Thermodynamic Studies on Amino Acid Solvation in Aqueous Urea

The present paper discusses the behaviour of transfer free energy of some amino acids from water to 4M, 6M and 8M aqueous urea. Dissection of transfer free energy into cavity term, interaction term and electrical term reveals that cavity forming free energy of transfer ΔG⁰_t (cav) plays an important role in dictating actual interaction of amino acids in aqueous urea. Cavity forming free energy of transfer has been estimated by using Scaled Particle Theory (SPT).     

Thermodynamic Studies on Amino Acid Solvation in some Aqueous Alcohols

Present paper discusses the behaviour of transfer free energy of some amino acids from water to aqueous solution of Ethanol, 2‐PrOH ad t‐BuOH at different compositions. Dissection of transfer free energy into cavity term, interaction term and electrical term reveals that cavity forming free energy of transfer ΔG_t⁰ (Cav.) plays an important role in dictating actual interaction of amino acids in these mixed solvents. Cavity forming free energy of transfer has been estimated by using Scaled Particle Theory (SPT).     

胶束溶液中钙黄绿素-荧光桃红间荧光共振能量转移的研究及应用

研究了钙黄绿素-荧光桃红体系的荧光共振能量转移机理及其在蛋白质测定中的应用.实验表明:在聚乙烯醇存在下,于HAc-NaAc缓冲液(pH 5.30)中,钙黄绿素与荧光桃红之间能发生有效的能量转移.根据Frster理论,探讨了钙黄绿素与荧光桃红分子间能量转移机理.结果表明:蛋白质的加入使钙黄绿素-荧光桃红体系发生荧光猝灭...     

Solubility of methane in water and in a medium for the cultivation of methanotrophs bacteria

Solubility of methane in water and in an aqueous growth medium for the cultivation of methanotrophs bacteria was determined over the temperature range 293.15 to 323.15 K and at atmospheric pressure. The measurements were carried out in a Ben-Naim/Baer type apparatus with a precision of about ±0.3%. The experimental results were determined using accurate thermodynamic relations. The mole fractions of the dissolved gas at the gas partial pressure of 101.325 kPa, the Henry coefficients at the water vapour pressure and the Ostwald coefficients at infinite dilution were obtained. A comparison between the solubility of methane in water and those observed in fermentation medium over the temperature range of 298.15 to 308.15 K has shown that this gas is about ±2.3% more soluble in water.The temperature dependence of the mole fractions of methane was also determined using the Clarke-Glew-Weiss equation and the thermodynamic quantities, Gibbs energy, enthalpy and entropy changes, associated with the dissolution process were calculated.Furthermore, the experimental Henry coefficients for methane in water are compared with those calculated by the scaled particle theory. The estimated Henry coefficients are about ±4% lower than the experimental ones.     

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor

The binding free energy calculation of protein–ligand complexes is necessary for research into virus–host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either inefficient or inaccurate in practice. Utilizing implicit solvent models in the molecular mechanics generalized Born surface area (MM/GBSA) framework allows for efficient calculations without significant loss of accuracy. Here, GBNSR6, a new flavor of the generalized Born model, is employed in the MM/GBSA framework for measuring the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor. A computational protocol is developed based on the widely studied Ras–Raf complex, which has similar binding free energy to SARS-CoV-2/ACE2. Two options for representing the dielectric boundary of the complexes are evaluated: one based on the standard Bondi radii and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein–ligand binding. Predictions based on the two radii sets provide upper and lower bounds on the experimental references: −14.7(ΔGbindBondi)<−10.6(ΔGbindExp.)<−4.1(ΔGbindOPT1) kcal/mol. The consensus estimates of the two bounds show quantitative agreement with the experiment values. This work also presents a novel truncation method and computational strategies for efficient entropy calculations with normal mode analysis. Interestingly, it is observed that a significant decrease in the number of snapshots does not affect the accuracy of entropy calculation, while it does lower computation time appreciably. The proposed MM/GBSA protocol can be used to study the binding mechanism of new variants of SARS-CoV-2, as well as other relevant structures.     

Thermodynamics of solvation and solvophobic effect in formamide

Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes.     

Thermodynamics for nonequilibrium solvation and numerical evaluation of solvent reorganization energy

This work presents a thermodynamic method for treating nonequilibrium solvation. By imposing an extra electric field onto the nonequilibrium solvation system, a virtual constrained equilibrium state is prepared. In this way, the free energy difference between the real nonequilibrium state and the con-strained equilibrium one is simply the potential energy of the nonequilibrium polarization in the extra electronic field, according to thermodynamics. Further, new expressions of nonequilibrium solvation energy and solvent reorganization energy have been formulated. Analysis shows that the present formulations will give a value of reorganization energy about one half of the traditional Marcus theory in polar solvents, thus the explanation on why the traditional theory tends to overestimate this quantity has been found out. For the purpose of numerical determination of solvent reorganization energy, we have modified Gamess program on the basis of dielectric polarizable continuum model. Applying the procedure to the well-investigated intramolecular electron transfer in biphenyl-androstane-naphthyl and biphenyl-androstane-phenanthryl systems, the numerical results of solvent reorganization energy have been found to be in good agreement with the experimental fittings.     

