ROBIA: a reaction prediction program

A reaction prediction program, ROBIA, has been developed. This interactive computer program predicts the products of organic reactions from the starting materials and the reaction conditions, on the basis of the selected transformations within its database. This mechanistic approach generates a large number of products, from which the most important are selected using filters and molecular modeling calculations. The procedure has been applied to the possible biosynthesis pathway of dolabriferol. [reaction: see text]     

Automation of the information content analysis of kinetic parameters

The aim of this work has been to automate the analysis of kinetic measurements in solving inverse problems in order to recognize the number and form of the independent combinations of reaction rate constants. Software for determining the basis of nonlinear parametric functions of the kinetic parameters of a mathematical model for the mechanism of a complex chemical reaction has been developed and described. The main stages of program construction with the use of a search algorithm for the independent combinations of the rate constants of elementary steps in the mechanism of a complex chemical reaction based on experimental data on the concentrations of reactants are considered.     

A possible construction of chemical reaction networks

The chemical reaction networks and the sequence networks represent the pathways of a complex chemical process. In order to study the pathways separately the systematization of the elementary processes included in the possible mechanism is inevitable.This systematization was realized by a special procedure based on linear algebraic methods and enabled us to select the corresponding processes from the possible mechanism. The efficiency of the procedure has been illustrated by its application to the liquid phase oxidation of ethylbenzene and the elementary processes have been selected using a computer program.     

硼氢化反应机理Ⅳ——甲基腈硼氢化反应的反应途径解析(英文)

利用量子化学从头计算法ＲＨＦ／４－３１Ｇ基组对ＣＨ３ＣＮ＋ＢＨ３反应进行了理论研究．ＩＲＣ分析表明：甲基腈与甲硼烷通过“类四中心”过渡态,直接加成生成产物．计算的活化能是３４６２６８ｋＪ／ｍｏｌ．计算发现在反应途径中,ＢＨ３分子片随着与ＣＨ３ＣＮ分子片的接近经历一个由电子受体到电子授体的变化,并用前线轨道理论作了解释．     

A new route to indazolone via amidation reaction of o-carboxyazobenzene

One new route for the synthesis of amino-substituted indazol-3,5-dione via the amidation reaction of o-carboxyazobenzenes is reported. Optimization which includes effects of the solvents, molar ratio of starting materials, and dehydrating agents on this reaction has been studied. A possible reaction mechanism has been proposed on the basis of the product's structure, and the steric hindrance could be the main reason for low yield.     

改进单纯形法的计算机模拟及其在化学发光分析中的应用

在分析化学中常常遇到具有交互作用的多因素实验的最优化问题。它往往使一些传统的优化方法陷入困境而很难找到最优化点。而改进单纯形法(MSM)特别适合于分析化学中具有交互作用的多因素最优化实验。MSM法已经用于分析化学的各个领域。本文试图根据改进单纯形法的数学原理,用计算机模拟其优化过程。     

1,4-二氧六环的光电离解离

采用同步辐射光源、飞行时间质谱和分子束方法研究了1．4-二氧六环的光电离解离过程．由光电离效率曲线得出离子产物的出现势，计算了产物的生成焓．若重分析了m／e=28,29.41等离子碎片的解离通道以及离子碎片的可能结构，提出1、4-二氧六环在光电离解离过程中发生了重排反应     

Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea

We present a high-level quantum chemical study of possible elimination reaction mechanisms associated with the catalytic decomposition of urea at the binuclear nickel active site cluster of urease. Stable intermediates and transition state structures have been identified along several possible reaction pathways. The computed results are compared with those reported by Suarez et al. for the hydrolytic catalyzed decomposition. On the basis of these comparative studies, we propose a monodentate coordination of urea in the active site from which both the elimination and hydrolytic pathways can decompose urea into CO2 and NH3. This observation is counter to what has been experimentally suggested based on the exogenous observation of carbamic acid (the reaction product from the hydrolysis pathway). However, this does not address what has occurred at the active site of urease prior to product release. On the basis of our computed results, the observation that urea prefers the elimination channel in aqueous solution and on the observation of Lippard and co-workers of an elimination reaction channel in a urease biomimetic model, we propose that the elimination channel needs to be re-examined as a viable reaction channel in urease.     

