碳源甲基苯热裂解机理的密度泛函动力学研究

在热力学研究的基础上,用UB3LYP/3-21G^*方法对甲苯热裂解机理进行了动力学研究。计算得到了甲苯的5种热裂解路径的活化能。用过渡状态理论,计算得到了这些路径在298～1223K温度范围内的速率常数。动力学计算结果表明：甲苯在热解温度低于963K时的主反应路径为甲苯热裂解生成苄基自由基的反应,其速控步的活化能△E~0^θ^≠=402.27kJ/mol;当温度高于963K达1223K左右时,主反应路径转为苯环上脱甲基生成苯基和甲基自由基的路径,该路径的活化能△E~0^θ^≠=456.91kJ/mol。以上研究结果与实验结果相一致。     

化学反应的内禀反应坐标法V. 顺-, 反-氟代乙烯基负离子异构化反应的反应路径解析

本文对顺-, 反-氟代乙烯基负离子异构化反应的反应途径进行了微观动力学解析。在RHF/4-31G水平上优化求得了反应物、过渡态及产物的平衡几何和总能量, 得到了活化能、反应热、A因子及活化熵等一些物理量, 从反应物到过渡态的振动相关表明: 正则振动模式是各自独立的; 键角H(1)-C-C的伸缩振动模式直接与内禀进动(IRC)相连结。这为模式选择化学反应的研究提供了信息。     

Thermodynamic origin of the increased rate of hydrolysis of phosphate and phosphorothioate esters in DMSO/water mixtures

The hydrolysis rates of the dianions of phosphate and phosphorothioate esters are substantially accelerated by the addition of polar aprotic solvents such as DMSO and acetonitrile. The activation barrier DeltaG is smaller due to a lower enthalpy of activation. The enthalpy of transfer of p-nitrophenyl phosphate (pNPP) and p-nitrophenyl phosphorothioate (pNPPT), from water to 0.6 (mol) aq DMSO (60 mol % water in DMSO) were measured calorimetrically. The enthalpies of activation for the hydrolysis reactions in the two solvents permitted the calculation of the enthalpy of transfer of the transition states. This transfer is thermodynamically favorable for both the reactants and the transition states but is more favorable for the transition states. In the case of pNPP, the enthalpy of transfer of the reactant is -23.9 kcal/mol, compared to -28.3 for the transition state. The difference is greater for pNPPT, where the enthalpy of transfer of the reactant is -23.2 kcal/mol and that for the transition state is -35.3. The results show that the reduced enthalpies of activation in both hydrolysis reactions arise not from a destabilization of the reactants in the mixed solvent, but from the fact that the enthalpy of transfer of the transition states to the mixed solvent is significantly more negative than the enthalpy of transfer of the reactants.     

IRC analysis of methanol carbonylation reaction catalyzed by rhodium complex

In the reaction cycle for methanol carbonylation catalyzed by Rh complex, the structure geometries of the reactant, intermediates, transition states and product of each elemental reaction have been studied by using the energy gradient method at HF/LANL2DZ level, and the changes of their potential profiles have also been calculated. Through IRC analyses of the transition states for each elemental reaction, it is confirmed that the various structure geometries obtained are stationary points on the cycle reaction pathway of methanol carbonylation catalyzed by Rh complex, and the changes are given in energies and structure geometries of the reactant molecules along the reaction pathway of lowest energy. It has been proposed that the geometrical conversions of intermediates play an important role during the cycle reaction. Through analyses of structure geometries, it has been suggested that, in addition to cis- and trans-structure exchange linkage of catalysis reactive species, the two pathways, cis- and tra     

A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: an analysis of tunneling and thermal activation

We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.     

Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined QM/MM molecular dynamics simulations have been carried out for the dehalogenation reaction of the nucleophilic displacement of dichloroethane catalyzed by haloalkane dehalogenase. The computed chlorine kinetic isotope effects and free energies of activation in the wild-type and the Phe172Trp mutant enzyme are found to be consistent with experiment. In comparison with the uncatalyzed model reaction in water, the enzyme lowers the activation barrier by about 16 kcal/mol. The enormous enzymatic action was attributed to a combination of contributions from a change in the solvation effect and transition state stabilization. The unique features of tryptophan's ability to interact favorably with hydrophobic substrates and to form hydrogen bonds to the leaving group chloride ion at the transition state enable both factors to make significant contributions to the barrier lowering mechanism in the enzyme. This is in contrast to the reference reaction in water, in which hydrogen bonding interactions are weakened at the transition state because of dispersed charge distribution at the transition state relative to that in the reactant and product states.     

1,2-C4H6→2-C4H6异构化反应机理的理论研究

采用自洽场分子轨道UHF/6-31G**从头算法,研究了1,2-C4H6→2-C4H6异构化反应机理,优化了基态势能面上反应物、过渡态、中间体和产物的几何构型,并对各驻点能量进行了零点能校准.结果表明该反应经历一个1-甲基环丙烯生成产物比经两步氢迁移反应历程更易发生.     

SiH_3NO_2－SiH_3ONO异构化的量子化学研究

用ＭＮＤＯ法研究了ＳｉＨ_３ＮＯ_２和其异构体ＳｉＨ_３ＯＮＯ之间的转化。结果表明，Ｓｉ－Ｎ键的断裂和Ｓｉ－Ｏ键的生成有较小的能垒，反应为放热过程。     

A dimensionless reaction coordinate for quantifying the lateness of transition states

The Hammond‐Leffler postulate asserts that transition states of exothermic reactions are reactant‐like (early), whereas transition states of endothermic reactions are product‐like (late). Related postulates have been proposed to describe the sensitivity of activation barriers for reactions occurring on catalytic surfaces to the catalyst structure. To evaluate the validity of these postulates for different chemical reactions, a general method for classifying transition states as either early or late is needed. One can envision a dimensionless reaction coordinate that changes continuously and monotonically from 0 to 1 along a minimum energy reaction pathway. The value of the dimensionless reaction coordinate for the transition state (W_TS) classifies transition states as (a) early when W_TS < 0.5, (b) late when W_TS > 0.5, and (c) equidistant between reactants and products when W_TS = 0.5. In this article, we derive such a dimensionless reaction coordinate and illustrate its usefulness for several different chemical reactions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

N-亚苯基氨基酰胺气相高温分解反应机理的密度泛函研究

利用密度泛函理论研究了N-亚苯基氨基酰胺气相高温分解生成苯腈和苯甲酰胺的反应机理。首先用B3LYP／6-31G(d,p)方法优化反应中反应物、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,并通过内稟反应坐标方法(IRC)确认能量最低的反应途径。本文报道了三条可能的反应通道,包括一条直接协同高温分解反应和两条先成环后协同高温分解反应途径,其中直接协同高温分解反应由于能垒低,因此发生的几率较大     

DFT Study on Intermolecular Cleavage Reaction of N-(2-Hydroxyphenyl)-phthalamic Acid

The reaction mechanisms of intermolecular cleavage reaction of N-(2-hydroxyphenyl)-phthalamic acid were studied via the density functional theory(DFT). All geometries of the reactant, transition states, and products were optimized at the B3LYP/6-31G(d, p) level. Vibration analysis was carried out to confirm its identity as transitions’ structure, and the intrinsic reaction coordinate method(IRC) was used to search the minimum energy path. Two possible reaction channels are reported in this article. The calc...     

