亚甲基硅烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet methylidenesilene and ethylene has been investigated with MP2/6-31G^＊ and B3LYP/6-31G^＊ methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies of the involved conformers were calculated by CCSD（T）//MP2/6-31G＊ and CCSD（T）//B3LYP/6-31 G＊ methods, respectively. The results show that the dominant reaction pathway of the cycloaddition reaction is that a complex intermediate is firstly formed between the two reactants through a barrier-free exothermic reaction of 13.3 kJ/mol, and the complex is then isomefized to a four-membered ring product P2,1 via a transition state TS2.1 with a barrier of 32.0 kJ/mol.     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

亚烷基锡烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet alkylidenestannylene and ethylene has been investigated with MP2/3-21 G^* and B3LYP/3-21 G* methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//MP2/3-2 IG^* and CCSD(T)//B3LYP/3-21G^* methods, respectively. The results show that the dominant reaction pathway of the cycloaddition is that an intermediate (INT) is firstly formed between the two reactants through a barrier-free exothermic reaction of 39.7 kJ/mol, and the intermediate then isomerizes to a four-membered ring product (P2.1) via a transition state TS2.1 with a barrier of 66.8 kJ/mol.     

Theoretical study of mechanism of forming a silapolycyclic compound between methylenesilylene and acetone

The mechanism of the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by CCSD(T)//MP2/6‐31G* method. From the potential energy profile, we predict that the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has two competitive dominant reaction pathways. First dominant reaction pathway consists of four steps: (I) the two reactants (R1, R2) first form an intermediate (INT1) through a barrier‐free exothermic reaction of 46.2 kJ/mol; (II) intermediate (INT1) then isomerizes to a planar four‐membered ring product (P3) via transition state (TS3) with an energy barrier of 47.1 kJ/mol; (III) planar four‐membered ring product (P3) further reacts with acetone (R2) to form an intermediate (INT4), which is also a barrier‐free exothermic reaction of 40.0 kJ/mol; (IV) intermediate (INT4) isomerizes to a silapolycyclic compound (P4) via transition state (TS4) with an energy barrier of 57.0 kJ/mol. Second dominant reaction pathway consists of three steps: (I) the two reactants (R1, R2) first form a four‐membered ring intermediate (INT2) through a barrier‐free exothermic reaction of 0.5 kJ/mol; (II) INT2 further reacts with acetone (R2) to form an intermediate (INT5), which is also a barrier‐free exothermic reaction of 45.4 kJ/mol; (III) intermediate (INT5) isomerizes to a silapolycyclic compound (P5) via transition state (TS5) with an energy barrier of 49.3 kJ/mol. P4 and P5 are isomeric compounds. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Ab initio Study of Mechanism of Forming Germanic Hetero-Polycyclic Compound between Germylene Carbene (H2Ge=C: ) and Formaldehyde

The mechanism of the cycloaddition reaction of forming germanic hetero‐polycyclic compound between singlet germylene carbene and formaldehyde has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by CCSD (T)//MP2/6‐31G* method. From the potential energy profile, we predict that the cycloaddition reaction of forming germanic hetero‐polycyclic compound between singlet germylene carbene and formaldehyde has two competitive dominant reaction pathways. First dominant reaction pathway consists of four steps: (1) the two reactants (R1, R2) first form an intermediate (INT1) through a barrier‐free exothermic reaction of 117.5 kJ/mol; (2) intermediate (INT1) then isomerizes to a four‐membered ring compound (P2) via a transition state (TS2) with an energy barrier of 25.4 kJ/mol; (3) four‐membered ring compound (P2) further reacts with formaldehyde (R2) to form an intermediate (INT3), which is also a barrier‐free exothermic reaction of 19.6 kJ/mol; (4) intermediate (INT3) isomerizes to a germanic bis‐heterocyclic product (P3) via a transition state (TS3) with an energy barrier of 5.8 kJ/mol. Second dominant reaction pathway is as follows: (1) the two reactants (R1, R2) first form an intermediate (INT4) through a barrier‐free exothermic reaction of 197.3 kJ/mol; (2) intermediate (INT4) further reacts with formaldehyde (R2) to form an intermediate (INT5), which is also a barrier‐free exothermic reaction of 141.3 kJ/mol; (3) intermediate (INT5) then isomerizes to a germanic bis‐heterocyclic product (P5) via a transition state (TS5) with an energy barrier of 36.7 kJ/mol.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