Kinetics of the reduction of water soluble colloidal MnO<Subscript>2</Subscript> by mandelic acid in the absence and presence of non-ionic surfactant triton X-100

Kinetics of the title reaction has been studied spectrophotometrically in presence of perchloric acid at 30°C both in the absence and presence of Triton X-100 (TX-100). The reaction-time curves suggest the involvement of non-autocatalytic and autocatalytic reaction paths. The reaction follows first-order kinetics with respect to colloidal MnO₂ and mandelic acid. The reaction has acid-dependent and acid-independent paths and, in the former case, the order is fractional in [H⁺]. Addition of nonionic surfactant (TX-100) catalysed the reaction which is explained on the basis of hydrogen bonding between the oxygen of polyoxyethylene chains of TX-100 and hydroxy groups of mandelic acid/colloidal MnO₂. The kinetic data are rationalized in terms of model proposed by Tuncay et al. On the basis of the observed results, a possible mechanism has been proposed and discussed.     

CVD Reactions of TiCl4 with Ammonia： a Quantum Chemical Study

Based on density functional calculations, the mechanism and the energetic course of the chemical vapor deposition （CVD） reaction of TiCl4 with NH3 were studied at the level of B3LYP with 6-311g（d） basis set. Furthermore, the polymerization processes of dimerization, trimerization and tetramerization were investigated. The calculation results indicate that the formation of polymers is favored at the elimination reaction. On the basis of the calculated energetics, a possible mechanism of the reduction reaction has been proposed.     

Theoretical Study of the Photochemical Reaction Mechanism of Bicyclo [4.1.0 ] heptane

IntroductionPhotochemical reactions, which involve a three-membered ring, have been of great interest to experi-mental photochemists[1—10]. A main reason for thisphenomenon is that the cyclopropane ring exhibits somereaction characteristics of double bon…     

A density functional theory study on the reaction mechanism of hydrazones with α-oxo-ketenes: Comparison between stepwise 1,3-dipolar cycloaddition and Diels–Alder pathways

Density functional theory calculations have been performed at the B3LYP/6-311+G(d,p) and M06-2X/6-31G(d,p) levels to obtain an insight into the nature of the stepwise cycloaddition reactions of hydrazones with α-oxo-ketenes. Three reaction pathways are possible, two Diels–Alder reactions and a 1,3-dipolar cycloaddition (1,3-DC) reaction. Despite the high energy required for 1,2-hydrogen shift in hydrazone to form an azomethine imine, 1,3-DC reaction among the possible pathways is the most favorable. The mechanism has been explained on the basis of transition state stabilities, global and local reactivity indices of the reactants, intrinsic reaction coordinate calculation, and the electron localization function topological analysis of the bonding changes along the 1,3-DC reaction. The computed free energies and enthalpies agree with the experimental outcome.     

Alkyl phosphines promoted reductive coupling of acyl cyanides: formation of O-acyl cyanohydrins

The reductive coupling of acyl cyanides promoted by alkyl phosphines has been discovered. Under mild reaction conditions, the substituted cyanohydrins were obtained in moderate to high yields by using trimethylphosphine or tributylphosphine as a promoter. The possible mechanism involved in the reaction was discussed on the basis of deuterium labeling and control experiments, indicating that one hydride transfer took place from alkyl phosphine to O-acyl cyanohydrin.     

Automatic estimation of heats of atomization and heats of reaction

Various additivity schemes for estimating heats of atomization have been evaluated to test their usefulness for designing a computer program. The approach is based on the Allen scheme and uses parameters obtained from thermochemical data. In addition, a method has been developed which allows the direct calculation of reaction enthalpies. Only the immediate environment of the bonds involved in the reaction has to be scanned. A program based on this method utilizes thermochemical parameters, too. Computation times with this program are extremely short and independent of the size of the molecules participating in the reaction. The procedure can be applied to a large variety of organic compounds. Examples demonstrate the accuracy of the predicted values.     

