The discovery of two kinds of ion pairs

The discovery and implications of the existence of two kinds of ion pairs in solutions of carbanion salts is described. Also discussed are the factors controlling tight–loose ion pair equilibrium: the nature of the carbanion and its counterion, temperature, pressure, solvent, and cation‐complexing additives. A few examples are presented of the effect of these ionic species on the mechanisms of anionic polymerization and proton transfer. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3655–3667, 2004     

La(Ⅲ)-乙醇溶液微团簇理论和光谱研究

利用分子光谱和基于密度泛函理论的第一性原理,采用改进的TPSSTPSS泛函方法对C、H、O原子用6-31G基组并添加极化和弥散函数,对La原子选用Def2-SV(P)赝势基组,研究La3+/乙醇溶液微团簇构型。优化计算La3+在水溶液中的溶剂化结构,得出气相中的优化结果可以近似代替液相结果的结论;理论优化计算La3+/乙醇溶液可能存在的结构构型的结果表明,溶剂化数n=6时结构最稳定。采用荧光光谱和核磁共振实验对结果进行了验证,表明La3+的加入使荧光强度显著增强,在高浓度时生成的团簇构型比较稳定,且随着溶剂化数目的增加,O—H键长增大,La3+使其附近的质子产生强大的屏蔽效应,化学位移向高场移动,溶剂化数n=6时绝对误差最小,最稳定,与理论计算结论相吻合。     

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 Phenomena of Potassium Thiocyanate in Methanol–Water Mixtures

This paper reports the results of a variety of experiments carried out for understanding the solvation behavior of potassium thiocyanate in methanol–water mixtures. Electrical conductivity, speed of sound, viscosity, and FT-Raman spectra of potassium thiocyanate solutions in 5 and 10% methanol–water (w/w) mixtures were measured as functions of concentration and temperature. The conductivity and structural relaxation time suggest the ion–solvent and solvent-separated ion–ion associations increase as the salt concentration increases in the mixtures. The Raman band shifts due to the C–O stretching mode of methanol for the solvent mixtures reveal the formation of methanol–water complexes. The significant changes in the Raman bands for the C–N, C–S and O–H stretching modes indicate the presence of SCN⁻−solvent interactions through the N-end, “free” SCN⁻ and the solvent-shared ion pairs as potassium thiocyanate is added to the methanol–water mixtures. The relative changes corresponding to H–O–H bending and C–O stretching frequencies indicate that K⁺ is preferentially solvated by water in these solvent mixtures. The appearance and increase of the intensity of a broad band at ≈940 cm⁻¹ upon salt addition was attributed to the SCN⁻–H₂O–K⁺ solvent-shared ion pairs. No Raman spectral evidence for K⁺(H₂O)_n species was observed. The preferential solvation of K⁺ and SCN⁻ in the methanol−water mixtures was verified by the application of the Kirkwood−Buff theory of solutions. This theory confirms that K⁺ is strongly preferentially solvated by water, whereas SCN⁻ is preferentially solvated by the methanol component.     

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

Fragment‐based quantum mechanical calculation of protein–protein binding affinities

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE‐GMFCC) method has been successfully utilized for efficient linear‐scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE‐GMFCC method for calculation of binding affinity of Endonuclease colicin–immunity protein complex. The binding free energy changes between the wild‐type and mutants of the complex calculated by EE‐GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6‐31G*‐D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein–protein binding affinities. Moreover, the self‐consistent calculation of PB solvation energy is required for accurate calculations of protein–protein binding free energies. This study demonstrates that the EE‐GMFCC method is capable of providing reliable prediction of relative binding affinities for protein–protein complexes. © 2018 Wiley Periodicals, Inc.     

Dielectric relaxation of electrolyte solutions in acetonitrile

Complex permittivity spectra in the frequency range 0.95v (GHz)89 for acetonitrile and its solutions of LiBr, NaI, NaClO₄, and Bu₄NBr at 25°C show one Debye equation for the neat solvent whereas the superposition of a Debye process for the solute and a Cole-Cole distribution for the solvent is necessary to account for the dielectric relaxation behavior of the solutions. The reorientation of bulk acetonitrile is diffusive and only weakly coupled to viscosity. The number of solvent molecules irrotationally bound to the electrolyte is in good agreement with conventional solvation numbers for all electrolytes, when kinetic depolarization is assumed to be negligible. The solute relaxation process is dominated by the formation kinetics and reorientation of contact ion pairs. There is evidence for solvent-shared ion pairs in dilute NaClO₄ solutions.     

Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics

In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for “biological water”, a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.     

Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition–elimination mechanism by ab initio calculations in gas phase and water

 Addition–elimination reactions involving a nucleophile and a remote leaving group [S^H _N(AE)^tele] are well-known under basic conditions, especially amongst electron-poor six-membered heterocycles, but are less commonly encountered for five-membered heterocycles and are rare under acidic conditions. Concentrated HCl converts 1-hydroxy-1H-pyrazolo[3,4-c] isoquinoline and 1-hydroxy-1H-pyrazolo[3,4-c]quinoline into 3-chloro-1H-pyrazolo[3,4-c]isoquinoline and 3-chloro-1H-pyrazolo[3,4-c]quinoline, respectively. However, apparently neither the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)-quinolines nor the parent 1-hydroxypyrazole undergo this reaction. Additionally, all these systems are refractory under basic conditions. We present a plausible mechanism for the reaction, involving the 3-addition of Cl^- to the diprotonated heterocycle, followed by the elimination of water. Calculations of the initial transition states and intermediates, using optimisation at B3LYP/6-311+G(d,p), including thermochemistry [HF/6-31+G(d)], and single-point Poisson–Boltzmann self-consistent reaction field determination of the free energy of solvation (Jaguar Poisson–Boltzmann self-consistent reaction field), support this mechanism and reproduce the observed order of reactivity, the addition step being 2–4 kcal less favourable for the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)quinolines and provide a rationalisation for the role of strong acid. Received: 27 June 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003