基于原子表面的蛋白质水合自由能预测模型

提出了一种计算蛋白质水合自由能的简化模型（SAWSA 2）.模型把蛋白质分子中的原子分为20种不同的原子类型,通过每类原子的溶剂可及化表面以及相应的溶剂化参数,就可以得到分子的水合自由能.不同原子类型的溶剂化参数通过110个蛋白质分子水合自由能拟合得到,水合自由能的标准值采用了基于求解Possion-Boltzmann方程（PB）以及分子表面计算（SA） 相结合的方法.采用得到的模型,预测了20个蛋白质分子的水合自由能,预测值的相对值和绝对值都能和PB/SA的计算值很好地吻合,大大优于两种已报导的水合自由能模型.     

一组和AMBER力场配合的普适波恩模型参数

提出了一套和AMBER力场相匹配的普适波恩模型参数.新的参数集包含21种原子类型的初始半径和屏蔽因子.参数通过遗传算法拟合359个小分子水合自由能的实验值得到.采用新的参数，预测了44个小分子的水合自由能，预测值和实验值能很好地吻合，而且大大优于采用Jayaram参数得到的结果.此外，采用新的参数，还预测了15个蛋白质的水合自由能，预测值和PB/SA预测得到的结果能很好地吻合.     

基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.     

Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia

The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pK_a of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be −1192 kJ mol^–1, whereas the absolute solvation enthalpy is evaluated to be −1214 kJ mol^–1. © 2019 Wiley Periodicals, Inc.     

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.     

Dramatic Increase in the Oxygen Reduction Reaction for Platinum Cathodes from Tuning the Solvent Dielectric Constant

Hydrogen fuel cells (FC) are considered essential for a sustainable economy based on carbon‐free energy sources, but a major impediment are the costs. First‐principles quantum mechanics (density functional theory including solvation) is used to predict how the energies and barriers for the mechanistic steps of the oxygen reduction reaction (ORR) over the fcc(111) platinum surface depend on the dielectric constant of the solvent. The ORR kinetics can be strongly accelerated by decreasing the effective medium polarizability from the high value it has in water. Possible ways to realize this experimentally are suggested. The calculated volcano structure for the dependence of rate on solvent polarization is considered to be general, and should be observed in other electrochemical systems.     

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.     

Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

A free energy perturbation (FEP) method was developed that uses ab initio quantum mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating the surroundings. Like our earlier results using AM1 semi empirical QMs, the ab initio QM/MM-based FEP method was shown to accurately calculate relative solvation free energies for a diverse set of small molecules that differ significantly in structure, aromaticity, hydrogen bonding potential, and electron density. Accuracy was similar to or better than conventional FEP methods. The QM/MM-based methods eliminate the need for time-consuming development of MM force field parameters, which are frequently required for drug-like molecules containing structural motifs not adequately described by MM. Future automation of the method and parallelization of the code for Linux 128/256/512 clusters is expected to enhance the speed and increase its use for drug design and lead optimization.     

Solvation of monovalent anions in acetonitrile and N,N-dimethylformamide: Parameterization of the IEF-PCM model

The present work reports the parameterization of the polarizable continuum model for predicting the free energies of solvation for monovalent anions in acetonitrile and N,N-dimethylformamide. The parameterization of the model for acetonitrile employed the experimental free energies of solvation for a set of 12 charged solutes, containing H, C, N, O, S, F, Cl, Br, and I atoms. For the N,N-dimethylformamide solutions, experimental solvation free energies for 11 monovalent anions were used. A mean absolute error of 0.7 kcal/mol in the solvation free energies has been achieved for the 12 anions in acetonitrile, whereas the mean absolute error for the 11 anions corresponds to 0.5 kcal/mol in N,N-dimethylformamide. These results indicate that the polarizable continuum model is a suitable methodology for the study of thermodynamic effects in solutions of monovalent anions in both solvents.     

Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed-charge Model and the Reference Potential Strategy

The IPolQ-Mod charges, which are the average of two charge sets fitted in vacuum state and condensed phase, take account of polarization effect implicitly in the solvation free energy calculation. However, the performance of the IPolQ-Mod charges sensitively depends on the QM levels used to generate the electrostatic potential from which the charges are fitted. In addition, the forces on atoms are not accurate theoretically in the molecular dynamics (MD) simulation as the solvent only feels the electrostatic potential of a half-polarized density of the solute according to the derivation of the IPolQ-Mod charges. To study these issues in detail, the IPolQ-Mod charges are combined with the reference potential (RP) strategy to predict the solvation free energies in the present study. It is found that the thermodynamic perturbation (TP) corrections utilizing total energy difference and interaction energy difference are almost the same and free of bias. The solvation free energies estimated by the RP method match very well with those obtained by applying IPolQ-Mod charges into MD simulation directly. By means of the RP strategy, the performances of the IPolQ-Mod charges with the change of the strength of the exact HF exchange in several DFT functionals are determined effectively. Although the “optimal” strengths are found in B3LYP and LC-ωPBE, the improvements over the default strength are not too much. In addition to the IPolQ-Mod charges, other charge models like bond charge correction (BCC) charges could also be combined with the RP strategy to study the thermodynamic properties like solvation free energy. © 2019 Wiley Periodicals, Inc.     

Theoretical investigation of isotopic scrambling mechanisms in 2-chloroethyl methyl sulfide

Ab initio and semiempirical molecular orbital calculations have been applied to study the concerted and stepwise isotopic scrambling mechanisms of 2-chloroethyl methyl sulfide in the gas phase and in aqueous solution. The calculations reveal the structural details of the reactants, transition structures, and intermediates involved in this reaction and provide relative energy estimates. The concerted mechanism is found to be competitive with the stepwise mechanism in the gas phase, but the stepwise mechanism is favored in aqueous solution as no true transition structure for the concerted mechanism could be found using the solvation models. A combined approach of evaluating solvation energies with the generalized-Bom-plus-surface-tensions SM _x solvation models of Cramer and Truhlar at ab initio optimized geometries is found to deliver the best agreement with experimentally determined reaction barriers. Together with the recent experimental results of McManus and co-workers, the present study provides insights into the controlling factors involved in the elementary reaction steps of sulfur mustards and a solid foundation for investigations into more complex reactions of related compounds.     

A Computational Protocol Combining DFT and Cheminformatics for Prediction of pH-Dependent Redox Potentials

Discovering new materials for energy storage requires reliable and efficient protocols for predicting key properties of unknown compounds. In the context of the search for new organic electrolytes for redox flow batteries, we present and validate a robust procedure to calculate the redox potentials of organic molecules at any pH value, using widely available quantum chemistry and cheminformatics methods. Using a consistent experimental data set for validation, we explore and compare a few different methods for calculating reaction free energies, the treatment of solvation, and the effect of pH on redox potentials. We find that the B3LYP hybrid functional with the COSMO solvation method, in conjunction with thermal contributions evaluated from BLYP gas-phase harmonic frequencies, yields a good prediction of pH = 0 redox potentials at a moderate computational cost. To predict how the potentials are affected by pH, we propose an improved version of the Alberty-Legendre transform that allows the construction of a more realistic Pourbaix diagram by taking into account how the protonation state changes with pH.     

Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction‐Field Method for the Solvation Free Energies of Amino Acid Side‐Chain Analogs

Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model’s accuracy in predicting conformational free‐energy differences. The solvation free energies of neutral and polar amino acid side‐chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol^?1. The new parameters were evaluated for charged side‐chain analogs. The HADES results were compared with explicit‐solvent, generalized Born, Poisson–Boltzmann, and QM‐based methods. The potentials of mean force (PMFs) between pairs of side‐chain analogs obtained by using HADES and explicit‐solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.     