硝基甲烷异构化反应势能面的ab initio研究

在B3LYP/6-311+ +G(2d,2p)水平上,优化得到硝基甲烷CH3NO2的10种异构体和23个异构化反应过渡态,并用G2MP2方法进行了单点能计算.根据计算得到的G2MP2相对能量,探讨了CH3NO2势能面上异构化反应的微观机理.研究表明,反应初始阶段的CH3NO2异构化过程具有较高的能垒,其中CH3NO2的两个主要异构化反应通道,即CH3NO2→CH3ONO和CH3NO2→CH2N(O)OH的活化能分别为270.3和267.8 kJ/mol,均高于CH3NO2的C-N键离解能.因而,从动力学角度考虑, CH3NO2的异构化反应较为不利.     

Theoretical study of mechanism of cycloaddition reaction between dichloro‐germylene carbene (Cl2GeC:) and aldehyde

The mechanism of the cycloaddition reaction between singlet dichloro‐germylene carbene and aldehyde has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by zero‐point energy and CCSD (T)//MP2/6‐31G* method. From the potential energy profile, it can be predicted that the reaction has two competitive dominant reaction pathways. The channel (A) consists of four steps: (1) the two reactants (R1, R2) first form an intermediate INT2 through a barrier‐free exothermic reaction of 142.4 kJ/mol; (2) INT2 then isomerizes to a four‐membered ring compound P2 via a transition state TS2 with energy barrier of 8.4 kJ/mol; (3) P2 further reacts with aldehyde (R2) to form an intermediate INT3, which is also a barrier‐free exothermic reaction of 9.2 kJ/mol; (4) INT3 isomerizes to a germanic bis‐heterocyclic product P3 via a transition state TS3 with energy barrier of 4.5 kJ/mol. The process of channel (B) is as follows: (1) the two reactants (R1, R2) first form an intermediate INT4 through a barrier‐free exothermic reaction of 251.5 kJ/mol; (2) INT4 further reacts with aldehyde (R2) to form an intermediate INT5, which is also a barrier‐free exothermic reaction of 173.5 kJ/mol; (3) INT5 then isomerizes to a germanic bis‐heterocyclic product P5 via a transition state TS5 with an energy barrier of 69.4 kJ/mol. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of mechanism of cycloaddition reaction between singlet dichlorosilylene carbene (Cl<Subscript>2</Subscript>Si=C:) and formaldehyde

The mechanism of the cycloaddition reaction between singlet dichlorosilylene carbene (Cl₂Si=C:) and formaldehyde has been investigated with MP2/6-31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by Zero-point energy and CCSD (T)//MP2/6-31G* method. From the potential energy profile, it can be predicted that the reaction has two competitive dominant reaction pathways. The first dominant reaction pathway consists of two steps: (1) the two reactants (R1, R2) firstly form a four-membered ring intermediate (INT4) through a barrier-free exothermic reaction of 387.9 kJ/mol; (2) intermediate (INT4) then isomerizes to H-transfer product (P4.2) via a transition state (TS4.2) with energy barrier of 4.7 kJ/mol. The second dominant reaction pathway as follows: on the basis of intermediate (INT4) created between R1 and R2, intermediate (INT4) further reacts with formaldehyde (R2) to form the intermediate (INT5) through a barrier-free exothermic reaction of 158.3 kJ/mol. Then, intermediate (INT5) isomerizes to a silicic bis-heterocyclic product (P5) via a transition state (TS5), for which the barrier is 40.1 kJ/mol.     

分子筛催化cis-2-丁烯的双键异构反应机理的DFT研究

基于含有两个Si和一个Al的分子筛3T簇模型, 利用密度泛函方法(DFT)研究了分子筛催化1-丁烯双键异构为cis-2-丁烯的反应机理. 在B3LYP/6-31G(d,p)计算水平上对反应各驻点进行了全优化, 并计算了反应的活化能. 研究发现, 分子筛上的酸性OH基团首先通过物理吸附靠近1-丁烯的双键, 形成了π配位复合物后, 丁烯双键的端基C原子逐渐抽取这个质子, 同时相邻酸性位的一个O原子也抽取丁烯碳链上的一个H原子, 形成吸附态的cis-2-丁烯, 最后通过脱附形成产物, 使分子筛复原, 反应按照协同反应机理发生. 计算得到的表观活化能是55.9 kJ/mol, 与实验结果接近.     

