An efficient fluctuating charge model for transition metal complexes

A fluctuating charge model for transition metal complexes, based on the Hirshfeld partitioning scheme, spectroscopic energy data from the NIST Atomic Spectroscopy Database and the electronegativity equalization approach, has been developed and parameterized for organic ligands and their high‐ and low‐spin Fe^II and Fe^III, low‐spin Co^III and Cu^II complexes, using atom types defined in the Momec force field. Based on large training sets comprising a variety of transition metal complexes, a general parameter set has been developed and independently validated which allows the efficient computation of geometry‐dependent charge distributions in the field of transition metal coordination compounds. © 2013 Wiley Periodicals, Inc.     

Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments

Cumulative Atomic Multipole Moments were calculated for all natural amino acids and symmetric cyclic hexapeptides within Self‐Consisted Field (SCF) and Density Functional Theory (DFT) approaches using a standard 6‐31G(d,p) basis set. These data were used to analyze in detail the quality and the conformational and the intermolecular transferability of molecular charge distributions expressed in the atomic multipole form. Intermolecular interaction energies were reproduced reasonably by CAMM transformed from other conformations. Good transferability of CAMM based model was also achieved between similar molecular environments, which opens a route to modeling electrostatic effects in highly symmetric (e.g., crystalline) systems. Transferability deficiencies of various charge distribution models were analyzed and attributed to different levels of multipole expansion. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1082–1097, 2001     

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform–water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER‐99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld‐I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld‐I method related to the unstable isolated anionic nitrogen pro‐atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc.     

利用双水相分离回收离子液体的研究进展

研究离子液体的分离与回收对于减少离子液体对环境的影响、提高离子液体的利用效率、降低离子液体的应用成本、促进离子液体的工业应用具有重要的意义.本文重点综述了利用无机盐-离子液体双水相、糖-离子液体双水相、聚合物-离子液体双水相和CO2诱导的离子液体双水相技术分离回收离子液体的研究进展,分析了影响离子液体分离回收的关键因素,评价了不同离子液体双水相体系的优缺点,展望了该领域的发展方向及面临的挑战.     

Temperature-controlled ionic liquid-liquid-phase microextraction for the pre-concentration of lead from environmental samples prior to flame atomic absorption spectrometry

Hydrophobic ionic liquid could be dispersed into infinite droplets under driving of high temperature, and then they can aggregate as big droplets at low temperature. Based on this phenomenon a new liquid-phase microextraction for the pre-concentration of lead was developed. In this experiment, lead was transferred into its complex using dithizone as chelating agent, and then entered into the infinite ionic liquid drops at high temperature. After cooled with ice-water bath and centrifuged, lead complex was enriched in the ionic liquid droplets. Important parameters affected the extraction efficiency had been investigated including the pH of working solution, amount of chelating agent, volume of ionic liquid, extraction time, centrifugation time, and temperature, etc. The results showed that the usually coexisting ions containing in water samples had no obvious negative effect on the recovery of lead. The experimental results indicated that the proposed method had a good linearity (R = 0.9951) from 10 ng mL⁻¹ to 200 ng mL⁻¹. The precision was 4.4% (RSD, n = 6) and the detection limit was 9.5 ng mL⁻¹. This novel method was validated by determination of lead in four real environmental samples for the applicability and the results showed that the proposed method was excellent for the future use and the recoveries were in the range of 94.8-104.1%.     

Python implementation of the restrained electrostatic potential charge model

The restrained electrostatic potential (RESP) charge model is widely used in molecular dynamics simulations, especially for the AMBER and GAFF force fields. We have implemented the RESP scheme using the accessible and widely used Python language and the NumPy numerical library. This article provides a programming-oriented introduction to the RESP scheme and highlights some of the features of NumPy that are useful in scientific computing.     

Effect of atomic charge,solvation, entropy,and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

The molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and MM-generalized-Born surface area (MM-GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM-PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM-PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO-3G and B3LYP/cc-pVTZ), (ii) the MM-GBSA approach over MM-PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer-aided drug design. © 2012 Wiley Periodicals, Inc.     

