(H_2O)_n(n=0～2)催化HS和HOCl反应机理的理论研究

在CCSD(T)/6-311+G(3df,2p)//M06-2X/6-311+G(3df,2p)水平上研究了(H_2O)n(n=0~2)催化HS和HOCl的反应机理.结果表明,HS与HOCl反应中HS夺取HOCl上的H原子形成产物H_2S和ClO.在无水催化时,该反应存在2种不同的路径(分别经过过渡态TS1和TS2,二者互为顺反结构),对应的能垒分别为100.28和100.91kJ/mol,到达产物(H_2S+ClO)需吸收18.99kJ/mol能量,反应不易发生;在单个水分子参与时,水分子可通过形成弱相互作用或者作为H原子转移桥梁影响反应机理,获得了4种水催化路径,能垒(间于53.97~92.39kJ/mol之间)均低于无水催化过程.同时发现,在反应到达产物前,水分子可以与产物形成中间体IM,IM相对能仅为0.46kJ/mol,有利于产物形成;有2个水分子参与反应时,找到了3条催化路径,最优反应路径过渡态TS7的能垒为45.05kJ/mol,低于无水催化过程,相比单个水分子最优路径能垒(53.97kJ/mol)并无显著降低.     

A theoretical study on the water-mediated asynchronous addition between urea and formaldehyde

The reaction between urea and formaldehyde in water solution was theoretically investigated by using B3LYP and MP2 methods.It was found that the addition of the nitrogen atom in urea to the carbonyl group in formaldehyde precedes the proton transfer and the proton migration from water to the carbonyl group occurs before the proton abstraction from the nitrogen.With one or two water molecules involved in the TS.the activation energy barrier is lowered compared to the TS of the mechanism with no water participation.The energy change along the reaction coordinate clearly shows that a zwitterionic-like intermediate does not exist on the PES.The reaction between urea and formaldehyde occurs in a concerted mechanism but with asynchronous characters.This is different from the stepwise mechanism recently found for the amination reactions of formaldehyde.     

Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water

The reaction mechanism for the dehydration of 1,4-butanediol in hot water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER). We have assumed that the proton transfers along the hydrogen bonds of the water molecules catalyze the reaction, where the transition state (TS) forms a singlet biradical electronic structure. It has been revealed by the simulation that the biradical electronic state at the TS changes to zwitterionic structure in solution due to the hydration of the polar solvent. Such the electronic structure change gives rise to the substantial stabilization of the TS in hot water. As a result, the water-catalytic path becomes more favorable in aqueous solution than another possible path that proceeds without proton transfers as opposed to the reaction mechanism in the gas phase. Furthermore, the activation free energy computed by the present method is in excellent agreement with the experimental result.     

Theoretical study of the reaction mechanism and solvent effect on the regioselectivity of 1,3‐dipolar cycloaddition reaction between azide and acetylene derivatives

The reaction mechanism and solvent‐dependant regioselectivity of 1,3‐dipolar cycloaddition reactions between azide and acetylene derivatives have been studied using computational methods. The two possible reaction transition states were located. Geometry and NBO analysis found that the reactions take place along a synchronous and concerted mechanism for TS1 and an asynchronous and less concerted mechanism for TS2 . SCRF analysis found that TS2 is more sensitive to the polarity of solvent. In less polar solvent such as CCl₄, the difference of activation barriers of the two transition states is small. However, when the reactions were conducted in water, the activation barriers for TS2 increase which leads to the observed regioselectivity. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:203–207, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20236     

4-氟苯甲醛、β-萘胺和Meldrum酸-锅反应生成1-(4-氟苯基)-1,2-二氢苯并[f]喹啉-3(4H)-酮的反应机理理论研究

采用密度泛函理论(DFT)研究了4-氟苯甲醛、β-萘胺和Meldrum酸一锅反应生成1-(4-氟苯基)-1,2-二氢苯并[f]喹啉-3(4H)-酮的微观反应机理.在B3LYP/6-311G*基组水平上优化了反应物、过渡态、中间体及产物的几何构型,通过振动分析确认了过渡态的结构,并用内禀反应坐标(IRC)确认反应途径.应用分子中的原子理论(AIM)分析了这些物质的成键特征.采用SCRF(PCM)方法研究了反应体系的溶剂化效应.报道了可能的反应路径,其中Re→TS1→IM1→TS2→IM2→TS3→IM3→TS4→IM5→TS7→IM9→TS13→IM10→TS14→P3具有相对较低的活化能,是反应的主要通道,理论预测的主要产物与实验吻合.     

