苯甲醛肟与炔丙醇偶极环加成反应的理论研究

用密度泛函理论(DFT)方法在B3LYP/6-31G*水平上研究了苯甲醛肟与炔丙醇加成反应的微观机制和热力学、动力学行为. 结果表明, 在苯甲醛肟与炔丙醇加成反应过程中, 8个可能反应通道的过渡态中均形成非平面五元环结构, 其中苯甲醛肟的Z、E构型特征得到了部分保留, 但主要部分的键长、键角均发生了变化, 电荷也进行了重新分布. 苯甲醛肟以羟基型参与反应的4个反应通道均为吸热反应和热力学非自发过程, 它们均具有较高的反应势垒、较慢的反应速率和较小的平衡常数; 而以离子型参与反应的四个反应通道均为放热反应和热力学自发过程, 它们的反应势垒较低, 反应速度较快, 平衡常数也较大, 故苯甲醛肟应主要以离子型参与反应. 炔丙醇的两种取向对应着加成反应的两种产物, 反应达到平衡后, 3-羟甲基二氢异噁唑为主要产物.     

对化学反应数据分类获取反应知识的新方法

尽管已有大量化学反应数据可供使用,但化学家仍常常感到很难便捷地从中得到所需的信息.这主要是由于反应数据库基于结构的检索方法与化学家解决问题的方法相去甚远.为解决这一问题而发展了一种通过对反应进行二级分类得到精细描述反应知识的层次模型的方法.第一次分类时不同的同类反应都在由一组普适性好的称作反应结构一级描述符构成的空间中进行.在第一次分类结果的基础上,得到每一类反应的公共结构特征作为第二次分类的结构描述符,利用它们进行更精细的分类,即可从原始反应数据中得到所需的基核反应.由特定反应、基核反应和基型反应就可将反应知识更合理地组织在同类反应知识库中,使它们得到更好的利用.     

关于反应分子数定义的讨论

There are two different views on the definition of reaction molecularity in physical chemistry textbooks and related literatures so far. We give a deep discussion about this conception herein. Starting with the development of chemical kinetics and the definition of elementary reaction and state-state reaction, we clarify that elementary reaction and state-state reaction are the conceptions belonging to macro-and micro-systems, respectively, and reaction molecularity is also belonging to micro-conception. Based on this conclusion, we think that the more reasonable definition of reaction molecularity should be "the number of chemical particles that take part in a state-state reaction (or an elementary chemi-physical reaction) as a reactant".     

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.     

钯催化的交叉偶联反应——2010年诺贝尔化学奖获奖工作介绍

钯催化的交叉偶联反应是非常实用的合成新方法.文章给出了Heck反应、Negishi反应和Suzuki反应的概念,对其反应机理作了详细的说明,并对其在复杂化合物和天然产物全合成中的应用作了评价.     

氟分子与乙烯反应的直接动力学模拟

Direct dynamics within the framework of DFT was used to study the long-time puzzling mechanism of the reaction between F2 and ethylene. Three types of reactions are widely accepted : F atom elimination reaction, HF elimination reaction and the addition reaction. Several reaction mechanisms have been proposed, but only the radical mechanism can reasonably explain the initial reaction at low temperature. In this article, our calculations support the radical mechanism and the reaction mechanisms of the three reactions, and they are described in detail by trajectory simulation. The reactions in a cryogenic matrix with the reaction mechanism were also discussed.     

用常温正丁烷异构化反应表征固体超强酸性

研究了室温下固体超强酸催化剂上正丁烷反应，发现转化率低于50％时，异构化选择性高于95％，正丁烷异构化反应动力学符合一级可逆反应规律，固体超强酸的酸强度与正丁烷异构化反应转化率和速率常数呈顺变关系，与反应表现活化能呈逆变关系．报出了一种新的表征固体超强酸性的实验方法．     

Detecting Reaction Pathways and Computing Reaction Rates in Condensed Phase

Methods for the computation of rate constants that characterize classical reactions occurring in the condensed phase are discussed. While microscopic expressions for these transport properties are well known, their computation presents challenges for simulation since reactive events often occur rarely, and the long time scales that are typical for reactive processes are not accessible using simple molecular dynamics methods. Furthermore, the underlying free energy surface is very complex with many saddle points that prevent sampling of possible reaction pathways. As a result, the reaction coordinate may be a complex many-body function of the system’s degrees of freedom. Since there is not an a priori way to define a “good” reaction coordinate, methods are being developed to assist in a systematic construction of a reaction coordinate. These methods are reviewed and examples of non-trivial reaction coordinates are presented.     