A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges

We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods.     

Plasmon resonances and plasmon‐induced charge transport in linear atomic chains

In linear hydrogen atomic chains, plasmon resonances and plasmon‐induced charge transport are studied by time‐dependent density functional theory. For the large linear chain, it is a general phenomenon that, in the longitudinal excitation, there are high‐energy resonances and a large low‐energy resonance. The energy of the large low‐energy resonance conforms to the results calculated by the classical Drude model. In order to explain the formation mechanism of the high‐energy resonances, we present a simple harmonic oscillator model. This model may reasonably account for the relationship between low‐energy and high‐energy resonances, and has a certain degree of universality. As the interatomic distance decreases, the current shows a gradual transition from insulator to metal. The current enhancement mainly depends on the local field enhancement associated with plasmon excitation, and the enhanced electron delocalization effect as a result of the decrease of the interatomic distance. © 2013 Wiley Periodicals, Inc.     

Design of functional guanidinium ionic liquid aqueous two-phase systems for the efficient purification of protein

A series of novel cationic functional hexaalkylguanidinium ionic liquids and anionic functional tetraalkylguanidinium ionic liquids have been devised and synthesized based on 1,1,3,3-tetramethylguanidine. The structures of the ionic liquids (ILs) were confirmed by ¹H nuclear magnetic resonance (¹H NMR) and 13C nuclear magnetic resonance (13C NMR) and the production yields were all above 90%. Functional guanidinium ionic liquid aqueous two-phase systems (FGIL-ATPSs) have been first designed with these functional guanidinium ILs and phosphate solution for the purification of protein. After phase separation, proteins had transferred into the IL-rich phase and the concentrations of proteins were determined by measuring the absorbance at 278 nm using an ultra violet visible (UV–vis) spectrophotometer. The advantages of FGIL-ATPSs were compared with ordinary ionic liquid aqueous two-phase systems (IL-ATPSs). The proposed FGIL-ATPS has been applied to purify lysozyme, trypsin, ovalbumin and bovine serum albumin. Single factor experiments were used to research the effects of the process, such as the amount of ionic liquid (IL), the concentration of salt solution, temperature and the amount of protein. The purification efficiency reaches to 97.05%. The secondary structure of protein during the experimental process was observed upon investigation using UV–vis spectrophotometer, Fourier-transform infrared spectroscopy (FT-IR) and circular dichroism spectrum (CD spectrum). The precision, stability and repeatability of the process were investigated. The mechanisms of purification were researched by dynamic light scattering (DLS), determination of the conductivity and transmission electron microscopy (TEM). It was suggested that aggregation and embrace phenomenon play a significant role in the purification of proteins. All the results show that FGIL-ATPSs have huge potential to offer new possibility in the purification of proteins.     

Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments

Summary In this paper a database of atomic residual charges has been constructed for all the molecular fragments defined previously in a combinatorial search of the Cambridge Structural Database. The charges generated for the atoms in each fragment are compared with charges calculated for whole molecules containing those fragments. The fragment atomic charges lie within 1 S.D. of the mean for 68%, and within 2 S.D. for 91%, of the atoms whose charges were computed for whole molecules. The actual charges on any atom are strongly influenced by the adjacent connected atoms. There is a large spread of atomic residual charge within the fragments database.     

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water.     