4-氟苯甲醛、β-萘胺和Meldrum酸一锅反应生成1-(4-氟苯基)-1,2-二氢苯并[f]喹啉-3(4H)-酮的反应机理理论研究

采用密度泛函理论(DFT)研究了4-氟苯甲醛、β-萘胺和Meldrum酸一锅反应生成1-(4-氟苯基)-1,2-二氢苯并[f]喹啉-3(4H)-酮的微观反应机理.在B3LYP/6-311G*基组水平上优化了反应物、过渡态、中间体及产物的几何构型,通过振动分析确认了过渡态的结构,并用内禀反应坐标(IRC)确认反应途径.应用分子中的原子理论(AIM)分析了这些物质的成键特征.采用SCRF(PCM)方法研究了反应体系的溶剂化效应.报道了可能的反应路径,其中Re→TS1→IM1→TS2→IM2→TS3→IM3→TS4→IM5→TS7→IM9→TS13→IM10→TS14→P3具有相对较低的活化能,是反应的主要通道,理论预测的主要产物与实验吻合.     

水催化2个酯分子相互转化反应的理论研究

从印楝植物内生真菌Phomopsis sp.培养液中分离得到的4-acetoxymultiplolide(1)和1-acetoxymultiplo-lide(2)在室温及水存在下能够相互转化. 提出二者相互转化最可能的4个途径(机理A~D). 在B3LYP/6-311+G(d,p)水平进行气相条件的优化, 结果表明, 无水催化的机理A中TS1和TS2的活化能均显著大于120 kJ/mol, 2个分子水催化的机理D中TS1和TS2的活化能则显著降低. 计算结果显示水的溶剂化效应能进一步降低机理D中TS1和TS2的活化能. 在MP2/6-311++G(2d,2p)//B3LYP/6-311+G(d,p)水平计算了单点能, 得到在水相时机理D中TS1和TS2的活化能分别为106.24和107.37 kJ/mol. 因此, 机理D是化合物1 和2在室温下及水存在时相互转化最可能的途径, 该途径是一种特殊的水催化分子内酯的醇解反应, 也是一种经典的亲核加成反应, 通过一种新的叔醇中间体实现.     

Diels-Alder ribozyme catalysis: a computational approach

A computational comparison of the Diels-Alder reaction of a maleimide and an anthracene in water and the active site of the ribozyme Diels-Alderase is reported. During the course of the catalyzed reaction, the maleimide is held in the hydrophobic pocket while the anthracene approaches to the maleimide through the back passage of the active site. The active site is so narrow that the anthracene has to adopt a tilted approach angle toward maleimide. The conformation of the active site changes marginally at different states of the reaction. Active site dynamics contribution to catalysis has been ruled out. The active site stabilizes the product more than the transition state (TS). The reaction coordinates of the ribozyme reaction in TS, RC1-CD1 and RC4-CD2, are 2.35 and 2.33 A, respectively, compared to 2.37 and 2.36 A in water. The approach angle of anthracene toward maleimide is twisted by 18 degrees in the TS structure of ribozyme reaction while no twisted angle is found in TS of the reaction in water. The free energy barriers for reactions in both ribozyme and water were obtained by umbrella sampling combined with SCCDFTB/MM. The calculated free energy barriers for the ribozyme and water reactions are in good agreement with the experimental values. As expected, Mulliken charges of the atoms involved in the ribozyme reaction change in a similar manner as that of the reaction in water. The proficiency of the Diels-Alder ribozyme reaction originates from the active site holding the two reactants in reactive conformations, in which the reacting atoms are brought together in van der Waals distances and reactants approach to each other at an appropriate angle.     

几种过渡态结构的有效优化方法

通过双桥反应机理、电环合反应和催化反应三个不同类型的过渡态优化，说明当标准方法难以给出结果时，对物理问题本身的分析有助于给出过渡态优化的线索．第一个例子根据化学问题给出限制条件，通过平衡几何构型优化方法优化得到过渡态；第二个例子是在使用标准过渡态优化方法失败后，根据物理问题从反应途径上用平衡几何构型优化方法选择过渡态优化的初始结构；第三个例子通过Gaussian 98程序中的标准方法QST2直接得到过渡态．     

Novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: free energy calculation for the Beckmann rearrangement promoted by proton transfers in the supercritical water

