A Gibbs free energy correlation for automated docking of carbohydrates

Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.     

Nano-scale grain growth kinetics

An empirical relation among three important properties of grain boundary (GB), i.e. GB free energy, energy change of GB segregation, and GB excess, was shown. Accordingly, GB energy reduces with grain growth. Once GB energy is equal to zero, GBs will be in thermodynamic equilibrium in the presence of solute atoms and, therefore, grain growth stops with saturated GBs. Applying a kinetic model for nano-scale grain growth, some published experimental data were successfully reinterpreted. With progressing grain growth, the activation energy of grain growth increases, in contrast with the reduction of GB energy. In connection with a semi-empirical relation according to the conjecture that GB energy is the difference between those responsible for diffusion in the lattice and the GB itself, proposed by Borisov, a conclusion can be drawn that, for alloy with strong segregation tendency, grain growth is inhibited due to the reduction of GB energy, even to zero.     

气流床粉煤气化的Gibbs自由能最小化模拟

用Gibbs自由能最小化方法对粉煤气化过程进行了热力学平衡分析。对一混合煤种,在3.0 MPa和气化温度限制在1 200 ℃～1 450 ℃时,研究了氧-煤比、蒸气-煤比对气化炉出口气体组成、温度和有效气产率的影响,并由此确定了可行的操作域是氧-煤比545m3/t～605 m3/t、蒸气-煤比为152.64 kg/t～313.92 kg/t及其对应的工艺指标。从操作域中选择有代表性的工艺条件为氧-煤比578 m3/t、蒸气-煤比为187 kg/t,对应的气化炉出口温度1 358 ℃,CO+H2干基体积分数为91.5%,有效气产率为2.123(CO+H2)m3/kg。同时,研究了碳转化率和热损失对气化工艺指标的影响,其影响是显著的。     

Gibbs free energy of formation of calcium rhodite

The Gibbs free energy of formation of CaRh₂O₄(s) has been determined using two techniques viz., quadrupole mass spectrometer coupled to a Knudsen cell and solid-state cell incorporating CaF₂(s) as the solid electrolyte. In the former method, equilibrium O₂(g) pressures were measured over the phase field Rh(s)+Rh₂O₃(s), in the temperature range 793.7-909.1 K and over the three phase mixture CaRh₂O₄(s)+Rh(s)+CaO(s) was measured from 862.1 to 1022.7 K.The Gibbs free energy of formation of Rh₂O₃(s) from elements in their standard state can be given by

     

对二甲苯＋环己烷及对二甲苯＋二甲基亚砜的固液相平衡和过量吉布斯自由能

测定了对二甲苯＋环己烷及对二甲苯＋二甲基亚砜体系（均为简单低共熔混合物）的固液平衡相图，计算出它们在３１３．１５Ｋ的过量吉布斯自由能。结果表明两体系对理想溶液均产生正偏差。     

甲酰胺溶剂中溶质间的过量Gibbs自由能相互作用参数

利用气液色谱方法测定了２９８．１５Ｋ时若干非电解质溶质在甲酰胺－乙酰胺、甲酰胺－尿素、甲酰胺－高氯酸钠固定液中的保留参数，采用ＭｃＭｉｌａａｎ－Ｍａｙｅｒ理论，将溶液热力学过量性质与溶液中粒子的对相互作用，参相互作用参数相联系，利用热力学方法求得了溶质的保留参数与Ｇｉｂｌｓ自由能相互作用参数的关系，并就溶质－溶质间的相互作用及溶剂性质的影响进行了讨论。     

四元系溶液中溶质间的Gibbs自由能相互作用参数的研究

用气液色谱法测定２９８．１５Ｋ下，有机溶质在尿素＋高氯酸钠＋甲酰胺固定液中的保留参数，用ＭｃＭｉｌｌａｎ－Ｍａｙｅｒ理论，将溶液的势力学过量性质与溶液中粒子间的对相互作用、三相互作用参数相联系，用热力学方法求得该四元体系中溶质的气液色谱保留参数与Ｇｉｂｂｓ自由能相互作用参数的联系，并就溶质间的相互作用及混合溶剂性质的影响进行了讨论。     

