真实溶剂似导体屏蔽模型(COSMO-RS)

真实溶剂似导体屏蔽模型（COSMO-RS, Conductor-like screening model for real solvents）是Klamt等人在连续介质溶剂化模式COSMO的基础上,结合统计力学方法发展起来的定量计算溶剂化现象的新方法。本文简单介绍了COSMO-RS的基本原理、概念,以及应用该模式的基本步骤。综述了COSMO-RS应用于离子性化合物、聚合物溶液体系、高温高压体系以及预测复杂生物体系的分配系数和药物设计的进展。评述了简化分子表面屏蔽电荷分布计算的COSMOfrag和GC-COSMO （group contribution COSMO）方法,对不同版本的COSMO-RS之间以及其与基团贡献方法的对比研究也作了详细的讨论,并指出了COSMO-RS的不足之处和进一步发展该模式的建议。     

Calculation of solvent shifts on electronic g-tensors with the conductor-like screening model (COSMO) and its self-consistent generalization to real solvents (direct COSMO-RS)

The conductor-like screening model (COSMO) was used to investigate the solvent influence on electronic g-values of organic radicals. The previously studied diphenyl nitric oxide and di-tert-butyl nitric oxide radicals were taken as test cases. The calculations employed spin-unrestricted density functional theory and the BP and B3LYP density functionals. The g-tensors were calculated as mixed second derivative properties with respect to the external magnetic field and the electron magnetic moment. The first-order response of the Kohn-Sham orbitals with respect to the external magnetic field was determined through the coupled-perturbed DFT approach. The spin-orbit coupling operator was treated using an accurate multicenter spin-orbit mean-field (SOMF) approach. Provided that important hydrogen bonds are explicitly modeled by a supermolecule approach and that the basis set is sufficiently saturated, the COSMO calculations lead to accurate predictions of isotropic g-shifts with deviations of not more than 100 ppm relative to experiment. Very accurate results were obtained by employing a recently developed self-consistent modification of the COSMO method to real solvents (COSMO-RS), which we briefly introduce in this paper as direct COSMO-RS (D-COSMO-RS). This model gives isotropic g-shifts of similar high accuracy for water without using the supermolecule approach. This is an important result because it solves many of the problems associated with the supermolecule approach such as local minima and the choice of a suitable model system. Thus, the self-consistent D-COSMO-RS incorporates some specific solvation effects into continuum models, in particular it appears to successfully model the effects of hydrogen bonding. Although not yet widely validated, this opens a novel approach for the calculation of properties which so far only could be calculated by the inclusion of explicit solvent molecules in continuum solvation methods.     

Blind prediction test of free energies of hydration with COSMO-RS

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with COSMO-RS, a statistical thermodynamics treatment of surface interactions, simulations, has been used for the direct, blind prediction of free energies of hydration within the SAMPL challenge. Straight application of the latest version of the COSMOtherm implementation in combination with a rigorous conformational sampling yielded a predictive accuracy of 1.56 kcal/mol (RMSE) for the 23 compounds of the blind prediction dataset. Due to the uncertainties of the extrapolations and assumptions involved in the derivation of the experimental data, the accuracy of the predicted data may be considered to be within the noise level of the experimental data.     

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.     

Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme

The treatment of the solvation charges using Gaussian functions in the polarizable continuum model results in a smooth potential energy surface. These charges are placed on top of the surface of the solute cavity. In this article, we study the effect of the solute cavity (van der Waals-type or solvent-excluded surface-type) using the Gaussian charge scheme within the framework of the conductor-like polarizable continuum model on (a) the accuracy and computational cost of the self-consistent field (SCF) energy and its gradient and on (b) the calculation of free energies of solvation. For that purpose, we have considered a large set of systems ranging from few atoms to more than 200 atoms in different solvents. Our results at the DFT level using the B3LYP functional and the def2-TZVP basis set show that the choice of the solute cavity does neither affect the accuracy nor the cost of calculations for small systems (< 100 atoms). For larger systems, the use of a vdW-type cavity is recommended, as it prevents small oscillations in the gradient (present when using a SES-type cavity), which affect the convergence of the SCF energy gradient. Regarding the free energies of solvation, we consider a solvent-dependent probe sphere to construct the solvent-accessible surface area required to calculate the nonelectrostatic contribution to the free energy of solvation. For this part, our results for a large set of organic molecules in different solvents agree with available experimental data with an accuracy lower than 1 kcal/mol for both polar and nonpolar solvents.     

Solvent system selection in counter-current chromatography using conductor-like screening model for real solvents

The aim of this investigation was to minimize the experimental effort for solvent system selection in counter-current chromatography. The separation mechanism in counter-current chromatography is based exclusively on the partitioning of the solute between the two liquid phases. Therefore, a quantum chemical method combined with statistical thermodynamics (conductor-like screening model for real solvents, COSMO-RS) was used for the prediction of the partition coefficient. A comparison of the experimental and predicted data for five model solutes systems demonstrated the potential of the use of COSMO-RS as a screening tool for the solvent system selection.     

