spatial, orientational, and hydrogen bond distributions of water in the two solvation regions. It is found that the water orientational profile in the ISS is typical of a cation hydration shell. The hydrogen bonded structure of water in the OSS is found to be very similar to that of the bulk water structure. Thus, the iodate ion essentially behaves like a positively charged iodine ion in water as if there is no anionic part. This explains why the cationic character of the iodate ion was prominently seen in earlier studies. The arrangement of water molecules in the two solvation shells and in the intervening regions around the iodate ion is further resolved by looking at structural cross‐correlations. The electronic properties of the solvation shells are also looked at by calculating the solute–solvent orbital overlap and dipole moments of the solute and solvation shell water. We have also performed BOMD simulations of iodate ion‐water clusters at experimentally relevant conditions. The simulation results are found to be in agreement with experimental results. © 2018 Wiley Periodicals, Inc.     

Further studies on the rotational barriers of Carbamates. An NMR and DFT analysis of the solvent effect for Cyclohexyl N,N-dimethylcarbamate

The solvent effect on the Gibbs energy of activation for rotation around the (C=O)–N bond in cyclohexyl N,N-dimethylcarbamate was investigated by dynamic NMR spectroscopy and density-functional theory at the B3LYP/6-311+G^** level. The experimental barriers were about 15 kcal mol⁻¹ with no appreciable variation when the solvent polarity was changed. A reaction field model was applied to theoretically mediate the solvent effect and the results were comparable to the experimental data. An analysis, based on the Onsager solvation theory, showed that the solvent effect on rotational barriers can be understood employing the total molecular dipole moment, the difference between the dipole moments of the ground and the transition state structures, or both, as appropriate.     

Photophysical properties of photoactive molecules with conjugated push-pull structures

The photophysical properties of two newly synthesized photoactive compounds with asymmetrical D-pi-A structure and symmetrical D-pi-A-pi-D structure are investigated in different aprotic solvents by steady-state and femtosecond fluorescence depletion measurements. It is found that the asymmetrical DA compound has larger dipole moment change than that of the symmetrical DAD compound upon excitation, where the dipole moments of the two compounds have been estimated using the Lippert-Mataga equation. Furthermore, the steady-state spectral results show that increasing solvent polarity results in small solvatochromic shift in the absorption maxima but a large red shift in the fluorescence maxima for them, indicating that the dipole moment changes mainly reflect the changes of dipole moment in excited-state rather than in ground state. The red-shifted fluorescence band is attributed to an intramolecular charge transfer (ICT) state upon photoexcitation, which could result in a strong interaction with the surrounding solvents to cause the fast solvent reorganization. The resulting ICT states of symmetrical compounds are less polar than the asymmetrical compounds, indicating the different extents of stabilization of solute-solvent interaction in the excited state. Femtosecond fluorescence depletion measurements are further employed to investigate the fast solvation effects and dynamics of the ICT state of these two novel compounds. The femtosecond fluorescence depletion results show that the DA compound has faster solvation time than that of DAD compound, which corresponds to the formation of relaxed ICT state (i.e., a final ICT state with rearranged solvent molecules after solvation) in polar solvents. It is therefore reasonably understood that the ICT compounds with asymmetrical (D-pi-A) structure have better performance for those photovoltaic devices, which strongly rely on the nature of the electron push-pull ability, compared to those symmetrical compounds (D-pi-A-pi-D).     

黄嘌呤及其互变异构体的密度泛函理论研究

嘌呤碱及其衍生物在生物系统中起重要作用。对人具有兴奋和利尿作用的茶碱和咖啡碱就是黄嘌呤的甲基衍生物。黄嘌呤存在多种互变异构体,从理论计算的角度研究这些互变异构体的几何结构、电子结构及相对稳定性,进一步研究溶剂对其结构和性质的影响是有意义旧。密度泛函理论方法既考虑了电子相关,又较其它CI（组态相互作用）或MPn（n级微扰）方法节省机时。其计算结果较好,被广泛应用于研究各种化合物。本文采用密度泛函B3LYP／6—311G方法对14种黄嘌呤可能的互变异构体（见图1）,分别在气相和水相中进行几何构型全自由度优化和能量计算,讨论了异构体的相对稳定性,水的溶剂化作用对异构体的能量、几何构型、电荷分布和偶极矩的影响,探讨了溶剂极性对异构体的能量和偶极矩的影响。     

