Theoretical modeling study for the phosphonylation mechanisms of the catalytic triad of acetylcholinesterase by sarin

Potential energy surfaces for the process of phosphonylation of the catalytic triad of acetylcholinesterase by sarin have been explored at the B3LYP/6-311G(d,p) level of theory through a computational study. It is concluded that the phosphonylation process involves a critical addition-elimination mechanism. The first nucleophilic addition process is the rate-determining step. The following elimination process of the fluoride ion comprises a composite reaction that includes several steps, and it occurs rapidly by comparison with the rate-determining step. The mobility characteristics of histidine play an important role in the reaction. A double proton-transfer mechanism is proposed for the catalytic triad during the phosphonylation process of sarin on AChE. The effect of aqueous solvation has been considered via the polarizable continuum model (PCM). One concludes that the energy barriers are generally lowered in solvent, compared to the gas-phase reactions.     

脂肪酰胺水解酶催化三联体膦酰化失活的机理：一个模型体系的理论研究

甲基花生四烯基氟代膦酸酯(MAFP)是脂肪酰胺水解酶(FAAH)的一个抑制剂. FAAH的丝氨酸241(Ser241)-丝氨酸217(Ser217)-赖氨酸142(Lys142)催化三联体被MAFP膦酰化后将导致FAAH失活. 本文采用B3LYP/6-311G(d,p)和MP2/6-311G(d,p)方法及一个简化的计算模型体系对这个膦酰化抑制反应进行理论研究. 考虑了两种反应途径. Path A涉及FAAH的催化三联体的所有残基, 是一个分步的加成-消除过程, 形成两性离子的三角双锥中间体, 其中第一步反应是决速步骤. 在这个反应途径中, Ser217和Lys142对亲核试剂Ser241起到碱催化活化的作用, 而Ser217充作Lys142和Ser241之间的桥梁. 此外, 溶剂中的一个水分子作为Lys142和MAFP间的“氢桥”具有关键的作用, 通过给出和接收质子促进了长距离的质子转移. Path B是催化三联体中的残基Lys142被突变为丙氨酸以后的膦酰化反应, 也是一个分步过程. 水的本体溶剂效应通过极化连续介质模型(PCM)估算. 计算结果显示膦酰化反应的Path A是优势途径, 在水溶液中其决速步骤的活化能垒为64.9 kJ·mol-1. FAAH催化三联体中残基Lys142的变异会降低膦酰化反应的速率, 这与实验结果相一致.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Induction heating enables efficient heterogeneous catalytic reactions over superparamagnetic nanocatalysts

Most catalytic processes are achieved by heating the whole reaction systems including the entire reactor,substrate and solvent, which leads to energy loss and obvious heat transfer limits. In this study, induction heating was employed to boost the catalytic Suzuki-Miyaura cross-coupling reactions by using conductive superparamagnetic microspheres with loaded Pd nanoparticles as heterogeneous catalysts. It was found that, at the same apparent reaction temperatures, the reactions by adopting the i...     

Solvent Impedes CO2 Cycloaddition on Metal–Organic Frameworks

The catalytic performance of metal–organic frameworks (MOFs) for the synthesis of cyclic carbonate from carbon dioxide and epoxides has been explored under solvent and solvent‐free conditions, respectively. It was found that MOF catalysts have significantly improved catalytic activities in solvent‐free CO₂ cycloaddition reactions than those in solvent. The mechanism was discussed with regard to the competition of solvent with substrate to adhere MOF catalysts during the reaction process.     