甲酰胺、乙酰胺、尿素在两种极性非水溶剂中的体积性质

以尿素、甲酰胺和乙酰胺为溶质,二甲基甲酰胺和二甲基亚砜为溶剂;或以二甲基甲酰胺、二甲基亚砜为溶质,以甲酰胺为溶剂,通过测定溶液在２９８．１５Ｋ下的密度数据,求得了溶质的表观摩尔体积以及与溶质－溶质相互作用相关的体积第二维里系数．利用定标粒子理论讨论了溶质分子的几何体积、溶质－溶剂相互作用对溶质偏摩尔体积的影响,结果表明,溶质的溶剂化与溶质－溶质相互作用的体积效应呈相反的变化趋势     

Thermodynamics,Charge Transfer and Practical Considerations of Solid Boosters in Redox Flow Batteries

Solid boosters are an emerging concept for improving the performance and especially the energy storage density of the redox flow batteries, but thermodynamical and practical considerations of these systems are missing, scarce or scattered in the literature. In this paper we will formulate how these systems work from the point of view of thermodynamics. We describe possible pathways for charge transfer, estimate the overpotentials required for these reactions in realistic conditions, and illustrate the range of energy storage densities achievable considering different redox electrolyte concentrations, solid volume fractions and solid charge storage densities. Approximately 80% of charge storage capacity of the solid can be accessed if redox electrolyte and redox solid have matching redox potentials. 100 times higher active areas are required from the solid boosters in the tank to reach overpotentials of <10 mV.     

Thermodynamics of molecular interactions in ethyl iodide+toluene mixtures

The excess Gibb's free energy of mixing, G^E, for ethyl iodide+toluene at 25°C have been obtained from the measured vapor pressuure data. The H^E and G^E values for ethyl iodide+toluene are positive throughout the ethyl iodide concentration range and G^E>H^E. The results have been analyzed in terms of Flory and ideal associated model theory of nonelectrolyte solutions. It has been observed that the ideal associated model approach which assumes the presence of AN and A₂B molecular species describes well (within±10 J-mol^–1 in the worst case) the general dependence of H^E on X_A (mole fraction of ethyl iodide) over the whole composition range for ethyl iodide+toluene mixtures. The equilibrium constants for A+A AB and 2A+BA₂B reactions along with the enthalpies of formation of AB and A₂B molecular species have been calculated.     

丙烷甲醇制烯烃共反应的热力学和动力学分析

通过计算和实验研究相结合的方法研究丙烷甲醇共进料制烯烃反应热力学及动力学过程.热力学过程采用Gibbs最小自由能法模拟丙烷甲醇制烯烃反应体系的平衡组成,同时结合响应面分析法建立了温度、压力、丙烷甲醇进料摩尔比对产物中丙烯的摩尔分数的函数关系,通过回归方程分析最佳工艺范围.热力学分析了反应条件对平衡产物的影响,随着反应温度升高,平衡产物丙烯的质量分数先增高后降低;平衡产物中丙烯的质量分数随着丙烷甲醇进料中丙烷摩尔比增高而增高,但是实际的反应状态和催化剂也是相关的,因此研究了存在催化剂情况下,丙烷脱氢和丙烷甲醇共进料反应的活化能.反应活化能动力学实验表明,通过添加少量甲醇可以降低耦合过程中丙烷脱氢表观活化能.     

Thermodynamics ofp-nitroanilinium ion and the acidity function in ethylene carbonate-water mixtures at 25°C

Hydrochloric acid solutions (0.05–1.18m) containing p-nitroaniline (8×10^–5M) as indicator base have H _o values which increase with increase of ethylene carbonate (EC) content in the solvent mixture for a fixed molality of the acid. This behavior confirms similar results obtained in AN-H₂O, MCS-H₂O, DMSO-H₂O and NMF-H₂O systems. This trend indicates that the solvent basicity increases by successive addition of the organic solvent. The partition of the proton between water and EC has been calculated using Sadek's theory. It is clear that [H₃O⁺] decreases gradually with increase of EC content. The change in the dissociation constant of p-nitroanilinium ion, decreases sharply with increasing dielectric constant. The free energy change of transfer, G _t ^o , has been attributed to an electrostatic, G _t(el) ^o , and a nonelectrostatic, electrostatic, G _t(non) ^o component. It has been found that G _t(non) ^o is negative.     