Solvent-Induced Symmetry-Breaking Charge Transfer in an Octupolar Triphenylamine Derivative Resolved with Transient Fluorescence Spectroscopy

The excited-state symmetry-breaking charge transfer (SBCT) dynamics in quadrupolar or octupolar molecules without clear infrared markers is usually hard to be tracked directly. In this work, on the basis of the evolution of instantaneous emission dipole moment obtained by femtosecond transient fluorescence spectroscopy, we presented a real-time characterization of the solvent-induced SBCT dynamics in an octupolar triphenylamine derivative. While the emission dipole moment of the octupolar trimer in weakly polar toluene changes little during the excited-state relaxation, it exhibits a fast reduction in a few picoseconds in strongly polar tetrahydrofuran. In comparison with the uorescence dynamics of dipolar monomer, we deduced that the emitting state of the octupolar trimer in strongly polar solvent, which undergoes solvent-induced structural uctuation, changes from exciton-coupled octupolar to excitation localized dipolar symmetry. In weakly polar solvent, the octupolar symmetry of the trimer is largely preserved during the solvation stabilization.     

Consequences of strong coupling between solvation and electronic structure in the excited state of a betaine dye

The electronic ground and excited-state structures of the betaine dye molecule pyridinium- N-phenoxide [4-(1-pyridinio)phenolate] are investigated both in the gas phase and in aqueous solution, using the reference interaction site model self-consistent-field (RISM-SCF) procedure within a CASSCF framework. We obtain the total free energy profiles in both the ground and excited states with respect to variation in the torsion angle between the phenoxide and pyridinium rings. We analyze the effect of solvent on the variation of the solute dipole moment and on the charge transfer character in the excited state. In the gas phase, it is shown that the potential energy profile in the excited-state decreases monotonically toward a perpendicular ring orientation and the dipole moment decreases along with decreasing charge localization. In water, the free energy surface for twisting is better characterized as nearly flat along the same coordinate for sterically accessible angles. These results are analyzed in terms of contributions of the solvation free energy, the solute electronic energy, and their coupling. Correspondingly, the dependence of the charge transfer character on solute geometry and solvation are analyzed, and the important roles in the excitation and subsequent relaxation processes for the betaine dye are discussed. It is found that there is considerable solute electronic reorganization associated with the evolution of solvation in the excited state, and it is suggested that this reorganization may contribute significantly to the early time evolution of transient spectra following photoexcitation.     

Nuclear-Electron Overhauser Effect in MC800 Liquid Asphalt Solutions

Experimental results on the extrapolated ultimate enhancement factors of o-, m-, and p-xylene protons at 1.53 mT are obtained for MC800 asphalt solutions. The ultimate enhancement factors are found such as ?26.9, ?25.7, and ?11.7 for o-, m-, and p-xylene, respectively. These results show that the solvent proton Overhauser effect cannot reach the extrapolated enhancement of ?330 in the extreme narrowing case because of occurrence of small scalar interactions in addition to the dipole–dipole interactions between solvent protons and asphalt electrons. The ortho, meta, and para positions of the –CH₃ group change the nature of the interactions. The nuclear magnetic resonance (NMR) signal enhancements exhibit a sensitive behavior depending on the chemical environment differing from isomer to isomer. The solvation or association of asphalt in xylene isomers at room temperature is revealed. Quantum chemical calculations for the xylene isomers with the electronic and optical properties; absorption wavelengths, excitation energy, atomic charges, dipole moment and frontier molecular orbital energies, molecular electrostatic potential; are carried out using the density functional theory (DFT) method (B3LYP) with the 6-311G(d,p) basis set by the standard Gaussian 09 software package program. The relative importance of scalar and translational dipolar interaction parameters determined in dynamic nuclear polarization experiments is explained by the electronic structure of HOMO–LUMO of the xylene isomers.     

