Effect of ion solvation on the diffuse layer structure in mixed electrolytes

A “solvionic” model of a multicomponent electrochemical system (mixed electrolyte) is considered. An ion in the solution is considered as a point charge rigidly fixed inside its solvation shell. The corresponding equations for the diffuse layer on an ideally polarizable electrode are derived, and an effective method of their numerical solution is formulated. The calculations are performed in order to follow the changes in the diffuse layer structure with variations in the electrode charge and electrolyte composition. Far from the zerocharge potential of solution, the dependences of distributions of solution components over the diffuse layer on the electrode charge radically differ from those within the classic Gouy-Chapman theory. Analytical equations (asymptotics at large electrode charges) for concentrations of solvated ions in the plane of their maximum approach and for their “surface excesses” (diffuse adsorption) are determined. Results of numerical calculations for a 0.2 M LiCl + 0.05 M BaCl₂ solution are plotted.     

Coupled reference interaction site model/simulation approach for thermochemistry of solvation: theory and prospects

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems.     

Photo absorption of ‐coumaric acid in aqueous solution: RISM‐SCF‐SEDD theory approach

Photo absorption properties of p‐coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated by means of reference interaction site model self‐consistent field with spatial electron density distribution (RISM‐SCF‐SEDD) method. RISM‐SCF‐SEDD is a combination methodology of electronic structure theory and statistical mechanics for molecular liquids. Here, time‐dependent density functional theory was coupled with RISM equation to study the electronic structure of p‐coumaric acid in aqueous system. Excitation energies of the chromophore in its neutral, two monoanionic and dianionic forms were computed to elucidate the effect of the deprotonation and solvation on the spectroscopic properties. We found that solvation strongly affects the excitation character of the chromophore, especially for phenolate anion and dianion. The free energy difference among the four protonation states is also discussed. © 2017 Wiley Periodicals, Inc.     

Structural Water Drives Self‐assembly of Organic Rosette Nanotubes and Holds Host Atoms in the Channel

We reveal how water solvent determines the self‐assembly pathway and stability of organic rosette nanotubes (RNTs) and show their possible functions, using three‐dimensional molecular theory of solvation (a.k.a. 3D‐RISM). Structural water molecules penetrate the pockets on the RNT outer surface, form a wetting monolayer in the RNT channel and bridge RNT rosettes. We predict that the inner water shell might stabilize rare gas atoms inside the RNT channel, and envision molecular devices with RNT channels transporting water or holding guest molecules for targeted delivery.     

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).     

Massively parallel implementation of 3D‐RISM calculation with volumetric 3D‐FFT

A new three‐dimensional reference interaction site model (3D‐RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D‐FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D‐RISM program has a limitation on the number of parallelizations because of the limitations of the slab‐type 3D‐FFT. The volumetric 3D‐FFT relieves this limitation drastically. We tested the 3D‐RISM calculation on the large and fine calculation cell (2048³ grid points) on 16,384 nodes, each having eight CPU cores. The new 3D‐RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D‐RISM program is effective to analyze the hydration properties of the large biomolecular systems. © 2014 Wiley Periodicals, Inc.     

Energies,structures, and electronic properties of molecules in solution with the C-PCM solvation model

The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method.     

Proton solvation in protic and aprotic solvents

Protonation pattern strongly affects the properties of molecular systems. To determine protonation equilibria, proton solvation free energy, which is a central quantity in solution chemistry, needs to be known. In this study, proton affinities (PAs), electrostatic energies of solvation, and pK_A values were computed in protic and aprotic solvents. The proton solvation energy in acetonitrile (MeCN), methanol (MeOH), water, and dimethyl sulfoxide (DMSO) was determined from computed and measured pK_A values for a specially selected set of organic compounds. pK_A values were computed with high accuracy using a combination of quantum chemical and electrostatic approaches. Quantum chemical density functional theory computations were performed evaluating PA in the gas‐phase. The electrostatic contributions of solvation were computed solving the Poisson equation. The computations yield proton solvation free energies with high accuracy, which are in MeCN, MeOH, water, and DMSO ?255.1, ?265.9, ?266.3, and ?266.4 kcal/mol, respectively, where the value for water is close to the consensus value of ?265.9 kcal/mol. The pK_A values of MeCN, MeOH, and DMSO in water correlates well with the corresponding proton solvation energies in these liquids, indicating that the solvated proton was attached to a single solvent molecule. © 2016 Wiley Periodicals, Inc.     