The Beckmann rearrangement of acetone oxime promoted by proton transfers in the supercritical water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER) recently developed. The transition state (TS) structures have been explored by ab initio calculations for the reaction of hydrated acetone oxime on the assumption that the reaction is catalyzed by proton transfers along the hydrogen bonds connecting the solute and the solvent water molecules. Up to two water molecules have been considered as reactants that take part in the proton transfers. As a result of the density functional theory calculations with B3LYP functional and aug-cc-pVDZ basis set, it has been found that participation of two water molecules in the reaction reduces the activation free energy by -12.3 kcal/mol. Furthermore, the QM/MM-ER simulations have revealed that the TS is more stabilized than the reactant state in the supercritical water by 2.7 kcal/mol when two water molecules are involved in the reaction. Solvation free energies of the reactant and the TS have been decomposed into terms due to the electronic polarization of the solute, electron density fluctuation, and others to elucidate the origin of the stabilization of the TS as compared with the reactant. It has been revealed that the promotion of the chemical reaction due to the hydration mainly originates from the interaction between the nonpolarized solute and the solvent water molecules at the supercritical state.     

Dynamics effects on an E2/E1cb borderline mechanism: unimolecular elimination of 2-aryl-3-chloro-2-R-propanols

The mechanistic dichotomy between concerted E2 and stepwise E1cb of the base-promoted elimination of 2-aryl-3-chloro-2-R-propanols was examined computationally at the HF, M05-2X, and MP2 levels of theory. Optimizations of transition states (TSs) and reaction intermediates, and intrinsic reaction coordinates (IRC) calculations showed that there was a single reaction route for each substrate, and that the mechanism could be changed from E2 to E1cb by making a carbanion intermediate more stable through the introduction of electron-withdrawing substituents. Molecular dynamics simulations revealed that trajectories started at a single TS led directly to two product regions; the carbanion intermediate region in the E1cb mechanism, and the alkene product region in the E2 mechanism, through path bifurcation after the TS. The present system is a new example of bifurcation in reactions of closed-shell molecules. The overall reaction mechanism changes dynamically from E2 to E1cb by a gradual change in the ratio of E2 and E1cb trajectories, rather than a path switch in concurrent pathways.     

Quantum mechanical design of enzyme active sites

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.     

Mechanism of pyridine protonation in water clusters of increasing size

This work presents a theoretical mechanistic study of the protonation of pyridine in water clusters, at the B3LYP/cc-pVDZ theory level. Clusters from one to five water molecules were used. Starting from previously determined structures, the reaction paths for the protonation process were identified. For complexes of pyridine with water clusters of up to three water molecules just one transition state (TS) links the solvated and protonated forms. It is found that the activation energy decreases with the number of water molecules. For complexes of four and five water molecules two transition states are found. For four water molecules, the first TS links the starting solvated structure with a new, less stable, solvated form through a concerted proton transfer between a ring of water molecules. The second TS links the new solvated structure to the protonated form. Thus, protonation is a two-step process. For the five water molecules cluster, the new solvated structure is more stable than the starting one. This structure exhibits two double hydrogen bonds involving the pyridinic nitrogen and several water molecules. The second TS links the new structure with the protonated form. Now the process occurs in one step. In all cases considered, the proton transfers involve an interconversion between covalent and hydrogen bonds. For four and five water molecules, the second TS is structurally and energetically very close to the protonated form. As evidenced by the vibration frequencies, this is due to a flat potential energy hypersurface in the direction of the reaction coordinate. Determination of DeltaG at 298.15 K and 1 atm shows that the protonation of pyridine needs at least four water molecules to be spontaneous. The complex with five water molecules exhibits a large DeltaG. This value yields a pKa of 2.35, relatively close to the reported 5.21 for pyridine in water.     