Nucleation-growth kinetics of the oxidation of silver nanocrystals to silver halide crystals

The electrochemical oxidation of silver nanocrystals to silver halide crystals proceeds by a process of nucleation and growth. The mechanism is confirmed by analyzing chronopotentiograms using a new extension of nucleation theory. The theory makes it possible to derive plots of nucleation-growth currents vs potential, and growth rates vs potential, directly from experimental data. Such plots yield powerful insights into the reaction kinetics. In situ AFM imaging reveals that a few thousand of silver nanocrystals are oxidized to only a few tens of silver halide crystals, without pronounced loss of active material. The mechanism of this remarkable process is described in this paper. In particular, it is shown that the decrease in crystal population proceeds via an oversaturated silver solution, i.e., a process that is mediated by “driven” Ostwald ripening across the electrode surface. At the same time, the low solubility of silver species in bulk solution means that few silver ions escape from the surface. This combination of features explains why the transformation from silver to silver halide is near-stoichiometric yet highly reconstructive.Dedicated to our friend and colleague Professor Dr. Alan Bond on the occasion of his 60th birthday     

正已醇-邻、间、对二甲苯二元系固液相平衡

Melting temperatures have been measured and the solid-liquid phase diagrams constructed for 1-hexanol＋o-xylene, 1-hexanol＋m-xylene and 1-hexanol＋p-xylene. They are simple eutectic systems. Excess mole Gibbs free energies were calculated at 298.15K, showing larger positive deviations from ideal-solution behavior. The largest values of GmE are 711、 650 and 800 J•mol-1 for {o-C6H4(CH3)2＋C6H13OH}、 {m-C6H4(CH3)2 ＋ C6H13OH} and {p-C6H4(CH3)2＋C6H13OH} respectively.     

C_8芳烃异构体+异丙醇体系在333.15K时的过量摩尔Gibbs自由能

采用CP-I型汽液平衡双循环釜,测定了333.15 K时乙苯+异丙醇、邻二甲苯+异丙醇、间二甲苯+异丙醇、对二甲苯+异丙醇四个体系的汽液平衡数据,计算了该温度下四个体系的过量摩尔Gibbs自由能,并对所测数据进行了恒温下热力学一致性检验。用Wilson方程关联了实验数据,拟合精度令人满意。     

Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLS-AA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.     

Quantum chemical study of the effect of N,N-acyl group nature on the structure and Gibbs free energy of the sulfur ketoylides and products of their transformations

With the purpose to study the effect of the nature of the imido-group of N,N-acyl-protected β-methyl-substituted keto-stabilized sulfonium ylides on the formation of methylthiopyrrolisinediones by cyclization, the structure features of these ylides are investigated by ab initio methods. The imido-group nature is shown to insignificantly affect in most cases the structure and the relative free energy of conformers of the ketoylides in question and the products of a cyclization reaction with their participation. The energy difference between the anti-peri-planar and syn-clinal orientation of nitrogen atoms in the imido-group and ylide carbon atom is negligible. The latter orientation is necessary for the reaction of intramolecular cyclization to proceed because in this case carbon atoms between which the bond forms are drawn together. The structure of cyclic pentanomial N,N-acyl group slightly affects the calculated values of Gibbs free energy of sulfur ketoylide reactions, and a temperature increase promotes the intramolecualr cyclization reactions. Wittig and Corey-Chaykovsky reactions typical of ylides are the least thermodynamically favorable for the sulfonium ketoylides under study.     

Relationship between heat of immersion and surface Gibbs energy of fluorite and cassiterite

Calorimetric measurements were made of the heat of immersion in water of cassiterite that was either untreated or treated with 60% HNO₃. The heats of immersion of cassiterite and fluorite were also calculated theoretically from the surface Gibbs energy components, and compared with the heat of immersion measured for cassiterite and that taken from the literature for fluorite. The results of the measurements and calculation revealed that the heat of immersion depends on the degree of hydration of the surface of cassiterite and fluorite. It was also found that it is possible to predict the heats of immersion in water of cassiterite and fluorite from the Lifshitz-van der Waals and acid-base components of the surface Gibbs energy.     

