Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction

This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy surface is a combined valence bond molecular mechanics (CVBMM) surface. Rate constants calculated with the CVBMM surface agree with the MPW54 rate constants within 12% for 534-2000 K and within 23% for 200-491 K. The full CVBMM potential-energy surface is now available for use in variety of dynamics calculations, and it provides a prototype for developing CVBMM potential-energy surfaces for other reactions.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.     

Experimental and theoretical multiple kinetic isotope effects for an SN2 reaction. An attempt to determine transition-state structure and the ability of theoretical methods to predict experimental kinetic isotope effects

The secondary alpha-deuterium, the secondary beta-deuterium, the chlorine leaving-group, the nucleophile secondary nitrogen, the nucleophile (12)C/(13)C carbon, and the (11)C/(14)C alpha-carbon kinetic isotope effects (KIEs) and activation parameters have been measured for the S(N)2 reaction between tetrabutylammonium cyanide and ethyl chloride in DMSO at 30 degrees C. Then, thirty-nine readily available different theoretical methods, both including and excluding solvent, were used to calculate the structure of the transition state, the activation energy, and the kinetic isotope effects for the reaction. A comparison of the experimental and theoretical results by using semiempirical, ab initio, and density functional theory methods has shown that the density functional methods are most successful in calculating the experimental isotope effects. With two exceptions, including solvent in the calculation does not improve the fit with the experimental KIEs. Finally, none of the transition states and force constants obtained from the theoretical methods was able to predict all six of the KIEs found by experiment. Moreover, none of the calculated transition structures, which are all early and loose, agree with the late (product-like) transition-state structure suggested by interpreting the experimental KIEs.     

Stationary fronts due to weak thermal effects in models of catalytic oxidation

We analyze the possible existence of an infinite number of stationary front solutions in a microkinetic model of a catalytic reaction coupled with weak enthalpy effects in the domain of kinetics bistability. The kinetic model incorporates three steps: dissociative oxygen adsorption, reactant adsorption and desorption, and surface reaction. The infinitude of stationary front solutions emerges due to the lack of intercrystallites communication of surface species in supported catalysts; thermal conductions and gas-phase diffusion are the only means of interaction. Incorporation of surface species diffusion leads to a very slow front motion. We complement this analysis with simulations of stationary states on one- (wire and ring) and two-dimensional (disk) systems which may be subject to control or to fluid flow. These results account for certain experimental results and may have implications for various technological problems.     

On the mechanism of dioxygen formation from a di-mu-oxo-bridged manganese dinuclear complex

Density functional theory (DFT) calculations, using the Becke-Perdew gradient-corrected functional with a triple-zeta-plus-polarization basis set, have been used to characterize the [(H(2)O)(H(3)N)(3)Mn(mu-O)(2)Mn(NH(3))(3)(OH(2))](q)(+) (q = 2-5) complexes. This structure has been proposed as a possible model for the oxygen-releasing site of the photosystem II (PSII) reaction center. We have performed full optimizations to locate stationary points in various spin states for each of the +2 to +5 charge states. Our calculations indicate that O(2) release from the vacuum-phase +5 charge state complex is barrier inhibited, in contrast to the results of a recent DFT study. We report several new di-mu-oxo-bridged stationary points with spin multiplicities of S = (1)/(2), (3)/(2), and (5)/(2) and effective metal oxidation states of Mn(IV)Mn(V) for the +5 charge state. Finally, calculations employing the 'conductorlike screening model' (COSMO), to address the inclusion of solvent effects, indicate that dissociative O(2) release from the +5 charge state model complex is inhibited by a major barrier and is therefore apparently highly disfavored.     

Theoretical study on the mechanism of the cycloaddition reaction between stannylene and ethylene or formaldehyde

The mechanism of the cycloaddition reaction of singlet stannylene and ethylene or formaldehyde has been studied by using density functional theory. The geometrical parameters, harmonic vibrational frequencies and energies of stationary points for potential energy surface are calculated by RB3LYP/3–21G* method. The results show that the two reaction processes are both two steps: (1) stannylene and ethylene or formaldehyde form an energy‐rich intermediate complex respectively, which is an exothermal reaction with no barrier; (2) two intermediate complexes isomerize to the product, respectively, with the barriers of these two reactions being 52.97 and 45.15 kJ/mol at RB3LYP/3–21G* level.     

FNC→FCN IRC途径中化学键的变化

利用电子密度分布函数的拓朴分析方法,研究化学反应中键的断裂与生成的变化过程,是理论化学的新课题。本文作者利用CNDO/2方法计算了若干基态分子体系,对其电子密度分布进行拓扑分析,所得结论与Bader等人精确从头算的结果定性一致。本文用CNDO/2及Abinitio(STO-3G)计算了FNC→FCN IRC途径上的若干点。一方面讨论这一反应过程中化学键特性的变化,一方面比较上述两种计算方法所得电子密度的拓扑性质的导同。     

Modeling Active Centers in Ammonia Synthesis. DFT Study of Dissociative Adsorption of N2 on Ru Clusters

Models of possible active centers (AC) of nitrogen adsorption on ruthenium clusters are suggested. An AC is represented by a labile Ru_n (n = 6, 7) cluster stabilized in carbon nanotubes. Nanotubes are modeled by the C₆₀ cluster. Density functional theory (DFT) is used to calculate the stationary points of the reaction path of dissociative adsorption of N₂ on the suggested AC. Optimal structures and transition state (TS) energies are determined. The effect of alkali metal (Cs) additions on the activation energy is investigated.     