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

Implicit solvent models for biomolecular simulations have been developed to use in place of more expensive explicit models; however, these models make many assumptions and approximations that are likely to affect accuracy. Here, the changes in free energies of solvation upon folding of several fast folding proteins are calculated from previously run μs–ms simulations with a number of implicit solvent models and compared to the values needed to be consistent with the explicit solvent model used in the simulations. In the majority of cases, there is a significant and substantial difference between the values calculated from the two approaches that is robust to the details of the calculations. These differences could only be remedied by selecting values for the model parameters—the internal dielectric constant for the polar term and the surface tension coefficient for the nonpolar term—that were system‐specific or physically unrealistic. We discuss the potential implications of our findings for both implicit and explicit solvent simulations. © 2015 Wiley Periodicals, Inc.     

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

The association of Mg²⁺ and H₂PO₄^? in water can give insights into Mg:phosphate interactions in general, which are very widespread, but for which experimental data is surprisingly sparse. It is studied through molecular dynamics simulations (>100 ns) by using the polarizable AMOEBA force field, and the association free energy is computed for the first time. Explicit consideration of outer‐sphere and two types of inner‐sphere association provides considerable insight into the dynamics and thermodynamics of ion pairing. After careful assessment of the computational approximations, the agreement with experimental values indicates that the methodology can be extended to other inorganic and biological Mg:phosphate interactions in solution.     

Physical quantity of residue electrostatic energy in flavin mononucleotide binding protein dimer

The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obtained by a molecular dynamics (MD) simulation. ES is one of the most important energies among the interaction energies in a protein. It is determined from the RES, the residues which mainly contribute to stabilize the structure of each subunit, and the binding energy between two subunits can be estimated. The RES of all residues in subunit A (Sub A) and subunit B (Sub B) were attractive forces, even though the residues contain net negative or positive charges. This reveals that the ES energies of any of the residues can contribute to stabilize the protein structure. The total binding ES energy over all residues among the subunits was distributed between −0.2 to −1.2 eV (mean = −0.67 eV) from the MD simulation time.     

热力学在无机化学“四大平衡”教学中的应用

利用化学反应吉布斯自由能变化?_rG_m~?来计算无机化学"四大平衡"的平衡常数,解释诸如沉淀-溶解平衡教学中为什么要求微溶强电解质等问题,并从化学反应等温式类推了电极反应的等温式,推导了复杂电极的标准电极电势与其简单电极的标准电极电势之间的关系,拓展了热力学在现行基础化学教学上的应用范围。     

壳聚糖大分子链的形态调控及其在微悬浮聚合中的分散稳定作用

以易去除可回用的壳聚糖(CS)为分散剂,通过微悬浮聚合制备微米级的软硬质聚合物胶粒.考察不同酸碱度下水相介质中CS大分子链的质子化程度、亲疏水性和形态结构,及其对油水界面处CS存在形态的影响,进而评估其对剪切均质化所制单体液滴的分散稳定作用.发现通过调节体系pH值可较容易地控制CS大分子链的质子化程度、亲疏水性以及在单体液滴表面的吸附效率和铺展程度,进而可在弱酸性环境下调控微悬浮聚合体系中CS的分散能力和稳定效果.特别是当pH值在6.0左右时,CS大分子链质子化程度和亲疏水性适中,链内易形成具有一定内聚密度的高分子链收缩构象、链间易形成由多根CS链缠结而成的疏松聚集状态.在此状态下的CS链对苯丙单体液滴具有较强的分散能力和稳定作用,因而通过微悬浮聚合可制得形态结构规整、分散状态良好的聚合物粒子.进一步与微悬浮聚合常用的无机粉末类和高分子类分散剂进行应用效果比较,发现CS具有形态调控性好、分散稳定效率高、易去除能回用、特别适合制备软质微米胶粒等优点,是一种有别于无机粉末类和高分子类分散剂的新型微悬浮聚合分散剂.     

Solubility of freons in polar and non-polar liquids at 298.15 K

The cavity formation energy (CFE) is the free energy invested in rearrangement of the solvent molecules when a solute is inserted into a solvent, which is very important to the solubility studies. The CFE of liquid solvents; n-heptane, n-octane, cyclohexane, tetrachloromethane, benzene and water at 298.15 K has been determined. The solubility (in terms of Henry’s law constant), Gibb’s free energy of solution and ΔG_s^*, the thermodynamical quantities for the solvation process defined by Ben-Naim and Marcus of fluorine containing gases; freon-11, freon-12, freon-13, freon-14, freon-21, freon-c-318 and sulpherhexafluoride (SF₆) in above liquid solvents at 298.15 K also been calculated with this cavity formation energy. It yields good agreement with experimental results. The calculation shows importance of CFE in determining the solution properties.