Recent advances in oxidative C–C coupling reaction of amides with carbon nucleophiles

The C–C coupling reaction of N-electron withdrawing group (EWG) protected amides with coupling partners is one of the most important methods for C–C bond formation at the α-position of amides to directly give α-substituted amides. Of the four reactions, namely, the reaction via the generation of carbanion with an electrophile, that via the generation of carbon radical with a radical donor, that via the generation of iminium ion species with a nucleophile (oxidative coupling reaction), and that using a transition metal carbenoid, the oxidative coupling reaction presents a challenge although the reaction products are very useful for the transformation of a wide range of nitrogen-containing derivatives. In this review, recent developments in the oxidative coupling reaction of N-EWG protected amides with nucleophiles are summarized with focus on the reaction using a transition metal, the transition-metal-free reaction, the enantioselective reaction using a chiral catalysts, and the organocatalyzed oxidative coupling reaction.     

Investigation of the rh-catalyzed asymmetric reductive aldol reaction. Expanded scope based on reaction analysis

[reaction: see text] A series of experiments are described that suggest that the Rh-catalyzed reductive aldol reaction proceeds by addition of a Rh(I) hydride, generated in situ, to the reacting acrylate followed by a stereochemistry-controlling aldol addition reaction. On the basis of this hypothesis, reaction conditions are engineered that allow for increased substrate scope.     

Domino reactions that combine an azido-Schmidt ring expansion with the Diels-Alder reaction

[reaction: see text] The combination of the intramolecular Schmidt reaction with the Diels-Alder reaction provides expedient access to a variety of heterocycles. Two different modes of reaction planning are presented. In one, the azide and ketone moieties necessary for the intramolecular Schmidt reaction originate on different molecules that are reacted and subsequently undergo a ring-adjustment step. Alternatively, an azido ketone can be used provided the ketone is deactivated by its presence in an enone.     

Integration of capacity fading in an electrochemical model of Li-ion batteries

We have developed a new method to describe a fading model integrated with a parasitic reaction of rechargeable Li-ion batteries in the present work. In our work, the Li-ion battery reactions and the parasitic reaction are incorporated into one model. A new governing equation and a new field variable are presented in the new model to characterize the parasitic reaction and the relationship to the battery fading. Due to the new variations, the parameters that are changed with the battery’s aging are able to be calculated and updated automatically in the model. The parasitic reaction is assumed to obey a Tafel equation. The simulating results show that the distribution of overpotential of the parasitic reaction as function of x shapes, a figure close to a “V,” suggests the nonuniform distribution of the parasitic current. The parasitic reaction’s equilibrium potential is proved to be one of most important factors that determine the rate of the reaction. In addition, the cutoff charging state of charge (SOC) has a large influence on the parameters related to the rate of the parasitic reaction. Therefore, controlling the charging SOC can be seen as an effective method to protect the battery from aging.     

Theoretical study on the alkaline hydrolysis of methyl thioacetate in aqueous solution

A base-catalyzed hydrolysis reaction of thiolester has been studied in both gas and solution phases using two ab initio quantum mechanics calculations such as Gaussian09 and CPMD. The free-energy surface along the reaction path is also constructed using a configuration sampling technique, namely, the metadynamics method. While there are two different reaction paths obtained for the potential profile of the base-catalyzed hydrolysis reaction for thiolester in the gas phase, a triple-well reaction path is computed for the reaction in the solution phase by two quantum mechanics calculations. Unlike the S(N)2 mechanism (a concerted mechanism) found for the gas-phase reaction, a nucleophilic attack from the hydroxide ion on the carbonyl carbon to yield a tetrahedral intermediate (a stepwise mechanism) is observed for the solution-phase reaction. Moreover, the energy profiles computed by these two theoretical calculations are found to be very comparable with those determined experimentally.     

A Simple Model for Barrier Frequencies for Enzymatic Reactions

We present a simple model to rationalize the effects of environment on the reaction barrier frequencies derived from free energy profiles. These frequencies are relevant in deviations of a rate constant from its transition state theory value and in determining which environmental dynamics participate in the reaction. In particular, this simple model can be used to understand the changes in the reaction barrier frequencies of an enzymatic catalyzed reaction and the corresponding uncatalyzed process in aqueous solution, a change which has implications for dynamical environmental effects on the enzymatic reaction. Two possible cases are analyzed, in which the polarity (charge separation/localization) of the reacting system increases or decreases as the reaction advances. A simple modeling of the environment′s effects allows the explanation of an unusual “inverse” effect on the reaction frequencies, that is, a free energy barrier lowering accompanied by an increase of the reaction frequency, a behavior observed in some enzymes. The model predictions are successfully compared with results from full simulations for four different enzyme reactions.     