Activation Energy and Transition State Determination of the Olefin Insertion Process of Metallocene Catalysts Using a Semiempirical Molecular Orbital Calculation

The transition state of the olefin insertion process of metallocene catalysts can be determined by adopting the semiempirical PM3 model. In computational chemistry, the computational methods most employed are the ab initio method and density functional theory, which are very time consuming. The semiempirical molecular orbital method requires much less computational resources than the above methods. However, the accuracy and reliability of the semiempirical molecular orbital method remains to be determined. The PM3 model is the most recently developed the semiempirical molecular orbital method and can also be applied to transition metal calculations. This study is intended to investigate the reliability of computational results determined using semiempirical PM3 model on metallocene catalysts through comparison with published results on the density functional theory (DFT). The saddle point finding procedure is adopted to find the transition state of the ethylene insertion process of metallocene catalysts. Results on the geometry and energy trends of the ethylene insertion process of metallocene catalysts determined using the PM3 model are in good agreement with the DFT results. In addition, the saddle point of the potential energy surface of ethylene insertion is verified in accordance with the eigenvalue of the vibrational frequency spectrum. Correct eigenvalues indicate that the correct saddle point of the potential energy surface of ethylene insertion has been successfully located. Hence, the eigenvalue of the vibrational frequency spectrum is a valuable reference in terms of saddle point justification. Computational results and vibrational frequency spectrum analysis demonstrate that the PM3 model can be used to locate the correct saddle point of the potential energy surface. The results obtained using the PM3 model confirm that the eigenvalue of the transition state lies nearly on the vibrational frequency spectrum. The eigenvalues are also analyzed, providing a valuable reference for further studies of the transition state of olefin insertion of metallocene catalysts. The activation energies for the olefin insertion reaction are also studied for evaluation of the catalyst.     

Ab initio and direct quasiclassical-trajectory study of the Cl + CH4-->HCl + CH3 reaction

We present an electronic structure and dynamics study of the Cl + CH(4)--> HCl + CH(3) reaction. We have characterized the stationary points of the ground-state potential-energy surface using various electronic structure methods and basis sets. Our best calculations, CCSD(T) extrapolated to the complete basis-set limit based on geometries and harmonic frequencies obtained at the CCSD(T)/aug-cc-pvtz level, are in agreement with the experimental reaction energy and indirect measurements of the barrier height. Using ab initio information, we have reparametrized a semiempirical Hamiltonian so that the predictions of the improved Hamiltonian agree with the higher-level calculations in various regions of the potential-energy surface. This improved semiempirical Hamiltonian is then used to propagate quasiclassical trajectories and characterize the reaction dynamics. The good agreement of the calculated HCl rotational and angular distributions with the experiment indicates that reparametrizing semiempirical Hamiltonians is a promising approach to derive accurate potential-energy surfaces for polyatomic reactions. However, excessive energy leakage from the initial vibrational energy of the CH(4) molecule to the reaction coordinate in the trajectory calculations calls into question the suitability of the standard quasiclassical-trajectory method to describe energy partitioning in polyatomic reactions.     

锗烯X2Ge(X=H、CH3、F、Cl、Br)与乙烯环加成反应的量子化学研究

利用量子化学密度泛函理论的B3LYP方法,在6-311G**的水平上,对锗烯X2Ge(X=H、CH3、F、Cl、Br)与C2H4的环加成反应进行了计算研究.结果表明,锗烯的基态是单重态,取代基的电负性越强,单-三态的能量差越大;控制反应的因素是电子效应,而不是立体效应;取代基的电负性越强,反应的活化能越高,放热越少;该反应由两步组成,第一步生成中间配合物,是一个无势垒的放热过程,第二步经过渡态生成产物.     

单重态二溴卡宾和甲醛环加成反应的量化研究

采用量子化学密度泛函理论,研究了单重态二溴卡宾和甲醛环加成反应的机理.在B3LYP/6-31G*基组水平上,优化得到了反应途径上反应物、过渡态、中间体和产物的几何构型;计算并考察了四种可能反应途径势能面上各驻点的构型参数、振动频率和能量;通过振动分析对过渡态和中间体构型进行了确认.计算结果表明,二溴卡宾和甲醛反应有四条反应通道,其中c反应通道(即0°-0°型)控制步骤的活化能仅为13.7 kJ·mol－1,反应容易进行.     