Phosphonylation mechanisms of sarin and acetylcholinesterase: a model DFT study

Potential energy surfaces for the phosphonylation of sarin and acetylcholinesterase (AChE) have been theoretically studied at the B3LYP/6-311G(d,p) level of theory. The obtained results show that the phosphonylation process involves a two-step addition-elimination mechanism, with the first step (addition process) being the rate-determining step, while by comparison, the ensuing steps are very rapid. Stable trigonal bipyramidal intermediates are formed in the studied pathways. It is also revealed that the catalytic triad of acetylcholinesterase plays the catalytic role in the reaction by speeding up the phosphonylation process, as it does in the acylation reaction of ACh and AChE. The effect of aqueous solvation was accounted for via the polarizable continuum model. It is concluded that the enzymatic reaction here is influenced strongly by the solvent environment.     

2-Nitrobenzylarsonium Compounds That Photorelease Heavy-Atom Cholinergic Ligands for Time-Resolved Crystallographic Studies on Cholinesterases

As heavy-atom analogues of caged cholinergic ligands, the arsonium compounds 1 – 3 were synthesized for potential time-resolved crystallographic studies on cholinesterases. Compounds 1 and 3 possess the desired properties for dynamic studies on the catalytic mechanism of cholinesterases: structural similarity with the N-homologue, strong X-ray diffracting effect of arsenic, inhibitory effects on cholinesterases, and excellent photofragmentation kinetics.     

Simple and Convenient Method for the Synthesis of Aryltellurophosphates Catalyzed by Cesium Hydroxide

In the presence of a catalytic amount cesium hydroxide, the corresponding aryltellurophosphates can be obtained by the reactions of dialkyl phosphites with diaryl ditellurides in excellent yield at room temperature, using dimethylsulfoxide as solvent. The possible reaction mechanism was discussed. The method could provide a new and expedient path for the preparation of aryltellurophosphates.     

Direct ab‐initio molecular dynamics study on the radiation effects on catalytic triad composed of Ser‐His‐Glu residues

High energy irradiation to the hydrogen bonded system is important in relevance with the initial process of DNA and enzyme damages. In the present study, the effects of radiation to catalytic triad have been investigated by means of direct ab‐initio molecular dynamics (AIMD) calculation. As a model of the catalytic triad, Ser‐His‐Glu residue, which is one of the important enzymes in the acylation reaction, was examined. The ionization and electron attachment processes in Ser‐His‐Glu were investigated as the radiation effects. The direct AIMD calculation showed that a proton of His is spontaneously transferred to carbonyl oxygen of Glu after the ionization. However, the whole structure of catalytic triad was essentially kept after the ionization. On the other hand, in the case of the electron capture in the model catalytic triad Ser‐His‐Glu, the dissociation of Glu residue from [Ser‐His]^? was found as a product channel. The mechanism of ionization and electron capture process in the catalytic triad was discussed on the basis of theoretical results. © 2015 Wiley Periodicals, Inc.     

Metal-free,noncovalent catalysis of diels-alder reactions by neutral hydrogen bond donors in organic solvents and in water

We examined the catalytic activity of substituted thioureas in a series of Diels-Alder reactions and 1,3-dipolar cycloadditions. The kinetic data reveal that the observed accelerations in the relative rates are more dependent on the thiourea substituents than on the reactants or solvent. Although the catalytic effectiveness is the strongest in noncoordinating, nonpolar solvents, such as cyclohexane, it is also present in highly coordinating polar solvents, such as water. In 1,3-dipolar cycloadditions, the thiourea catalysts demonstrate only very moderate selectivity for reactions with inverse electron demand. Our experiments emphasize that both hydrophobic and polar interactions can co-exist, making these catalysts active, even in highly coordinating solvents. This class of catalysts increases the reaction rates and endo-selectivities of Diels-Alder reactions, in a similar manner to weak Lewis acids, without concomitant product inhibition.     