Solvation of N3- at the water surface: the polarizable continuum model approach

We present a new quantum mechanical model to introduce Pauli repulsion interaction between a molecular solute and the surrounding solvent in the framework of the Polarizable Continuum Model. The new expression is derived in a way to allow naturally for a position-dependent solvent density. This development makes it possible to employ the derived expression for the calculation of molecular properties at the interface between two different dielectrics. The new formulation has been tested on the azide anion (N3-) for which we have calculated the solvation energy, the dipole moment, and the static polarizability at the interface as a function of the ion position. The calculations have been carried out for different ion-surface orientations, and the results have also been compared with the parallel electrostatic-only solvation model.     

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: equilibrium fluctuation of cytochrome c

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein-water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein-water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.     

Study on Preferential Solvation of Water by Electrochemical Method

The preferential solvation of water plays an important role in ferrocene research which is a subject of current interest. Voltammetric investigations were carried out for Au electrode in acetonitrile/water, showing preferential solvation of water. In our work, the preferential solvation of water in acetonitrile/water was studied by electrochemical methods including cyclic volitammetry, electrochemical impedance spectra and double‐step chronoamperometry. Ferrocenemethanol (FcCH₂OH) molecules as a solute spontaneously adsorb on the electrode surface in anhydrous acetonitrile, resulting from acetonitrile molecules tend to form an acetonitrile solvent layer on the surface of the electrode and acetonitrile solvent layer has a lower energy barrier than the aqueous solvent layer, which has been obtained by modeling solvation. The solvent strongly influences electrochemical behavior of solute. Once there is an amount of water in acetonitrile solvent, FcCH₂OH that adsorbed on the electrode surface desorb. This is because water preferentially solvate with FcCH₂OH in term of intermolecular forces between solvent and solute. Moreover, hydrogen bond between water molecules and FcCH₂OH molecules is stronger than dipole‐dipole interaction between acetonitrile molecules and FcCH₂OH molecules in solvation effect. Through electrochemical behavior of FcCH₂OH changing, preferential solvation of water is analyzed by electrochemical methods.     

Solvent dependence of the one-electron reduction of substituted benzo- and naphthoquinones

Potentials for the one-electron reduction of a series of substituted benzo- and naphthoquinones were measured in 10 aprotic solvents by cyclic voltammetry and used to construct Hammett plots. Hammett reaction constants, ρ, were determined in each solvent and used as indicators of the solvent-mediated stabilization of the charged radical-anion product of the reduction reaction. Correlations of Hammett ρ values with solvent parameters suggest that the Lewis acidity of the solvent, in particular the solvent's ability to donate a partially positive proton, is a consistent predictor of the degree of charge stabilization of the quinone radical anion. Other mechanisms of charge stabilization, including solvent–solute charge transfer complexes and dipole–dipole interactions involving the molecular dipole moment (or an induced dipole moment) of the solvent, were found to be inconsistent predictors of the effect of solvent on one-electron quinone reduction in aprotic media.     

Shells theory of solvation and the long-range Born correction

A new solvation model, named shells theory of solvation, is proposed. In this approach, the solvent is divided in two regions, the S₁ shell, close to the solute and describing specific solute–solvent interactions, and the S₂ shell, representing the remain solvent and accounting for the long-range interaction contribution. A simple theoretical equation can be derived which allows the computation of the solvation free energy using two-point thermodynamic integration and configurations generated from molecular dynamics simulation. The discrete/continuum version of this theory provides rigorous theoretical foundations for the popular long-range Born correction and presents a new reliable expression for including this contribution. Further, it converges to the full discrete representation of the solvent when the number of solvent molecules goes to infinity. The method can be easily applied when the solute–solvent interaction (S₁ shell) is treated by full quantum mechanics, while the S₂ shell is described by a dielectric continuum solvation method. A simple test of the theory was done for solvation of fluoride ion in benzene solution. The S₁ shell was composed of the fluoride ion plus 32 benzene molecules, and the interaction with the S₂ shell was calculated at Hartree–Fock level with the MINI basis set and using the polarizable continuum model.