Molecular simulation of the hydration Gibbs energy of barbiturates

In the present work, molecular dynamics calculations of the Gibbs energy of hydration of 10 different substituted barbiturates in SPC/E water were performed using thermodynamic integration. Given that experimental determination of the Gibbs hydration energy for this class of compounds is currently unfeasible, computer simulations appear as the only alternative for the estimation of this important quantity. Several simulation parameters are discussed and optimized based on calculations for barbituric acid. It is concluded that accounting for electrostatic interactions with the Reaction-Field method can be up to two times faster than with Particle-Mesh-Ewald method, without loss of accuracy. Different number of solvent molecules and simulation lengths were also tested. Lennard-Jones and electrostatic contributions were scaled down to zero in an independent way. It is shown that the electrostatic contribution is dominant (representing approximately 90% of the total Gibbs energy of hydration) and that barbiturate intra-molecular interactions cannot be neglected. The importance of the electrostatic contribution is attributed to the formation of hydrogen bonds between the barbiturates and water, which play an important role in the solvation process. The influence of the different substituents and their contribution to the Gibbs energy of hydration was assessed. Finally, the Lennard-Jones contributions and the total hydration Gibbs energy can both be correlated against molecular weight or partition coefficient data for mono- and di-substituted barbiturates.     

A model for the Gibbs energy of aqueous solutions of polyelectrolytes

A new model for the excess Gibbs energy of aqueous solutions of polyelectrolytes is presented and applied for the correlation of the activity of water in aqueous solutions of polyelectrolytes without as well as with an added (single) salt. The model considers the phenomenon of counterion condensation, i.e., the partial dissociation of highly charged polyelectrolytes in water. Three parameters (a binary interaction parameter between polymer segments, the equilibrium constant of the dissociation reaction and a parameter which accounts for the polymer configuration) were fitted to the experimental results. The model allows for a reliable correlation of experimental results for the osmotic coefficient of aqueous solutions of a single polyelectrolyte (without as well as with an added salt).     

糖与非电解质在甲酰胺中相互作用的Gibbs自由能参数

用气液色谱法测定了298.15K时10个非电解质溶质在不同浓度甲酰胺糖(葡萄糖,果糖,蔗糖)溶液中的保留参数.依据McMillanMayer理论,求得非电解质溶质与糖间的Gibbs自由能相互作用参数g_ij和g_ijj.采用OkamotoWood的基团加合法,求得各基团的Gibbs自由能相互作用参数G_x,y,讨论了非电解质溶质与糖间的相互作用以及溶剂性质的影响.     

Evaluation of Excess Gibbs Energy of Mixing in Binary Mixtures of Di-Isobutyl Ketone (Dibk) and Nonpolar Solvents

Abstract

Excess Gibbs energy of mixing in binary mixture of Di-isobutyl ketone (DIBK) in nonpolar solvents namely n-heptane, p-xylene, cyclohexane, dioxane, benzene and tetra-chloromethane have been evaluated at 303°K. The results indicate that (ΔG_AB)_maxima is in the order, n-heptane > p-xylene > cyclohexane > benzene > dioxane > tetra-chloromethane.     

Evaluation of Gibbs free energy for the transfer of a highly hydrophilic ion from an acidic aqueous solution to an organic solution based on ion pair extraction

A method to determine the standard Gibbs free energy for the transfer, ΔG°_tr, of a highly hydrophilic metal ion from an aqueous solution, W, in the presence of high concentration of H⁺ to an organic solution, O, was proposed based on the theoretical consideration of the distribution process of ions between W and O. The usefulness of the proposed method was verified experimentally by comparing ΔG°_tr of Mg²⁺ determined by the method with that obtained by voltammetry for the ion transfer at the W|O interface. The O examined were nitrobenzene (NB) and 1,2-dichloroethane (DCE). By applying the proposed method, ΔG°_tr of NpO₂⁺, UO₂²⁺, NpO₂²⁺ and PuO₂²⁺ from an acidic W to NB were determined.