Theoretical studies of metallo (Li and Na)-ene reaction mechanisms

The reaction mechanisms of allyl-lithium and allyl-sodium with ethylene were studied by ab initio molecular orbital (MO) methods. The reaction mechanisms were analyzed by a CiLC-IRC method on the basis of ab initio CASSCF MOs. The ene reaction pathways of allyl-Li and allyl-Na with ethylene were located. The complex between allyl-metal and ethylene for both systems is found in the first step of the reaction, and then the metal migration and new C-C bond formation occur synchronously through the transition state. The complexation energies are -13.2 and -9.6 kcal/mol for Li and Na systems, respectively. The activation energy barriers from the reactants are 3.5 kcal/mol for the Li system and 2.0 kcal/mol for the Na system at the MRMP2 calculation level. These barriers are significantly lower than that of the ene reaction of propene with ethylene as the parent reaction. The CiLC-IRC analysis shows that the reaction of allyl-metal with ethylene is a concerted ene reaction mechanism, not a metal catalysis and/or a stepwise reaction.     

Kinetics and mechanism of nucleophilic halogen exchange in furan derivatives

Studies are made of the reaction of 5-bromofurfurylidenaniline with aromatic amines (reaction 1), of the disproportionation of 5-bromofurfurylidenaniline (reaction 2), and of the reaction of 5-bromofurfurylidenaniline and 5-bromofurfural with saturated secondary amines (reaction 3). It is shown that these reactions are of the autocatalytic type (the catalyst being a reaction product, the hydrobromide of the amine), that addition of acid accelerates them, while they are retarded by addition of alkali. The hypothesis is advanced that in these reactions the active form of the substrate is the salt containing the fragment. The latter arises by protonation of the Schiff's base (reactions 1 and 2), or by quaternization of aminoacetals (which are products formed by addition of a secondary amine across the (double) bonds in through the action of the hydrohalide salt of the amine (reaction 3).     

迈克尔反应受体分子化学生物学研究

迈克尔受体是烯键或炔键与吸电子基团共轭相连形成的官能团,含有这样官能团的化学小分子能与亲核试剂发生迈克尔加成反应,因此称为迈克尔反应受体分子。迈克尔反应受体分子是一类重要的生理活性分子,它们直接或间接参与许多生命过程,同时也是细胞中许多信号转导途径的调节者,在化学生物学研究中起着重要的作用。本文对迈克尔反应受体分子化学生物学研究进展进行了综述。     

Synthesis of organosulfides using transition-metal-catalyzed substitution reactions: to construct exergonic reactions employing metal inorganic and organic co-substrate/co-product methods

A catalyst changes the course of a reaction without affecting the relative thermodynamic stability of substrates and products, and a catalytic reaction must be exergonic in order to obtain high yields of the product and to attain reasonable reaction rates. In the case that the desired reaction is in equilibrium or is endergonic, devices for making products thermodynamically more stable than substrates are needed. In this review, the transition-metal-catalyzed synthesis of organosulfides using a substitution reaction is summarized, where metal inorganic and organic co-substrate/co-product methods are used in developing exergonic reactions.     

Topological studies on IRC paths of the isomerization reaction of silicon methyl-nitrene

On the basis of kinetic study of isomerization reaction of H_3Si-N, ab initio (RHF, UHF/6-31G) calculations on some points of the singlet and triplet reaction paths were carried out. The breakage and formation of chemical bond in the reaction are discussed. The calculated results show that there is a transitional structure of three-membered ring on each of reaction paths. A 'structural transition region' and a 'structural transition state' in both of studied reaction are found. Our previous conclusion that the structure transition state (STS) always appears before the energy transition state (ETS) in endothermic reaction and after ETS in exothermic reaction is further confirmed. The relationship between the change of spin density distribution and the structural transition state are investigated.     

化学反应的几何分析 I:动态堆积模型研究

本文首次提出了化学反应过程中几何可能性的定量研究.在下列条件下:(1)反应过程中,惰性配位体的键长,立体角系数等参数保持不变;(2)惰性配位体的压缩性很小;(3)在不压缩其它配位体的条件下,某一配位体在配位球面漂移所需的活化能低于这一配位体所形成的化学键断裂时所需的相应能量.我们提出动态堆积模型.以此来模拟反应过程中各个配位体间的相对位置和运动、配位体之间间隙的大小与受压缩的程度,并计算在反应中间过程中能够容纳新的配位体的最大空缺.考虑到使惰性配位体压缩将产生很大的空间势垒,以UCp3X为例说明了Lewis碱的配合与解离;金属-碳σ键的热分解以及一氧化碳插入反应的可能性.