New insights into iron release from ferritin: direct observation of the neurotoxin 6-hydroxydopamine entering ferritin and reaching redox equilibrium with the iron core

Iron release from the iron storage protein ferritin has been studied extensively because of its important role in oxidative stress and its possible role in the progression of Parkinson's disease. For many years external indicators, notably strong iron(II) chelators, have been used to investigate this reaction. Such chelators can, however, drastically affect the electrochemical and thermodynamic properties of iron. The present study is unique in that it has been possible to follow a reaction taking place within the ferritin shell. This was made possible by our serendipitous discovery that, at physiological pHs, the oxidation product of 6-hydroxydopamine (a deprotonated quinone) acts as its own indicator (G. N. L. Jameson and W. Linert, J. Chem. Soc., Perkin Trans. 2, 2001, 563-568). The redox equilibrium data and the kinetics of the formation of this red-coloured species can only be explained on the basis that reduction of the iron(III) takes place within the ferritin shell. This is, in fact, the first time that a reaction actually taking place inside the ferritin shell has been followed. It has also been established that, at least in vitro, all eight hydrophilic channels are capable of being simultaneously involved in the reaction. It has also been possible to calculate the rate of oxidation of the 6-hydroxydopamine within the ferritin and it is demonstrated that a redox equilibrium is established within the protein. Finally, evidence is provided confirming that chelators are in fact intrinsically linked to iron removal from ferritin.     

Quantum-chemical study of the equilibrium geometry and electronic structure of certain γ-pyrone derivatives

Full ab initio optimization of molecular geometry has been carried out for certain γ-pyrone derivatives: comenic, meconic, chelidonic, and kojic acids and 5-methoxy-γ-pyrone-2-carboxylic acid in the forms of free acids, their anions, sodium and calcium salts, chelate complexes with Ca²⁺, and sodium and calcium salts of the chelate complexes. The calculations were carried out by the restricted Hartree-Fock method with the 6-31G* basis using the GAMESS program. The effect of salt and complex formation on the geometric and electronic structure of the molecules under consideration has been examined. To study the effect of solvation, full geometry optimization of comenic acid and its derivatives in media with the dielectric constants ? 10 and 78.3 has been was carried out in terms of the polarizable continuum model. The energy effects of salt and complex formation has been estimated. A possible mechanism of binding of the molecules under consideration with opioid receptors has been proposed on the basis of the calculation results.     

量子化学研究NO在铜负载金红石表面降解反应

应用密度泛函方法结合嵌入簇模型对NO在铜负载金红石表面的吸附与降解进行了研究，计算结果表明NO分子解离以氧端吸附形成N₂O中间体然后解离N₂和 O₂.过程，另一条途径为NO双分子直接解离。通过能量学计算揭示了生成N₂O中间体对降解NO更为有利。     

Modeling the stereoselectivity of the beta-amino alcohol-promoted addition of dialkylzinc to aldehydes

The title reaction has been modeled by a Q2MM force field, allowing for rapid evaluation of several thousand TS conformations. For 10 experimental systems taken from the literature, the pathway leading to the major enantiomer has been identified. Furthermore, several possible contributions to the minor enantiomer have been investigated, providing an identification of the reasons for the sometimes moderate enantioselectivity of the title reaction, and allowing for future rational improvement of existing ligands. The favored pathways to the minor enantiomer, which must be blocked for significant selectivity improvement, differ strongly among ligands. Thus, design ideas are not necessarily transferable between ligand classes, but must be developed for each reaction on the basis of the pathway that needs to be blocked in each specific case. However, we have identified some general structure-selectivity relationships.     

Graph-theoretic study of certain interstellar reactions

Certain interstellar reactions have been studied through the graph-theoretic method using a Fortran-77 program. A plausible mechanism has been proposed for the reactions. The criterion of the conversion of edge to loop and vice versa proposed by the Bratislava group [Theor. Chim. Acta 79 , 65 (1991)] has been given a reasonable chemical insight. In the reaction scheme the nucleophilic/electrophilic/carbene (singlet, triplet) or biradical loops have been generated by the fragmentation of reactant. Subsequently, Pearson's hard and soft acids bases (HSAB) theory and frontier orbital (FO) theory have been applied to explain the reaction mechanism. Few possible reactions of the interstellar and circumstellar molecules have been investigated with illustrations involving carbene intermediate and Woodward-Hoffmann rule. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 495–508, 1997