过充电保护添加剂1,4-二甲氧基苯的反应机理

采用密度泛函理论(B3LYP/6-311+G(d,p))和MP2/6-311+G(d,p)方法,研究锂离子电池过充电保护添加剂1,4-二甲氧基苯(p-DMOB)的作用机理.计算结果表明,在过充时,p-DMOB优先于溶剂分子(乙基甲基碳酸酯、二甲基碳酸酯、碳酸乙酯)发生氧化反应.用B3LYP和MP2计算所得的p-DMOB理论氧化电位接近,分别为4.12和4.05V(vsLi/Li+).p-DMOB氧化时首先失去一个电子,生成p-DMOB+·正离子自由基,用B3LYP和MP2方法计算所得的相应能量变化分别为701.24和728.27kJ·mol-1.失去电子后苯环的共轭性受到破坏,随后p-DMOB+·苯环上的C―H键发生断裂,失去H+并形成p-DMOB·自由基.用B3LYP和MP2方法计算所得的相应能量变化分别为1349.78和1810.99kJ·mol-1.p-DMOB·自由基很不稳定,会在电极表面发生聚合反应形成聚合物膜,用B3LYP和MP2方法计算所得的相应能量变化分别为-553.37和-1331.20kJ·mol-1.     

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.     

Facile ketene-ketene and ketene-ketenimine rearrangements: a study of the 1,3-migration of alpha-substituents interconverting alpha-imidoylketenes and alpha-oxoketenimines, a pseudopericyclic reaction

Theoretical calculations (B3LYP/6-311+G(3df,2p)//B3LYP/6-31G) of the 1,3 migration of NR(2) transforming alpha-oxoketenimines 1 to alpha-imidoylketenes 3 and vice versa indicate that this process is a pseudo-pericyclic reaction with a low activation energy (NH(2) 97 kJ mol(-1), N(CH3)(2) 62 kJ mol(-1)). The oxoketenimines were found to be more stable (by 18-35 kJ mol(-1)) which is in line with experimental observations. The hindered amine rotation in the amide and amidine moieties adjacent to the cumulenes are important in the migration of the NR(2) group, as one of the rotation transition states is close to the 1,3 migration pathway. This gives an interesting potential energy surface with a valley-ridge inflection (VRI) between the orthogonal hindered amine rotation and 1,3 migration transition states. The imidoylketene may also undergo ring closure to an azetinone 5; however, this is metastable, and under the conditions that allow the 1,3-migration, the oxoketenimine 1 will be favored. The imine NH E/Z-interconversion of the ketenimine group takes place by inversion and has a low activation barrier ( approximately 40 kJ mol(-1)). In all the amidines examined the E/Z-interconversion of the imine function was predicted to be by rotation with a high barrier (>80 kJ mol(-1)), in contrast to all other reported imine E/Z-interconversions which are by inversion.     

Computational methods in organic thermochemistry. 1. Hydrocarbon enthalpies and free energies of formation

Standard state enthalpies and free energies of formation can be computed with reasonable accuracy (usually within 4 and often 2 kJ/mol) using high level model chemistries. A comparison set of nearly 300 organic compounds ranging from 1 to 10 carbon atoms having a variety of functional groups for which enthalpy and free energy literature values are available has been examined using G2, G2MP2, G3, G3MP2, G3B3, G3MP2B3, CBS-QB3, and density functional (B3LYP/6-311+G(3df,2p)) model chemistries. G3 gives an average mean absolute deviation of 3.0 and 13.4 kJ/mol for the enthalpies and free energies, respectively, using the atomization method and 3.1 and 3.7 kJ/mol when bond separation reactions are employed. G3 and G3B3 are the most accurate overall; the related G3MP2 and G3MP2B3 are nearly as accurate and can compute larger molecules. CBS-QB3 was also found to be accurate but is more limited in the size of molecules that can be computed. The density functional energies were found to have large deviations from the literature values using either the atomization or the bond separation method. Regardless of the model employed, the free energies are increasingly underestimated by computation as the size of the molecule increases. A series of corrections applied to the aliphatic hydrocarbons is presented, which usually reduces the deviations to less than 4 kJ/mol regardless of the size of the molecule.     