基态氧(3^O2)氧化硅烯的密度泛函计算研究

采用密度泛函[B3LYP(full)/6-311+G^*]方法研究了基态氧(3^O2)氧化硅烯(Si2H4)的机理。计算了三重态初始中间体(IM(T1)到单重态中间体IM2(S0)反应交叉势能面,报道了各反应中间体、产物和过渡态的构型和能量,用频率分析方法对各过渡态进行了验证,进一步用IRC方法对主要的基元反应进行了考察,确定了历经生成1,2-二氧环氧硅烷中间体的氧化过程的主要反应通道。     

Gas‐phase pyrolysis mechanisms of 3‐anilino‐1‐propanol: Density functional theory study

The gas‐phase pyrolytic decomposition mechanisms of 3‐anilino‐1‐propanol with the products of aniline, ethylene, and formaldehyde or N‐methyl aniline and aldehyde were studied by density functional theory. The geometries of the reactant, transition states, and intermediates were optimized at the B3LYP/6‐31G (d, p) level. Vibration analysis was carried out to confirm the transition state structures, and the intrinsic reaction coordinate method was performed to search the minimum energy path. Four possible reaction channels are shown, including two concerted reactions of direct pyrolytic decomposition and two indirect channels in which the reactant first becomes a ring‐like intermediate, followed by concerted pyrogenation. One of the concerted reactions in the direct pyrolytic decomposition has the lowest activation barrier among all the four channels, and so, it occurs more often than others. The results appear to be consistent with the experimental outcomes. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics

We present a quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution in the framework of mixed quantum-classical molecular dynamics, where the reactant and product states are explicitly defined by dividing the double-well potential into the reactant and product wells. The equation can describe quantum reaction processes such as tunneling and thermal excitation and relaxation assisted by the solvent. Fluctuations of the zero-point energy level, the height of the barrier, and the curvature of the well are all included in the equation. Here, the equation was combined with the surface hopping technique in order to describe the motion of the classical solvent. Applying the present method to model systems, we show two numerical examples in order to demonstrate the potential power of the present method. The first example is a proton transfer by tunneling where the high-energy product state was stabilized very rapidly by solvation. The second example shows a thermal activation mechanism, i.e., the initial vibrational excitation in the reactant well followed by the reacting transition above the barrier and the final vibrational relaxation in the product well.     

Efficient exploration of reaction paths via a freezing string method

The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants. Existing surface walking techniques to locate such transition states typically require an extremely good initial guess that is often beyond human intuition to estimate. To alleviate this problem, automated techniques to locate transition state guesses have been created that take the known reactant and product endpoint structures as inputs. In this work, we present a simple method to build an approximate reaction path through a combination of interpolation and optimization. Starting from the known reactant and product structures, new nodes are interpolated inwards towards the transition state, partially optimized orthogonally to the reaction path, and then frozen before a new pair of nodes is added. The algorithm is stopped once the string ends connect. For the practical user, this method provides a quick and convenient way to generate transition state structure guesses. Tests on three reactions (cyclization of cis,cis-2,4-hexadiene, alanine dipeptide conformation transition, and ethylene dimerization in a Ni-exchanged zeolite) show that this "freezing string" method is an efficient way to identify complex transition states with significant cost savings over existing methods, particularly when high quality linear synchronous transit interpolation is employed.     

化学反应的内禀反应坐标法（X）：氨基卡宾脱氢反应的从头计算研究

氨基卡宾作为重要的反应中间体引起了人们的兴趣,它可分别通过1,1-H_2消除和1,2-H_2消除2种脱氢方式分别生成氰和异氰,但对这两个反应过程的细致研究至今未见报道,本文利用内禀反应坐标(IRC)法对氨基卡宾的2种脱氢反应途径进行微观动力学解析,并对反应途径上的振动相关问题做了理论探讨。     

Reaction ergodography for the additions of HLi and its dimer to acetylene

The ab initio calculation has been performed with the addition pathways of HLi and its dimer to acetylene at the RHF/3-21G basis set. It shows that the reaction mechanisms of these two reactions are rather similar. In either of two reaction pathways, there is a meta-stable molecular complex near the isolated reactant state. This kind of addition can be treated approximately as the unimolecular reaction in which the molecular complex rearranges into the product. We have estimated the activation entropies and the statistical A factors of these two reactions by the use of RRKM theory. Frontier molecular orbital analysis of these two transition states reveals their HOMOS to be formed from both HOMO-LUMO and HOMO-HOMO interactions.     