Chromatographic and spectroscopic methods for the determination of solvent properties of room temperature ionic liquids

Room temperature ionic liquids are novel solvents with favorable environmental and technical features. Synthetic routes to over 200 room temperature ionic liquids are known but for most ionic liquids physicochemical data are generally lacking or incomplete. Chromatographic and spectroscopic methods afford suitable tools for the study of solvation properties under conditions that approximate infinite dilution. Gas-liquid chromatography is suitable for the determination of gas-liquid partition coefficients and activity coefficients as well as thermodynamic constants derived from either of these parameters and their variation with temperature. The solvation parameter model can be used to define the contribution from individual intermolecular interactions to the gas-liquid partition coefficient. Application of chemometric procedures to a large database of system constants for ionic liquids indicates their unique solvent properties: low cohesion for ionic liquids with weakly associated ions compared with non-ionic liquids of similar polarity; greater hydrogen-bond basicity than typical polar non-ionic solvents; and a range of dipolarity/polarizability that encompasses the same range as occupied by the most polar non-ionic liquids. These properties can be crudely related to ion structures but further work is required to develop a comprehensive approach for the design of ionic liquids for specific applications. Data for liquid-liquid partition coefficients is scarce by comparison with gas-liquid partition coefficients. Preliminary studies indicate the possibility of using the solvation parameter model for interpretation of liquid-liquid partition coefficients determined by shake-flask procedures as well as the feasibility of using liquid-liquid chromatography for the convenient and rapid determination of liquid-liquid partition coefficients. Spectroscopic measurements of solvatochromic and fluorescent probe molecules in room temperature ionic liquids provide insights into solvent intermolecular interactions although interpretation of the different and generally uncorrelated "polarity" scales is sometimes ambiguous. All evidence points to the ionic liquids as a unique class of polar solvents suitable for technical development. In terms of designer solvents, however, further work is needed to fill the gaps in our knowledge of the relationship between ion structures and physicochemical properties.     

Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS

Performance of COSMO-RS method as a tool for partition and distribution modeling in 20 solvent pairs—composed of neutral or acidic aqueous solution and organic solvents of different polarity, ranging from alcohols to toluene and hexane—was evaluated. Experimental partition/distribution data of lignin-related and drug-like compounds (neutral, acidic, moderately basic) were used as reference. Several aspects of partition modeling were addressed: accounting for mutual saturation of aqueous and organic phases, variability of systematic prediction errors across solvent pairs, taking solute ionization into account. COSMO-RS was found to predict extraction outcome for both ligneous and drug-like compounds in various solvent pairs fairly well without any additional empirical input. The solvent-specific systematic errors were found to be moderate, despite being statistically significant, and related to the solvent hydrophobicity. Accounting for mutual solubilities of the two liquids was proven crucial in cases where water was considerably soluble in the organic solvent. The root mean square error of a priori logP prediction varied, depending mainly on the solvent pair, from 0.2 to 0.7, overall value being 0.6 log units. The accuracy was higher in case of hydrophilic than hydrophobic solvents. The logD predictions were less accurate, due to pK_a prediction being an additional source of error, and also because of the complexity of modeling the behaviour of ionic species in the two-phase system. A simple correction for partitioning of free ions was found to notably improve logD prediction accuracy in case of the most hydrophilic organic phase (butanol/water).     

Quantum chemical model of solvation for calculation of electrode potentials of redox processes involving ferrocene,cobaltocene, and their ions

Quantum chemical calculations of solvation energy for ferrocene and cobaltocene molecules and their ionic forms in water, acetonitrile, methanol, and acetone are performed in terms of the B3LYP density functional method by taking into account solvation effects and using the polarized continuum model (PCM). Standard electrode potentials of the corresponding redox pairs, the effect of solvent on them, and the overall energy of the transfer of cobaltocene cation and anion between two solvents are calculated. The calculation results well agree with the available experimental data. The present study provides sufficiently reliable grounds for the application of an ion—metallocene molecule redox pair as a pilot system for the comparison of electrode potentials and solvation energies in different solvents.     

Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms

Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.     

COSMOsim: bioisosteric similarity based on COSMO-RS sigma profiles

A novel approach for the quantification of drug similarity is proposed, which makes use of the surface polarities, that is, conductor surface polarization charge densities sigma, as defined in the quantum chemically based conductor-like screening model for realistic solvation(COSMO-RS). The histogram of these surface polarities, the so-called sigma profiles, have been proven to be the key for the calculation of all kinds of partition and adsorption coefficients and, therefore, of relevant absorption, distribution, metabolism, and excretion parameters such as solubility, pKa, log BB, and many others. They also carry a large part of the information required for the estimation of desolvation and binding processes responsible for receptor binding and enzyme inhibition of drug molecules. Thus, a large degree of similarity with respect to the sigma profiles appears to be a necessary condition for drugs of similar physiological action. Driven by this insight, we propose a sigma-profile-based drug similarity measure COSMOsim for the detection of new bioisosteric drug candidates. In several examples, we demonstrate its statistical and pharmaceutical plausibility, its practicability for real drug research projects, and its unique independence from the chemical structure, which enables scaffold hopping in a natural way.     