The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin

The mechanism of cis-trans isomerization of prolyl peptides catalyzed by cyclophilin (CyP) was studied computationally via molecular dynamics (MD) simulations of the transition state (TS) and the cis and trans forms of the ground state (GS), when bound to CyP and when free in aqueous solution. The MD simulations include four enzyme-bound species of tetrapeptide (Suc-Ala-XC([double bond]O)-NPro-Phe-pNA; X = Gly, Trp, Ala, and Leu). In water, the prolyl amide bond is favorably planar with the presence of conformers exhibiting +/-20 degrees twist of the C-N dihedral. In the active site a hydrogen bond between the cis-prolyl amide carbonyl O and the backbone amide N-H of Asn102 retains the 20 degrees twist of the C-N dihedral. The TS structure is characterized by a 90 degrees twist of the amide C-N bond and a more favorable interaction with Asn102 due to the shorter distance between Asn102(HN) and the amide carbonyl O. The conformational change of cis --> TS also involves pyramidalization of the amide N, which results in the formation of a hydrogen bond between the amide N and the guanidino group of Arg55. Both Asn102 and Arg55 are held in the same position in CyP.cis-isomer as in CyP.TS. In the ligand-free CyP the Arg55 guanidino group is highly disorganized and Asn102 is displaced 1 A from the position in the ligand-bound CyP. Thus, the organization of Arg55 and Asn102 occurs upon substrate binding. The geometrical complimentarity of the organized enzyme structure to the TS structure is a result of preferential binding of the proline N and the amide carbonyl of the TS compared to that of GS. However, the N-terminal part (Suc-Ala) becomes repositioned in the TS such that two hydrogen bonds disappear, one hydrogen bond appears and two other hydrogen bonds becomes weaker on the conversion of CyP.cis to CyP.TS. During this conversion, total hydrophobic contact between enzyme and the peptide is preserved. Thus, the interaction energies of GS and TS with enzyme are, as a whole, much alike. This does not support the contention that TS is bound more tightly than GS by K(m)/K(TS) = 10(6) in the cis --> trans reaction. Repositioning of the N-terminal part of the peptide on CyP.TS formation becomes more pronounced when the substrate X residue is changed from Gly < Trp < Ala < Leu. We propose that the larger turning of the N-terminus is responsible for the larger value of the experimentally observed Delta S(++) and Delta H(++), which sum up to little change in Delta G(++). The positioning of the Arg55 and the degree of 20 degrees twist of the amide C-N bond are considered as criteria for Near Attack Conformers (NACs) in cis-trans isomerization. NACs account for approximately 30% of the total GS populations of the cis-isomer. Similar NAC populations were observed with four different substrates. This is consistent with the insensitivity of enzymatic activity to the nature of the X residue. Also, the NAC population in CyP.trans-AAPF was comparable to that in CyP.cis-AAPF, in accord with similar experimentally measured rates of the cis --> trans and trans --> cis reaction in CyP. These NACs, found in CyP.cis and CyP.trans, resemble only one of the four possible TS configurations in the water reaction. The identity of this TS structure (syn/exo) is in accord with experimentally determined KIE values in the enzymatic reaction. However, the geometry of the active site was also complementary to another TS structure (anti/exo) that was not detected in the active site by the same KIE measurements, implying that the geometrical fitness of the TS cannot be a single determining factor for enzymatic reactions.     

CF3O2自由基和NO反应机理的理论研究

用密度泛函理论(DFT)的B3LYP方法, 分别在6-31G、6-311G、6-311+G(d)基组水平上研究了CF3O2自由基和NO反应机理. 研究结果表明, CF3O2自由基和NO反应存在三条可行的反应通道, 优化得到了相应的中间体和过渡态. 从活化能看, 通道CH3O2+NO→IM1→TS1→IM2→TS2→CF3O+ONO的活化能最低, 仅为70.86 kJ•mol-1, 是主要反应通道, 主要产物是CF3O和NO2. 而通道CH3O2+NO→IM1→TS3→CF3ONO2和CH3O2+NO→TS4→IM3→TS5→IM4→TS6→CF3O+NOO的活化能较高, 故该反应难以进行.     

Computational study on the reaction pathway of α-bromoacetophenones with hydroxide ion: possible path bifurcation in the addition/substitution mechanism

The reaction of an α-haloketone with a nucleophile has three reaction channels: carbonyl addition, direct substitution, and proton abstraction. DFT calculations for the reaction of PhCOCH(2)Br with OH(-) showed that there exists an addition/substitution TS on the potential energy surface, in which OH(-) interacts with both the α- and carbonyl carbons. The intrinsic reaction coordinate calculations revealed that the TS serves as the TS for direct substitution for XC(6)H(4)COCH(2)Br with an electron-donating X or a X less electron-withdrawing than m-Cl, whereas the TS serves as the TS for carbonyl addition for derivatives with a X more electron-withdrawing than m-CF(3). Trajectory calculations starting at respective TS indicated that the single TS can serve for the two mechanisms, substitution and addition, through path bifurcation after the TS for borderline substrates. The reaction is the first example of dynamic path bifurcation for fundamental reaction types of carbonyl addition and substitution.     