Role of stereoelectronic features of imine and enamine in (S)-proline catalyzed Mannich reaction of acetaldehyde: an in silico study

A detailed mechanistic investigation of sixteen possible diastereomeric pathways for the C-C bond formation step in (S)-proline catalyzed Mannich reaction of acetaldehyde with N-acetyl protected benzaldimine in acetonitrile solvent has been carried out to understand how stereoelectronic features invoke enantioselectivity of the final product. Both kinetic and thermodynamic factors of the reaction obtained using various density functional theory methods point out that si-enantiofacial nucleophilic attack of anti-enamine on the iminium carbon of the E, s-cis N-acetyl protected imine is the stereoselective pathway. Structural features of the transition states predicted that enamine in anti conformation attacks the imine through a Burgi-Dunitz trajectory to yield the stereocenter. Computations at B3LYP-PCM/6-311++G(3df,2p)//B3LYP-PCM/6-31G(d,p) level showed a strong linear correlation between Burgi-Dunitz angle and activation energy when anti-enamine is used as nucleophile to react with all the configurations of the imine. Further, energy decomposition analysis has been carried out at B3LYP/TZ2P+ level for all the transition states, which revealed that the most dominant factor that control the enantioselectivity of the (S)-proline catalyzed Mannich reaction is steric effect. Though the less favored transition states showed high amount of stabilizing orbital interaction, the destabilizing steric effects from both Pauli repulsion and preparation energy for the reactant molecules are very high and overshadowed the stabilizing effects. However, in the most favored transition state, a balanced outcome of electronic and steric effects was observed. Solvation effect was nearly same for all the transition states and electrostatic effects showed no correlation to the rank order of the energy of the transition states.     

卡宾与氢氰酸加成反应机理的量子化学研究

用MNDO法研究单线态卡宾与氢氰酸的反应途径,通过两条不同反应途径的能量比较,得到了此反应可行的反应机理。     

DFT studies of the methyl exchange reaction between Cp2M-CH3 or Cp*2M-CH3 (Cp = C5H5, Cp* = C5Me5, M = Y, Sc, Ln) and CH4. Does M ionic radius control the reaction?

The activation energies for the methyl exchange reactions between Cp2M-CH3 and H-CH3 have been calculated for M = Sc, Y and representative metals of the lanthanide family (La, Ce, Sm, Ho, Yb and Lu) with DFT(B3PW91) calculations with large-core pseudopotentials for M. The sigma-bond metathesis reactions are calculated to have lower activation energies for early lanthanides than for late lanthanides and any of group 3 metals. The relative activation barriers are analyzed using the NBO charge distributions in the reactant and in the transition states. It is shown that the methane needs to be polarized in the transition state as H((+delta))-CH3((-delta)) by the reactant, because this sigma-bond metathesis is best viewed as heterolytic cleavage of methane, leading to a proton transfer between two methyl groups in the field of an electropositive M metal. Early lanthanides, which are involved in strongly ionic metal-ligands bonds are thus associated with the lowest activation energies. The ionic radius and the steric effects influence the relative rates of reaction for the complexes of Sc, Y and Lu. In agreement with earlier works of Sherer et al., the experimental reactivity trends found by Tilley are reproduced best with Cp*2M-CH3 (Cp* = C5Me5) rather than Cp2M-CH3 (Cp = C5H5) because the steric bulk of C5Me5 deactivates most the complex where the metal has the smallest ionic radius (Sc). While the steric effects and the influence of the metal ionic radius cannot be neglected, these factors are not the only ones involved in determining the activation barriers of the sigma-bond metathesis reaction.