Intrinsic minimal atomic basis representation of molecular electronic wavefunctions

The problem of finding an effective minimal atomic basis that spans the exact occupied wavefunctions of a mean‐field theory at a given molecular geometry, which has a number of special properties, is studied and a new general procedure is developed that (1) solves for a raw minimal set of strongly atom‐centered functions—products of spherical harmonics and molecule‐optimized radial parts—that approximately span the occupied molecular wavefunctions and minimize the sum of their energies, (2) uses projection operators to get a new set of deformed atom‐centered functions that exactly span the occupied space and fall into core and valence subsets, (3) applies a new zero‐bond‐dipole orthogonalization scheme to the core‐orthogonalized valence subset so that for each two‐center product of these functions the projection of its dipole moment along the line going through the two centers is zero. The resulting effective minimal atomic basis is intrinsic to the molecular problem and does not need a free‐atoms input. Some interesting features of the zero‐bond‐dipole orthogonalization are showing up in the atomic population analysis of a diverse set of molecules. The new procedure may be useful for the interpretation of electronic structure, for the construction of model Hamiltonians in terms of transferable molecular integrals, and for the definition of active valence space in the treatment of electron correlation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

计算离子液体溶液汽液相平衡的分子热力学模型

用平均球近似理论、微扰理论和UNIFAC基团贡献方法分别考虑离子之间的长程静电作用、离子与溶剂之间的中程静电作用以及所有粒子之间的短程作用,本文提出了一种新的分子热力学模型,可用于离子液体溶液中溶剂活度系数的计算.通过对含烷基咪唑磷酸酯类离子液体与水、甲醇或乙醇组成的9个二元体系的饱和蒸汽压数据进行关联,获得了相关的模型参数,即溶剂的分子直径和基团之间的交互作用能参数.溶剂活度系数及饱和蒸汽压的计算结果与实验值的平均偏差为1.40%,符合良好,因此本模型可望用于含离子液体体系汽液相平衡的预测.     

Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations

We present an alternative approach to determine "density-dependent property"-derived charges for molecules in the condensed phase. In the case of a solution, it is essential to take into consideration the electron polarization of molecules in the active site of this system. The solute and solvent molecules in this site have to be described by a quantum mechanical technique and the others are allowed to be treated by a molecular mechanical method (QM/MM scheme). For calculations based on this scheme, using the forces and interaction energy as density-dependent property our charges from interaction energy and forces (CHIEF) approach can provide the atom-centered charges on the solute atoms. These charges reproduce well the electrostatic potentials around the solvent molecules and present properly the picture of the electron density of the QM subsystem in the solution system. Thus, the CHIEF charges can be considered as the atomic charges under the conditions of the QM/MM simulation, and then enable one to analyze electrostatic interactions between atoms in the QM and MM regions. This approach would give a view of the QM nuclei and electrons different from the conventional methods.     

Characterization of hexacationic imidazolium ionic liquids as effective and highly stable gas chromatography stationary phases

Polycationic ionic liquids (ILs) are an attractive class of ILs with great potential applicability as gas chromatography stationary phases. A family of hexacationic imidazolium ILs derived from the cycloalkanol family was chemically first prepared in a straightforward manner and then applied for analytical separation purposes. Four tuneable engineering vectors, namely cation ring size structure, anion nature, spatial disposition of cycloalkanol substituents and O‐substitution, were considered as experimental parameters for the design of the desired ionic liquids. A total number of five new phases based on a common benzene core respectively exhibited column efficiencies around to 2500 plates/m, broad operating temperature ranges and also, even more importantly, good thermal stabilities (bleeding temperature between 260 and 365°C), finding variations in the selectivity and analytes elution orders depending on the IL structures. Their solvation characteristics were evaluated using the Abraham solvation parameter model, establishing clear correlations between their cation structure and retention capability with respect to certain analytes. The study of relationships between the ILs structure and solvation parameters gives us an idea of the IL stationary phase to be used for specific separations.     

Fast tools for calculation of atomic charges well suited for drug design1

Two novel approaches to construct empirical schemes for partial atomic charge calculation were proposed. The charge schemes possess important benefits. First, they produce both topologically symmetrical and environment dependent charges. Second, they can be parameterised to reasonably reproduce ab initio molecular electrostatic potential (MEP), which guarantees their successful use in molecular modelling. To validate the approaches, the parameters of the proposed charge schemes were fitted to best reproduce MEP simultaneously on grids around a set of 227 diverse organic compounds. The residual errors in MEP reproduction due to calculated atomic charges were compared to those due to charges from known charge schemes.