A morphometric approach for the accurate solvation thermodynamics of proteins and ligands

We have developed a versatile method for calculating solvation thermodynamic quantities for molecules, starting from their atomic coordinates. The contribution of each atom to the thermodynamic quantities is estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem, and the coefficients reflecting their solvation properties. This treatment enables us to calculate the solvation free energy with high accuracy despite of the limited computational load. The method can readily be applied to macromolecules in an all‐atom molecular model, allowing the stability of these molecules' structures in solution to be evaluated. © 2013 Wiley Periodicals, Inc.     

Preferential solvation of acridine in binary mixtures

Preferential solvation studies of acridine have been investigated using optical absorption technique. The preferential solvation parameter shows that in dimethyl formamide (DMF)+ethanol mixture, the acridine is preferentially solvated by ethanol in DMF rich region and by DMF in ethanol rich region. In the case of DMF+Carbon tetrachloride mixture acridine is preferentially solvated by DMF.     

Li＋在PC＋DMF混合溶剂中优先溶剂化的13C NMR研究

利用¹³C NMR光谱技术研究了Li^＋在碳酸丙烯酯(PC)＋N,N-二甲基甲酰胺(DMF)混合溶剂中的优先溶剂化现象. 根据溶剂分子中碳原子的化学位移随锂盐浓度的变化关系, 确定了与Li^＋发生配位的原子. 碳原子的配位位移值随混合溶剂组成的变化关系表明, 在LiClO₄＋PC＋DMF混合物中, DMF分子对Li^＋的溶剂化作用较PC分子强. 定量计算得到, 在n(PC)∶n(DMF)＝1∶1(摩尔比)的混合溶剂中, PC与DMF分子数在Li^＋第一溶剂化层中的比率为0.12, 说明Li^＋优先被DMF分子溶剂化.     

Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy

The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme-ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen-atom scheme to GB calculations, a buffer region within the frozen-atom zone is generated based on a user-definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 A for the frozen-atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand-receptor binding conformations and energies in a solvated environment.     

Calculation of solvation free energy using RISM theory for peptide in salt solution

We developed a robust, highly efficient algorithm for solving the full reference interaction site model (RISM) equations for salt solutions near a solute molecule with many atomic sites. It was obtained as an extension of our previously reported algorithm for pure water near the solute molecule. The algorithm is a judicious hybrid of the Newton–Raphson and Picard methods. The most striking advantage is that the Jacobian matrix is just part of the input data and need not be recalculated at all. To illustrate the algorithm, we solved the full RISM equations for a dipeptide (NH₂(SINGLE BOND)CHCH₃(SINGLE BOND)CONH(SINGLE BOND)CHCH₃(SINGLE BOND)COOH) in a 1 M NaCl solution. The extended simple point charge (SPC/E) model was employed for water molecules. Two different conformations of the dipeptide were considered. It was assumed for each conformation that the dipeptide was present either as an un-ionized form or as a zwitterion. The structure of the salt solution near the dipeptide and salt effects on the solvation free energy were also discussed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1724–1735, 1998     

A smooth permittivity function for Poisson–Boltzmann solvation methods

This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid‐based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian‐based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions. 1 © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 608–640, 2001     

Solvatochromism and preferential solvation of Brooker's merocyanine in water–methanol mixtures