Solvation enthalpies of neutral solutes in water and octanol

The balance between electrostatic and non-electrostatic enthalpic contributions to the free energy of solvation of a series of neutral solutes in water and n-octanol is examined by means of continuum solvation calculations based on the Miertus–Scrocco–Tomasi (MST) method. The experimental data indicate that the solvation enthalpy of hydrocarbons is very similar in water and n-octanol, and that the enthalpic contribution measured for polar compounds is larger in water than in n-octanol. According to MST calculations, the different magnitude of the solvation enthalpy found for polar compounds in the two solvents can be largely attributed to the electrostatic contribution. Moreover, the results point out that there is close resemblance between the non-electrostatic components for both hydrocarbons and polar compounds in the two solvents. Finally, the results show the power of current continuum models like MST to dissect the total free energy of solvation in entropic and enthalpic contributions and suggest that new refinements of continuum solvation models should include not only the fitting to solvation free energies, but also their enthalpic components.     

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.     

Nonequilibrium solvation for vertical photoemission and photoabsorption processes using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model

In this paper, we present the theory and implementation of a nonequilibrium solvation model for the symmetry-adapted cluster (SAC) and symmetry-adapted cluster-configuration interaction (SAC-CI) method in the polarizable continuum model. For nonequilibrium solvation, we adopted the Pekar partition scheme in which solvent charges are divided into dynamical and inertial components. With this nonequilibrium solvation scheme, a vertical transition from an initial state to a final state may be described as follows: the initial state is described by equilibrium solvation, while in the final state, the inertial component remains in the solvation for the initial state; the dynamical component will be calculated self-consistently for the final state. The present method was applied to the vertical photoemission and absorption of s-trans acrolein and methylenecyclopropene. The effect of nonequilibrium solvation was significant for a polar solvent.     

Thermodynamics of chemical reactions with COSMO‐RS: The extreme case of charge separation or recombination

Many technically relevant chemical processes in the condensed phase involve as elementary reactive steps the formation of ions from neutral species or, as the opposite, recombination of ions. Such reactions that generate or annihilate charge defy the standard gas phase quantum chemical treatment, and also continuum solvation models are only partially able to account for the right amount of stabilization in solution. In this work, for such types of reaction, a solvation treatment involving the COSMO‐RS method is assessed, which leads to improved results, i.e., errors of only around 10 kJ/mol for both protic and aprotic solvents. The examples discussed here comprise protolysis reactions and organo halide heterolysis, for both of which a comparison with reliable experimental data is possible. It is observed that for protolysis, the quality of results does not strongly depend on the quantum chemical method used for energy calculation. In contrast, in the case of heterolytic carbon‐chlorine bond cleavage, clearly better results are obtained for higher correlated (coupled cluster) methods or the density functional M06‐2X, which is well known for its accuracy if applied to organic chemistry. This hints at least that the right answer is obtained for the right reason and not due to a compensation of errors from gas phase thermodynamics with those from the solvation treatment. Problems encountered with certain critical solvents or upon decomposing Gibbs free energies into heats or entropies of reaction are found to relate mostly to the parameterization of the H‐bonding term within COSMO‐RS. © 2012 Wiley Periodicals, Inc.     

Monte Carlo simulations of the solution structure of simple alcohols in water-acetonitrile mixtures

Monte Carlo simulations have been performed to explore the solution structure of ethyl, isopropyl, isobutyl, and tertiary butyl alcohols in pure water, pure acetonitrile, and different mixtures of the two solvents. The explicit solvent studies in NpT ensembles at T = 298 K illustrate that the solute "discriminates" the solvent's components and that the composition of the first solvation shell differs from that of the bulk solution. Since the polarizable continuum dielectric method (PCM) does not presently model the solvation of molecules with both polar and apolar sites in mixed protic solvents, we suggest a direction for further program development wherein a continuum dielectric method would accept more than one solvent and the solute sites would be solvated by user-defined solvent components. The prevailing solvation model will be determined upon the lowest free energy calculated for a particular solvation pattern of the solute having a specific conformational/tautomeric state. Characterization of equilibrium hydrogen-bond formation becomes a complicated problem that depends on the chemical properties of the solute and its conformation, as well as upon the varying nature of the first solvation shell. For example, while the number of hydrogen bonds to secondary and tertiary alcohol solutes are nearly constant in pure water and in water-acetonitrile mixtures with at least 50% water content, the number of hydrogen bonds to primary alcohols gradually decreases for most of their conformations when acetonitrile content is increased. Nonetheless, the calculations indicate that O-H...O(water) hydrogen bonds are still possible in a small fraction of the arrangements for the solution models with water content of 30% or less. The isopentene solute does not form any observable hydrogen bonds, despite having an electron-rich, double-bond site.