CHF_2Br与激发态氧原子O(~1D)的反应机理研究

利用密度泛函理论(DFT)研究了CHF2Br与O(1D)的反应机理.首先在B3LYP/6-311+G(d)水平上优化了各驻点的几何结构,并通过频率分析加以确认;然后利用内稟反应坐标理论,以相同的方法计算了反应的最小能量途径,进而确认了过渡态所连接的反应物和产物;最后在B3LYP/aug-cc-pvtz水平上对所有驻点的能量进行了校正.     

CH3S与HO2气相反应机理的理论研究

采用密度泛函理论的B3LYP方法, 在6-311＋＋G(d,p)基组水平上研究了CH3S自由基与HO2自由基的微观反应机理, 全参数优化了反应势能面上各驻点的几何构型, 振动分析和内禀反应坐标(IRC)分析结果证实了中间体和过渡态的真实性, 计算所得的键鞍点电荷密度的变化情况也确认了反应过程. 找到了五条可能的反应通道, 对结果的分析表明: 单线态反应通道(5) CH3S＋HO2→CH3SOOH (1P), 是所有通道中的主要反应通道. 该通道不需要克服过渡态能垒, 属于放热反应, 在动力学和热力学上都是最为有利的. 对于三线态反应通道来说, 通道(1)CH3S＋HO2→COM11→TS1→COM12→CH3SH＋O2 (3P)为主要反应通道, 控制步骤的活化能为53.5 kJ/mol, 能垒最低, 属于放热反应, 在动力学和热力学上都是有利的.     

Substituent effects on heats of formation, group interactions, and detonation properties of polyazidocubanes

We have calculated the heats of formation (HOFs) for a series of polyazidocubanes by using the density functional theory (DFT), Hartree-Fock, and MP2 methods with 6-31G* basis set as well as semiempirical methods. The cubane skeleton was chosen for a reference compound, that is, the cubane skeleton was not broken in the process of designing isodesmic reactions. There exists group additivity for the HOF with respect to the azido group. The semiempirical AM1 method also produced reliable results for the HOFs of the title compounds, but the semiempirical MINDO3 did not. The relationship between HOFs and molecular structures was discussed. It was found that the HOF increases 330-360 kJ/mol for each additional number of the azido group being added to the cubane skeleton. The distance between azido groups slightly influences the values of HOFs. The interacting energies of neighbor azido groups in polyazidocubanes are in the range of 2.3 approximately 6.6 kJ/mol, which are so small and less related to the substituent numbers. The average interaction energy between nearest neighbor --N3 groups in the most stable conformer of octaazidocubane is 2.29 kJ/mol at the B3LYP/6-31G* level. The relative stability related to the number of azido groups of the title compounds was assessed based on the calculated HOFs, the energy gaps between the frontier orbitals, and the bond orders of the C--N3 and C--C bonds. The predicted detonation velocity of hepta- and octa-derivatives is over 9 km/s, and the detonation pressure of them is ca. 40 GPa or over.     

Six-dimensional quantum dynamics of dissociative chemisorption of H2 on Ru(0001)

Six-dimensional quantum dynamics calculations on dissociative chemisorption of H(2) on Ru(0001) are performed. The six-dimensional potential energy surface is generated using density functional theory. Two different generalized gradient approximations are used, i.e., RPBE and PW91, to allow the results to be compared. The dissociation probability for normally incident H(2) on a clean Ru(0001) surface is calculated. Large differences between the reaction probabilities calculated using the RPBE and PW91 are seen, with the PW91 results showing a much narrower reaction probability curve and a much higher reactivity. Using the reaction probabilities and assuming normal energy scaling reaction rates are generated for temperatures between 300 and 800 K. The rate generated using the PW91 results is higher by about a factor 5 than the rate based on the RPBE results in the range of temperatures relevant to ammonia production.     

Conformational behavior of some hydroxamic acids

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.     

DFT研究SiN与ClO反应的产物通道

利用量子化学从头算和密度泛函理论(DFT)对SiN和ClO反应机理进行了理论研究.在B3LYP/6-311 G(d,p)水平上优化得到了反应势能面上各驻点的几何构型;通过频率分析和内禀反应坐标(IRC)计算对过渡态与反应物和产物的连接关系进行确认.在CCSD(T)/cc-pVTZ水平上对各物种的能量进行校正,得到了反应势能面.计算结果表明：该反应体系存在单态和三态势能面,其中单态势能面上反应通道(1)和(2)是主反应通道,P4为主产物.     

Theoretical studies of furoxan-based energetic nitrogen-rich compounds

Density functional theory calculations were performed to study the effects of different substituents and nitrogen-containing heterocyclic rings on the heats of formation (HOFs), energetic properties, and thermal stability for a series of furoxan derivatives. The isodesmic reaction method was employed to calculate the HOFs of the derivatives using total energies obtained from electronic structure calculations. The detonation velocities and pressures were evaluated by using the semiempirical Kamlet–Jacobs equations, based on the theoretical densities and HOFs. The bond dissociation energies and bond orders for the weakest bonds were analyzed to investigate the thermal stability of the furoxan derivatives. These results provide basic information for the molecular design of novel high energy density materials.