The excitation energy of Brooker's merocyanine in water–methanol mixtures shows nonlinear behavior with respect to the mole fraction of methanol, and it was suggested that this behavior is related to preferential solvation by methanol. We investigated the origin of this behavior and its relation to preferential solvation using the three‐dimensional reference interaction site model self‐consistent field method and time‐dependent density functional theory. The calculated excitation energies were in good agreement with the experimental behavior. Analysis of the coordination numbers revealed preferential solvation by methanol. The free energy component analysis implied that solvent reorganization and solvation entropy drive the preferential solvation by methanol, while the direct solute–solvent interaction promotes solvation by water. The difference in the preferential solvation effect on the ground and excited states causes the nonlinear excitation energy shift. © 2017 Wiley Periodicals, Inc.     

Universal solvation model based on conductor‐like screening model

Atomic surface tensions are parameterized for use with solvation models in which the electrostatic part of the calculation is based on the conductor‐like screening model (COSMO) and the semiempirical molecular orbital methods AM1, PM3, and MNDO/d. The convergence of the calculated polarization free energies with respect to the numerical parameters of the electrostatic calculations is first examined. The accuracy and precision of the calculated values are improved significantly by adjusting two parameters that control the segmentation of the solvent‐accessible surface that is used for the calculations. The accuracy of COSMO calculations is further improved by adopting an optimized set of empirical electrostatic atomic radii. Finally, the electrostatic calculation is combined with SM5‐type atomic surface tension functionals that are used to compute the nonelectrostatic portions of the solvation free energy. All parameterizations are carried out using rigid (R) gas‐phase geometries; this combination (SM5‐type surface tensions, COSMO electrostatics, and rigid geometries) is called SM5CR. Six air–water and 76 water–solvent partition coefficients are added to the training set of air–solvent data points previously used to parameterize the SM5 suite of solvation models, thereby bringing the total number of data points in the training set to 2266. The model yields free energies of solvation and transfer with mean unsigned errors of 0.63, 0.59, and 0.61 kcal/mol for AM1, PM3, and MNDO/d, respectively, over all 2217 data points for neutral solutes in the training set and mean unsigned errors of 3.0, 2.7, and 3.1 kcal/mol, respectively, for 49 data points for the ions. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 340–366, 2000     

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.     

The solvation number of ions obtained from their entropies of solvation

The entropy of solvation of an ion contains contributions from i) the change of the volume at its disposal, ii) long-range electrostatic effects, iii) immobilization of solvent molecules in the first solvation shell, and iv) effects on the structure of the solvent. The last item is important in water, but can be ignored in less structured solvents. Standard ionic entropies of transfer from water to a dozen solvents are used for the estimation of the entropy of solvent immobilization, and the (extrapolated) entropy of freezing of the solvent is then used to estimate the number of solvent molecules immobilized.Presented in part at the IX ICNAS (International Conference on Non-Aqueous Solutions), Pittsburgh, PA, August 1984.     

Highly Stable Lithium Metal Batteries Enabled by Regulating the Solvation of Lithium Ions in Nonaqueous Electrolytes

Safe and rechargeable lithium metal batteries have been difficult to achieve because of the formation of lithium dendrites. Herein an emerging electrolyte based on a simple solvation strategy is proposed for highly stable lithium metal anodes in both coin and pouch cells. Fluoroethylene carbonate (FEC) and lithium nitrate (LiNO₃) were concurrently introduced into an electrolyte, thus altering the solvation sheath of lithium ions, and forming a uniform solid electrolyte interphase (SEI), with an abundance of LiF and LiN_xO_y on a working lithium metal anode with dendrite‐free lithium deposition. Ultrahigh Coulombic efficiency (99.96 %) and long lifespans (1000 cycles) were achieved when the FEC/LiNO₃ electrolyte was applied in working batteries. The solvation chemistry of electrolyte was further explored by molecular dynamics simulations and first‐principles calculations. This work provides insight into understanding the critical role of the solvation of lithium ions in forming the SEI and delivering an effective route to optimize electrolytes for safe lithium metal batteries.