富氮多孔有机聚合物催化制备α⁃氰基肉桂酸乙酯

α-氰基肉桂酸乙酯作为含多种官能团的缺电子烯烃, 是一种极具应用价值的有机合成反应底物, 主要通过催化Knoevenagel缩合反应获得. 本文以多聚甲醛和三聚氰胺为前驱体, 采用溶剂热法制备富氮多孔有机聚合物mPMF, 经K₂CO₃处理得到K₂CO₃-mPMF-X(X=1, 10, 50). 考察了mPMF在苯甲醛和氰乙酸乙酯Knoevenagel缩合反应中的催化性能, 通过mPMF与K₂CO₃-mPMF-X催化活性的比较, 探讨了碱性强弱对Knoevenagel缩合反应的影响, 并对催化反应机理进行了探索. 结果表明, 催化剂中丰富的氮物种为反应提供了碱性环境和大量的碱性活性位点, 催化剂碱性强弱的控制是催化合成α-氰基肉桂酸乙酯的关键因素. mPMF在甲醇溶剂中于60 ℃反应3 h后, 苯甲醛转化率为97%, 目标产物选择性在99.9%以上.     

ReBr(CO)_5-Catalyzed Knoevenagel Condensation

Knoevenagel condensations are especially important reactions for the synthesis of alkene compounds having electron-withdrawing groups such as COR,CN,COOR,NO2 etc. Recently, transition metal hydride ruthenium1, hydride and polyhydride rhenium2, and polyhydride iridium complexes have been found to be the efficient catalysts for Knoevenagle condensation. However the mentioned-above transition metal hydride complexes are not easily prepared. In addition, all of them are oxygen and H2O-sensit…     

Facile synthesis of TMS-protected trifluoromethylated alcohols using trifluoromethyltrimethylsilane (TMSCF3) and various nucleophilic catalysts in DMF

Organofluorine compounds are becoming increasingly important in different fields, such as material science, agro chemistry, and the pharmaceutical industry. Nucleophilic trifluoromethylation is one of the widely used methods to incorporate a trifluoromethyl moiety into organic molecules. We have carried out extensive studies to develop varieties of easily accessible nucleophilic catalysts to promote such reactions. TMS-protected trifluoromethylated alcohols were prepared from both aldehydes and ketones in excellent yields using catalytic amount of amine N-oxide. Carbonate and phosphate salts also showed efficient catalytic activity toward this reaction. These reactions were highly solvent dependent, and DMF was found to be the most suitable one among the various solvents studied. All these reactions proceeded under very mild conditions, giving clean products and avoiding the use of any fluoride initiators or expensive catalysts, and extremely water-free conditions. The mechanism for the reaction is discussed in detail. DFT calculations were performed on the possible reaction intermediates using the Gaussian 03 program at B3LYP/6-311+G* level to support the proposed mechanism.     

Dramatic solvent and hydration effects on the transition state of soybean peroxidase

Enzymes are shown to function in nonaqueous media; however, relatively little information is available on the influence of the organic solvent as well as its associated water content on the properties of the enzymatic transition states. A better understanding of these effects will be useful in developing kinetic models that can then be used to predict optimal solvent and substrate choices for enzymatic reactions in organic media. The influence of the reaction media on soybean peroxidase-catalyzed oxidation of para-substituted phenols was studied using Hammett analysis for several organic solvent systems. The catalytic activity and substrate specificity of the enzyme are influenced by the nature of the solvent and its associated hydration. These findings may allow one to draw conclusions about the reaction mechanism and the roles of solvent and solvent hydration on enzyme function.     