二氯亚甲基锗烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet dichloromethylene germylene and ethylene has been investigated with B3LYP/6-31G＊ method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD（T）//B3LYP/6-31G＊ method. On the basis of the surface energy profile obtained with CCSD（T）// B3LYP/6-31G＊ method for the cycloaddition reaction between singlet dichloromethylene germylene and ethylene, it can be predicted that the dominant reaction pathway is that an intermediate INT1 is firstly formed between the two reactants through a barrier-free exothermic reaction of 61.7 kJ/mol, and the intermediate INT1 then isomerizes to an active four-membered ring product P2.1 via a transition state TS2, an intermediate INT2 and a transition state TS2.1, in which energy barriers are 57.7 and 42.2 kJ/mol, respectively.     

A theoretical study on the mechanism of the addition reaction between carbene and epoxyethane

The mechanism of addition reaction between carbene and epoxyethane has been investigated employing the MP2 and B3LYP/6-311+G* levels of theory. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Based on the calculated results at the MP2/6-311+G* level of theory, it can be predicted that there are two reaction mechanisms (1) and (2). In the first reaction carbene attacks the atom O of epoxyethane to form an intermediate 1a (IM1a), which is a barrier-free exothermic reaction. Then, IM1a can isomerize to IM1b via a transition state 1a (TS1a), where the potential barrier is 48.6 kJ/mol. Subsequently, IM1b isomerizes to a product epoxypropane (Pro1) via TS1b with a potential barrier of 14.2 kJ/mol. In the second carbene attacks the atom C of epoxyethane firstly to form IM2 via TS2a. Then IM2 isomerizes to a product allyl alcohol (Pro2) via TS2b with a potential barrier of 101.6 kJ/mol. Correspondingly, the reaction energies for the reactions (1) and (2) are −448.4 and −501.6 kJ/mol, respectively. Additionally, the orbital interactions are also discussed for the leading intermediate. The results based on the B3LYP/6-311+G* level of theory are paralleled to those on the MP2/6-311+G* level of theory. Furthermore, the halogen and methyl substituent effects of H₂C: on the two reaction mechanisms have been investigated. The calculated results indicate that the introductions of halogen or methyl make the addition reaction difficult to proceed.     

Theoretical Study of the AlEt3-Promoted Tandem Reductive Rearrangement of Epoxides

The AlEt3-promoted tandem reductive rearrangement reactions of epoxides was studied at B3LYP/6-31G(d,p) level. For the model compound σ-hydroxy epoxides, two possible reaction pathways I and II were calculated. The main difference is the order of ethylene release and six- to five-member ring rearrangement.The ring contraction rearrangement in pathway I is the first step and this step is the rate controlling step with a free energy barrier of 116.62 kJ/mol. For pathway II, the ethylene release occurs first, and is followed by a six-member ring opening reaction which is the rate controlling step, and the barrier is 251.38 kJ/mol.The reason for such high barrier is that the ethylene release results in the following reaction being moredifficult. The results show that pathway I (C-C rearrangement and then ethylene release) is more favorable,which is consistent with experimental results.     

木质素模化物紫丁香酚热解机理的量子化学研究

采用密度泛函理论方法B3LYP/6-31G++(d,p),对木质素模化物紫丁香酚的热解反应机理进行了量子化学理论研究。提出了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化。计算了各热解反应途径的标准动力学参数,分析了各种主要热解产物的形成演化机理。键离解能计算结果表明,紫丁香酚中CH₃-O键的键离解能最小,各种键离解能的大小顺序为CH₃-O < O-H < CH₃O-C_aromatic < CH₂-H < HO-C_aromatic < C_aromatic-H。在反应路径(1)中,主要热解产物是3-甲氧基邻苯二酚,其形成反应的总能垒为366.6 kJ/mol;在反应路径(2)中主要热解产物是2-甲氧基-6-甲基苯酚,其形成反应的总能垒为474.8 kJ/mol;在反应路径(3)中形成邻甲氧基苯酚的总能垒很低,为21.4 kJ/mol,这表明,在连接甲氧基的碳原子上加氢后能够有效地降低木质素芳环模化物紫丁香酚去甲氧基反应的反应能垒。     

Transition state for the gas-phase reaction of uranium hexafluoride with water

Density functional theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transition states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF 6, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F 5, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structures and relative energies of the reacting complex and transition state. However, a significant change in the structure of the product complex was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF 4, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF 6 with water.