Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

Factors affecting the strengths of σ-hole electrostatic potentials

A σ-hole is a region of diminished electronic density on the extension of a covalent bond to an atom. This region often exhibits a positive electrostatic potential, which allows attractive noncovalent interactions with negative sites. In this study, we have systematically examined the dependence of σ-hole potentials upon (a) the atom having the σ-hole, and (b) the remainder of the molecule. We demonstrate that not only relative electron-attracting powers need to be considered, but also relative charge capacities (or polarizabilities), and that other factors can also have significant roles.     

PHOTOELECTRON SPECTROSCOPY STUDY OF AMMONIA-INDUCED CHANGES IN ELECTROSTATICALLY-ASSEMBLED CONJUGATED POLYMER FILMS

ABSTRACT

Exposure of electrostatically assembled polyelectrolyte films comprised of the anionic carboxylic conjugated polymer poly[2-(3-thienyl)-ethanolhydroxycarbonylmethyl-urethane], hereafter referred to as H-PURET, and polycations such as poly(diallyldimethylammonium) chloride, here after referred to as PDADMAC, to aqueous ammonia vapor leads to dra matic changes in the ultraviolet-visible absorption spectrum. In the case of H-PURET/PDADMAC, a shift from 442 to 494 nm is observed upon overnight ammonia exposure. X-ray photoelectron spectroscopy has been used to investigate the mechanism of the changes in optical properties. The C1s, O1s and S2p core levels exhibit negligible ammonia-induced changes. Two N1s peaks are observed in virgin H-PURET/PDADMAC assemblies, and ammonia exposure causes the nitrogen peak corresponding to the H-PURET side chain to become more intense relative to that of the PDADMAC layer. This selective change in the N1s feature suggests that ammonia interacts with the polythiophene side-chain, presumably by deprotonating the fraction of carboxylic acid groups that remain in the H-PURET layer. This deprotonation apparently leads to structural or single chain conformational changes in the conjugated polymer layers that alter the electronic absorption spectrum.     

Halogen Bonding: An Interim Discussion

Halogen bonding is a noncovalent interaction that is receiving rapidly increasing attention because of its significance in biological systems and its importance in the design of new materials in a variety of areas, for example, electronics, nonlinear optical activity, and pharmaceuticals. The interactions can be understood in terms of electrostatics/polarization and dispersion; they involve a region of positive electrostatic potential on a covalently bonded halogen and a negative site, such as the lone pair of a Lewis base. The positive potential, labeled a σ hole, is on the extension of the covalent bond to the halogen, which accounts for the characteristic near‐linearity of halogen bonding. In many instances, the lateral sides of the halogen have negative electrostatic potentials, allowing it to also interact favorably with positive sites. In this discussion, after looking at some of the experimental observations of halogen bonding, we address the origins of σ holes, the factors that govern the magnitudes of their electrostatic potentials, and the properties of the resulting complexes with negative sites. The relationship of halogen and hydrogen bonding is examined. We also point out that σ‐hole interactions are not limited to halogens, but can also involve covalently bonded atoms of Groups IV–VI. Examples of applications in biological/medicinal chemistry and in crystal engineering are mentioned, taking note that halogen bonding can be “tuned” to fit various requirements, that is, strength of interaction, steric factors, and so forth.     

Quantum topology phase diagrams for molecules,clusters, and solids

The need to make more quantitative use of the total electronic charge density distribution is demonstrated in this short perspective. This is framed in the perspective of the ground breaking early work of Bader and coworkers, along with mathematicians who captured the essential nature of a molecule in a suitably compact form in real space. We see that this simple form is the Poincaré–Hopf relation for molecules and clusters and the Euler–Hopf relation in solids. Thom's theory of elementary catastrophes combined with the Poincaré–Hopf relation provides the inspiration for the new quantum topology. An alternative use of the Poincaré–Hopf relation, molecular recognition, is discussed. Quantum topology is then used to create a topology phase diagram for both molecules and solids. The author adds their perspectives of the huge potential of the quantum topology approach by demonstrating the ease with which new theoretical ideas can be generated. © 2013 Wiley Periodicals, Inc.     

Comment on “Extending Hirshfeld‐I to bulk and periodic materials”

In recent years, several methods have been developed that partition the electron density among atoms using spherically symmetric atomic weights. D. E. P. Vanpoucke, P. Bultinck, and I. Van Driessche (J. Comput. Chem. 2012, doi: 10.1002/jcc.23088) recently reported a periodic implementation of the Hirshfeld‐I method that uses a combination of Becke‐style and uniform integration grids and modified atomic reference densities to compute net atomic charges in periodic materials. Herein, this method is discussed in the context of earlier periodic implementations of the Hirshfeld‐I method, the Iterated Stockholder Atoms method, and the density derived electrostatic and chemical method.     

A numerically stable restrained electrostatic potential charge fitting method

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)‐based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill‐conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges. © 2012 Wiley Periodicals, Inc.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

电极电势:从电化学势说起*

对于原电池,电极电势的本质是化学体系对电极材料上电子势能的影响,其正负极电势差反映化学能向电能转化的趋势。电极界面上化学物质的氧化/还原反应是通过何种途径影响到电极上电子势能的,现有的教材和论著没有给出明确的解释。本文基于相间电化学势平衡原则阐明了固液界面上离子平衡与电极上电子电势的关系,并由此给出了标准电势的物理含义:它是构成电极体系一系列物性参数的组合,包括被测电极的电子、离子化学势,工作电极电解液的离子化学势,参比电极的电子、离子化学势和参比电极电解液的离子化学势等。     

高效液相色谱-四极杆/静电场轨道阱高分辨质谱法快速分析三子散的入血成分及代谢产物

蒙药三子散由诃子、川楝子、栀子3味药材等比例组成,其临床用药主要采用口服给药方式,药物在体内的吸收、分布、代谢、排泄过程与药物发挥药理作用和疗效的产生密切相关,因此考察灌胃给药后的入血成分有助于阐明三子散的药效物质基础。研究采用血清药物化学研究思路,将Wistar大鼠分成空白组和给药组,给药组给予三子散水提物,腹主动脉取血,离心制备血清样品,采用高效液相色谱-四极杆/静电场轨道阱高分辨质谱(HPLC-Q/Orbitrap HRMS),在SHIMADZU GIST C₁₈色谱柱(150 mm×4.6 mm, 5 μm)上进行色谱分离;以甲醇和0.1%(v/v)甲酸水溶液为流动相进行梯度洗脱,柱温30 ℃,流速0.5 mL/min,进样量10 μL,采用加热电喷雾电离(HESI)源,正、负离子同时扫描。通过比对三子散含药血清和空白血清的图谱差异,查阅数据库、各类成分体内代谢途径、三子散成分的相关文献,采用Xcalibur 3.0软件进行峰提取、峰匹配等质谱数据处理,结合Compound Discover 3.0软件对化合物代谢途径的预测分析和裂解规律的推断,解析三子散水提液经大鼠灌胃后血清中的原型成分和代谢产物。结果表明,在给药大鼠血清样品中鉴定出55种入血成分,其中41种原型成分,14种代谢产物。入血的原型成分主要为鞣质类、环烯醚萜类和小分子酚酸类。该研究较为全面地阐释了三子散水提液在大鼠血中的移行成分,有助于揭示三子散的药效物质基础,为该药的临床应用提供参考。