果糖一步转化制备呋喃基燃料：溶剂效应及离子液体修饰活性金属对产物选择性的决定作用

在众多生物基化合物中,2,5-二甲基呋喃(DMF)是一种有实用前景的可再生液体生物质燃料,也是一种具有重要价值的化学品,可作为生产对苯二甲酸的原料.2,5-二甲基四氢呋喃(DMTF)是DMF进一步加氢产物,该化合物比DMF更稳定,适合长期保存;由于具有更高的氢碳比,用作生物燃料燃烧时能够释放更多能量.研究生物质资源制备DMF和DMTF对可再生资源制备液体燃料和化学品具有重要意义.从生物质多糖出发制备这两类化合物,中间经历了水解、脱水、加氢、加氢脱氧等多个反应步骤,每一步反应都十分复杂,包含许多副反应途径.此外,由于每一步反应条件的不兼容性,大多数研究集中在分步反应阶段,鲜有文献能够实现从碳水化合物原料直接转化为DMF和DMTF.发展由生物质一锅法多步耦合转化技术制备化学品和燃料,不仅具有科学意义,而且可大大简化反应过程,避免中间产物分离和损失,节省资源和时间,历来受到化学家和工业界的关注.本文利用离子液体对Ru/C催化剂电子性质的修饰作用以及溶剂效应的影响,设计了离子液体/THF双相体系中果糖直接催化转化制备2,5-二甲基呋喃(DMF)和2,5-二甲基四氢呋喃(DMTF)的新路线.该转化过程耦合了果糖脱水制HMF、HMF加氢及加氢脱氧生成DMF和DMTF等多步反应.通常在HMF加氢转化过程中, Ru/C催化剂的高活性易导致HMF深度加氢生成大量开环产物及气体,我们借助离子液体与有机溶剂的不同溶解性,筛选出[BMIm]Cl/THF双相溶剂体系,使极性HMF在离子液体层反应,生成弱极性的DMF和DMTF能及时被THF萃取出来,有效稳定了目标产物.其次,果糖转化为HMF会产生少量水,通常水的存在易导致HMF发生水合等副反应,对下一步的加氢转化是不利因素;然而在本催化体系中,由于[BMIm]Cl能与水以较强的氢键结合形成水合物,对水分子起到了束缚作用,减少了HMF发生水解、水合等副反应的机会.另一方面,离子液体粘度较大,微量水的存在能降低离子液体层粘度,改善传质,从而提高反应速率.在HMF加氢处理过程中,离子液体对DMF和DMTF的生成起了决定作用.当反应体系中不添加离子液体,以THF为溶剂,反应结束后未检测到DMF生成, DMTF的收率仅为2%,但HMF已经完全转化.取气体样品进行GC分析,发现有部分气相产物生成,包括CO2、CH4和C2H6等.液体混合物进行GC-MS检测,发现产物主要包括DHMTF、5-甲基四氢糠醇(MTFA)、四氢糠醇(TFA)、1,2-戊二醇、DMTF、2-己醇和少量戊醇,产物中所有呋喃环结构的双键都发生加氢反应.以上结果表明,没有离子液体的THF中, Ru/C催化的HMF涉氢反应平衡已发生改变.当反应体系中添加0.2 g离子液体[BMIm]Cl进行HMF的加氢时,此时开始有DMF生成,随着[BMIm]Cl量依次增加, DMF以及DMTF的收率也呈上升趋势.1.0 g离子液体获得两种产物最高收率为68%.然而,如果进一步增加[BMIm]Cl的量到2.0 g,呋喃基液体燃料DMF和DMTF的收率却开始下降.综合以上实验结果,我们认为适量的[BMIm]Cl存在有可能会对催化剂物理化学性质造成影响,从而对产物的选择性起了决定性作用.通过对催化剂进行元素分析、XPS、H2-TPR表征以及一系列对比实验证明,离子液体不仅促进果糖脱水转化为HMF,同时在HMF选择性加氢反应中可修饰活性金属电子性质,改变催化路径,是多步串联反应能够耦合的关键因素.在[BMIm]Cl/THF双相溶剂体系中,离子液体的“溶剂笼效应”促进DMF和DMTF高效生成, THF的萃取功能对目标产物的稳定起了关键作用.以上对催化剂和溶剂的合理设计共同促进高产率呋喃基燃料的获得.该研究实现由六碳糖直接选择转化获取DMF和DMTF,为生物质高效催化转化制备生物基能源化学品提供了新思路.     