Toward robust computational electrochemical predicting the environmental fate of organic pollutants

A number of density functionals was utilized for the calculation of electron attachment free energy for nitrocompounds, quinones and azacyclic compounds. Different solvation models have been tested on the calculation of difference in free energies of solvation of oxidized and reduced forms of nitrocompounds in aqueous solution, quinones in acetonitrile, and azacyclic compounds in dimethylformamide. Gas‐phase free energies evaluated at the mPWB1K/tzvp level and solvation energies obtained using SMD model to compute solvation energies of neutral oxidized forms and PCM(Pauling) to compute solvation energies of anion‐radical reduced forms provide reasonable accuracy of the prediction of electron attachment free energy, difference in free solvation energies of oxidized and reduced forms, and as consequence yield reduction potentials in good agreement with experimental data (mean absolute deviation is 0.15 V). It was also found that SMD/M05‐2X/tzvp method provides reduction potentials with deviation of 0.12 V from the experimental values but in cases of nitrocompounds and quinones this accuracy is achieved due to the cancelation of errors. To predict reduction ability of naturally occurred iron containing species with respect to organic pollutants we exploited experimental data within the framework of Pourbaix (E_h ? pH) diagrams. We conclude that surface‐bound Fe(II) as well as certain forms of aqueous Fe(II)_aq are capable of reducing a variety of nitroaromatic compounds, quinones and novel high energy materials under basic conditions (pH > 8). At the same time, zero‐valent iron is expected to be active under neutral and acidic conditions. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations

Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calculations lead to large variations of calculated absolute and relative electrostatic binding free energies. Hence, parametrization of solvation effects based on hydration data, although a necessary condition, is not sufficient to guarantee its transferability to the calculation of binding free energies in solution.     

Breaking the polar‐nonpolar division in solvation free energy prediction

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature‐function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson–Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave‐one‐out test gives an optimal root‐mean‐square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94 molecules and its associated training set, the present approach was carefully compared with a classic solvation model based on weighted solvent accessible surface area. © 2017 Wiley Periodicals, Inc.     

The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method

We present a model to calculate the free energies of solvation of small organic compounds as well as large biomolecules. This model is based on a generalized Born (GB) model and a self-consistent charge-density functional theory-based tight-binding (SCC-DFTB) method with the nonelectrostatic contributions to the free energy of solvation modeled in terms of solvent-accessible surface areas (SA). The parametrization of the SCC-DFTB/GBSA model has been based on 60 neutral and six ionic molecules composed of H, C, N, O, and S, and spanning a wide range of chemical groups. Effective atomic radii as parameters have been obtained through Monte Carlo Simulated Annealing optimization in the parameter space to minimize the differences between the calculated and experimental free energies of solvation. The standard error in the free energies of solvation calculated by the final model is 1.11 kcal mol(-1). We also calculated the free energies of solvation for these molecules using a conductor-like screening model (COSMO) in combination with different levels of theory (AM1, SCC-DFTB, and B3LYP/6-31G*) and compared the results with SCC-DFTB/GBSA. To assess the efficiency of our model for large biomolecules, we calculated the free energy of solvation for a HIV protease-inhibitor complex containing 3,204 atoms using the SCC-DFTB/GBSA and the SCC-DFTB/COSMO models, separately. The computed relative free energies of solvation are comparable, while the SCC-DFTB/GBSA model is three to four times more efficient, in terms of computational cost.     

Evaluation of DFT Methods and Implicit Solvation Models for Anion‐Binding Host‐Guest Systems

Although supramolecular chemistry is traditionally an experimental discipline, computations have emerged as important tools for the understanding of supramolecules. We have explored how well commonly used density functional theory quantum mechanics and polarizable continuum solvation models can calculate binding affinities of host‐guest systems. We report the calculation of binding affinities for eight host–guest complexes and compare our results to experimentally measured binding free energies that span the range from ?2.3 to ?6.1 kcal mol^?1. These systems consist of four hosts (biotin[6]uril, triphenoxymethane, cryptand, and bis‐thiourea) with different halide ions (F^?, Cl^?, Br^?) in various media including organic and aqueous. The mean average deviation (MAD) of calculated from measured ΔG_a is 2.5 kcal mol^?1 when using B3LYP‐D3 with either CPCM or PCM. This MAD value lowers even more by eliminating two outliers: 1.1 kcal mol^?1 for CPCM and 1.2 kcal mol^?1 for PCM. The best DFT and implicit solvation model combination that we have studied is B3LYP?D3 with either CPCM or PCM.