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions

Chorismate mutase is at the centre of current controversy about fundamental features of biological catalysts. Some recent studies have proposed that catalysis in this enzyme does not involve transition state (TS) stabilization but instead is due largely to the formation of a reactive conformation of the substrate. To understand the origins of catalysis, it is necessary to compare equivalent reactions in different environments. The pericyclic conversion of chorismate to prephenate catalysed by chorismate mutase also occurs (much more slowly) in aqueous solution. In this study we analyse the origins of catalysis by comparison of multiple quantum mechanics/molecular mechanics (QM/MM) reaction pathways at a reliable, well tested level of theory (B3LYP/6-31G(d)/CHARMM27) for the reaction (i) in Bacillus subtilis chorismate mutase (BsCM) and (ii) in aqueous solvent. The average calculated reaction (potential energy) barriers are 11.3 kcal mol(-1) in the enzyme and 17.4 kcal mol(-1) in water, both of which are in good agreement with experiment. Comparison of the two sets of reaction pathways shows that the reaction follows a slightly different reaction pathway in the enzyme than in it does in solution, because of a destabilization, or strain, of the substrate in the enzyme. The substrate strain energy within the enzyme remains constant throughout the reaction. There is no unique reactive conformation of the substrate common to both environments, and the transition state structures are also different in the enzyme and in water. Analysis of the barrier heights in each environment shows a clear correlation between TS stabilization and the barrier height. The average differential TS stabilization is 7.3 kcal mol(-1) in the enzyme. This is significantly higher than the small amount of TS stabilization in water (on average only 1.0 kcal mol(-1) relative to the substrate). The TS is stabilized mainly by electrostatic interactions with active site residues in the enzyme, with Arg90, Arg7 and Glu78 generally the most important. Conformational effects (e.g. strain of the substrate in the enzyme) do not contribute significantly to the lower barrier observed in the enzyme. The results show that catalysis is mainly due to better TS stabilization by the enzyme.     

Topological structure of mechanisms of complex reactions

A new concept is proposed, the topological structure of the mechanism of chemical reactions (TS), reflecting the set of interrelations of intermediates and reactants. In order to identify the TS of a mechanism, topological information must be obtained through kinetic methods for describing the process, through certain chemical and physical methods of identifying individual links in the TS and through chemical modeling of the stages. Feasibility has been demonstrated for application of graph theory methods in classifying, codifying, and determining the complexity of TS of reaction mechanisms. Techniques are described for identifying the TS of mechanisms of catalytic reactions, involving analysis of the structure of hypothetical nodes of conjugation of stage sequences in the formation of products, and also techniques for purposeful changes in the TS of the mechanism of a complex reaction.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 3, pp. 282–291, May–June, 1988.     

A spin-coupled study of the Claisen rearrangement of allyl vinyl ether

The spin-coupled (SC) form of modern valence bond (VB) theory is utilised to examine the electronic structure of the transition state (TS) and the electronic reaction mechanism of the Claisen rearrangement of allyl vinyl ether. The differences between the spin-coupling patterns and orbital overlap integrals at the optimised TS geometries obtained using B3LYP/6-31G^*, MP2/6-31G^* and MP4(SDQ)/6-31G^* wavefunctions are minimal, and the SC picture suggests that the TS is non-aromatic. SC calculations along the intrinsic reaction coordinates computed at these three levels of theory also produce near identical results. The SC wavefunctions at different stages of the reaction provide easily interpretable orbital diagrams which, in combination with the changes in the orbital overlap integrals, indicate an electronic reaction mechanism involving concerted, though not entirely synchronous, bond breaking and bond formation processes. The evolution of the active space spin-coupling pattern, which is closely related to the classical VB concept of resonance, combined with the changes in the orbital overlap integrals, show that the reaction path involves a region in which the electronic structure of the reacting system becomes similar to that of benzene. This suggests that during the Claisen rearrangement the reacting system can attain moderately aromatic character but that this does not necessarily happen at the TS. The results of the SC analysis indicate that the most appropriate schematic representation of the Claisen rearrangement is furnished by a homolytic mechanism in which six harpoons describe the changes in the bonding pattern from reactant to product     

A quantum mechanics study on the reaction mechanism of chalcone formation from p-coumaroyl-CoA and malonyl-CoA catalyzed by chalcone synthase

Chalcone synthase catalyzes formation of phenylpropanoid chalcone from one p-coumaroyl-coenzyme A (CoA) and three malonyl-CoA molecules. In order to elucidate structural and energetic features of the reaction mechanism, we performed the quantum mechanics calculations and obtained the following results. In loading step, only a tetrahedral intermediate is located without transition state (TS). Our results indicate that His303 acts as a H₃₁ donor, but not a hydrogen bond donor, to stabilize the intermediate formation. In decarboxylation step, the reaction proceeds via a TS and is sensitive to the environment. In elongation step, a tetrahedral TS is located. All of the results above support the reaction mechanism and further complement the proposal of Noel JP et al.