Catalytic reactions of C4 hydrocarbons on the fluid catalytic cracking catalyst

利用小型固定流化床实验装置,对C4烃类在催化裂化催化剂上催化转化反应规律进行了实验研究,考察了不同反应温度及空速对C4烃类催化转化反应的产物分布和组成的影响。实验结果表明,催化裂化催化剂对C4烃类具有一定芳构化和裂化性能,在适宜的反应条件下,可增产芳烃和丙烯;在C4烃类催化转化过程中,丁烯是主要的反应物,而丁烷几乎不反应;低反应温度有利于增产芳烃,高反应温度有利于增产丙烯。较低的空速对增产芳烃和丙烯都有利。根据双分子反应机理和反应结果,建立了C4烃类在催化裂化催化剂上催化转化过程的反应网络。对C4烃类催化转化历程分析表明,中间产物碳五和碳六烯烃较弱的二次裂化性能是C4烃类在催化裂化催化剂上催化转化过程中乙烯和丙烯产率较低的主要原因。     

催化反应中休眠期与诱导期之区别

许多化学反应中都存在一个被定义为"诱导期"的起始反应速率较低的阶段，例如一些自由基反应、放热反应和催化反应。与之相比，在极少数的催化反应中研究者观察到一个反应速率始终为零的特殊阶段，在这个阶段之后反应自发开始。这两种阶段形成的原因与反应的机理尤其是催化剂的活化和失活有关。然而，这两个具有明显不同特征的阶段往往被混淆。本文通过所选取的一些代表性的催化反应分别介绍了"诱导期"和"休眠期"的动力学特征，讨论了两者之间的区别。期待这些隐藏在稳态催化循环之前的阶段能够得到更多的关注，这将有利于研究人员深度理解有机化学反应中的前催化循环和详细的反应机理。     

The reactant state for substrate-activated turnover of acetylthiocholine by butyrylcholinesterase is a tetrahedral intermediate

Secondary beta-deuterium kinetic isotope effects have been measured as a function of substrate concentration for recombinant human butyrylcholinesterase-catalyzed hydrolysis of acetyl-L3-thiocholine (L = 1H or 2H). The isotope effect on V/K is inverse, D3V/K = 0.93 +/- 0.03, which is consistent with conversion of the sp2 hybridized carbonyl carbon of the scissile ester bond of the E + A reactant state to a quasi-tetrahedral structure in the acylation transition state. In contrast, the isotope effect on Vmax under conditions of substrate activation is markedly normal, D3(betaVmax) = 1.29 +/- 0.06, an observation that is consistent with accumulation of a tetrahedral intermediate as the reactant state for catalytic turnover. Generally, tetrahedral intermediates for nonenzymatic ester hydrolyses are high-energy steady-state intermediates. Apparently, butyrylcholinesterase displays an unusual ability to stabilize such intermediates. Hence, the catalytic power of cholinesterases can largely be understood in terms of their ability to stabilize tetrahedral intermediates in the multistep reaction mechanism.     

KOtBu‐Catalyzed Michael Addition Reactions Under Mild and Solvent‐Free Conditions

Designed transition metal complexes predominantly catalyze Michael addition reactions. Inorganic and organic base‐catalyzed Michael addition reactions have been reported. However, known base‐catalyzed reactions suffer from the requirement of solvents, additives, high pressure and also side‐reactions. Herein, we demonstrate a mild and environmentally friendly strategy of readily available KO^tBu‐catalyzed Michael addition reactions. This simple inorganic base efficiently catalyzes the Michael addition of underexplored acrylonitriles, esters and amides with (oxa‐, aza‐, and thia‐) heteroatom nucleophiles. This catalytic process proceeds under solvent‐free conditions and at room temperature. Notably, this protocol offers an easy operational procedure, broad substrate scope with excellent selectivity, reaction scalability and excellent TON (>9900). Preliminary mechanistic studies revealed that the reaction follows an ionic mechanism. Formal synthesis of promazine is demonstrated using this catalytic protocol.