Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of diazomethane to ethene

The electronic mechanism for the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane (CH2N2) to ethene (C2H4) is described through spin-coupled (SC) calculations at a sequence of geometries along the intrinsic reaction coordinate obtained at the MP2/6-31G(d) level of theory. It is shown that the bonding rearrangements occurring during the course of this reaction follow a heterolytic pattern, characterized by the movement of three well-identifiable orbital pairs, which are initially responsible for the pi bond in ethene and the C-N pi bond and one of the N-N pi bonds in diazomethane and are retained throughout the entire reaction path from reactants to product. Taken together with our previous SC study of the electronic mechanism of the 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne (C2H2) (Theor. Chim. Acc. 1998, 100, 222), the results of the present work suggest strongly that most gas-phase concerted 1,3-dipolar cycloaddition reactions can be expected to follow a heterolytic mechanism of this type, which does not involve an aromatic transition state. The more conventional aspects of the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane to ethene, including optimized transition structure geometry, electronic activation energy, activation barrier corrected for zero-point energies, standard enthalpy, entropy and Gibbs free energy of activation, have been calculated at the HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p), QCISD/6-31G(d) and CCD/6-31G(d) levels of theory. We also report the CCD/6-311++G(2d, 2p)//CCD/6-31G(d), MP4(SDTQ)/6-311++G(2d,2p)//CCD/6-31G(d) and CCSD(T)/6-311++G(2d, 2p)//CCD/6-31G(d) electronic activation energies.     

Cyclic vinyl p-tolyl sulfilimines as chiral dienophiles: theoretical study on the stereoselectivity, Lewis acid catalysis, and solvent effects in their Diels-Alder reactions

The theoretical study reported in the present work deals with chiral cyclic vinyl sulfilimines and their reactivity as dienophiles in [4 + 2] cycloaddition reactions, using B3LYP/6-31G(d)//AM1 and B3LYP/6-31G(d)//B3LYP/6-31G(d) model chemistries. Consideration of Lewis acid catalysis, illustrated by BF(3), decreases the activation energies of the cycloaddition process while the charge transfer from the diene to the sulfilimine is augmented. The [4 + 2] cycloaddition reactions of sulfilimines with both furan and cyclopentadiene occur in the gas phase with endo stereoselectivity, which is more pronounced with the latter diene. Endo-exo energy differences in the gas phase with the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31G(d)//AM1 model chemistries are almost the same. Solvent effects are responsible for the inversion of the stereoselectivity in the reactions of sulfilimines with furan because of the great difference in the dipole moments in endo and exo approaches.     

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.     

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)).     

亚烷基卡宾与甲醛环加成反应机理的理论研究

用二阶微扰理论研究了单重态亚烷基卡宾与甲醛发生的三种环加成反应的机理 ，采用MP2/6－31G~*方法计算了势能面上各驻点的构型参数、振动频率和能量。根 据能量数据可以预言环加成反应（1）的a途径将是单重态亚烷基卡宾与甲醛环加成 反应的主要反应通道，该反应由两步组成：（I）亚烷基卡宾与甲醛生成了一富能 中间体（INT1a），是一无势垒的放热反应，（II）中间体异构化为产物亚烷基环 乙烷，其势垒为24.1 kJ·mol~(-1)(MP2/6-31G~*)。     

Thermal and Sc(OTf)3 catalyzed 1,3-dipolar cycloaddition of open-chain nitrones to α,β-unsaturated lactones: combined experimental and computational studies

The stereoselectivity of 1,3-dipolar cycloaddition reactions of C-phenyl open-chain nitrones and α,β-unsaturated γ- and δ-lactones was investigated under thermal and catalytic conditions. It was found that under thermal conditions, the endo approach of the reactants was preferred leading to the thermodynamic product. In the presence of Sc(OTf)₃ the exo adduct was obtained in high yield and selectivity. The energies of the cycloaddition reactions were investigated by means of molecular orbital calculations at the B3LYP/6-31+G(d,p) and MP3/6-31+G(d,p) theory level. Different reaction channels and reactant approaches, fitting the individual regio- and stereochemical preferences, are discussed. The computational results were compared with the corresponding experimental data and found to be in good agreement.     

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.     

Origins of stereoselectivity in the Diels-Alder addition of chiral hydroxyalkyl vinyl ketones to cyclopentadiene: a quantitative computational study

Modest basis set level MP2/6-31G(d,p) calculations on the Diels-Alder addition of S-1-alkyl-1-hydroxy-but-3-en-2-ones (1-hydroxy-1-alkyl methyl vinyl ketones) to cyclopentadiene correctly reproduce the trends in known experimental endo/exo and diastereoface selectivity. B3LYP theoretical results at the same or significantly higher basis set level, on the other hand, do not satisfactorily model observed endo/exo selectivities and are thus unsuitable for quantitative studies. The same is valid also with regard to subtle effects originating from, for example, conformational distributions of reactants. The latter shortcomings are not alleviated by the fact that observed diastereoface selectivities are well-reproduced by DFT calculations. Quantitative computational studies of large cycloaddition systems would require higher basis sets and better account for electron correlation than MP2, such as, for example, CCSD. Presently, however, with 30 or more non-hydrogen atoms, these computations are hardly feasible. We present quantitatively correct stereochemical predictions using a hybrid layered ONIOM computational approach, including the chiral carbon atom and the intramolecular hydrogen bond into a higher level, MP2/6-311G(d,p) or CCSD/6-311G(d,p), layer. Significant computational economy is achieved by taking account of surrounding bulky (alkyl) residues at 6-31G(d) in a low HF theoretical level layer. We conclude that theoretical calculations based on explicit correlated MO treatment of the reaction site are sufficiently reliable for the prediction of both endo/exo and diastereoface selectivity of Diels-Alder addition reactions. This is in line with the understanding of endo/exo selectivity originating from dynamic electron correlation effects of interacting pi fragments and diastereofacial selectivity originating from steric interactions of fragments outside of the Diels-Alder reaction site.     

Addition reaction of adamantylideneadamantane with Br2 and 2Br2: a computational study

Ab initio calculations were carried out for the reaction of adamantylideneadamantane (Ad=Ad) with Br2 and 2Br2. Geometries of the reactants, transition states, intermediates, and products were optimized at HF and B3LYP levels of theory using the 6-31G(d) basis set. Energies were also obtained using single point calculations at the MP2/6-31G(d)//HF/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31+G(d)//B3LYP/6-31G(d) levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Only one pathway was found for the reaction of Ad=Ad with one Br2 producing a bromonium/bromide ion pair. Three mechanisms for the reaction of Ad=Ad with 2Br2 were found, leading to three different structural forms of the bromonium/Br3- ion pair. Activation energies, free energies, and enthalpies of activation along with the relative stability of products for each reaction pathway were calculated. The reaction of Ad=Ad with 2Br2 was strongly favored over the reaction with only one Br2. According to B3LYP/6-31G(d) and single point calculations at MP2, the most stable bromonium/Br3- ion pair would form spontaneously. The most stable of the three bromonium/Br3- ion pairs has a structure very similar to the observed X-ray structure. Free energies of activation and relative stabilities of reactants and products in CCl4 and CH2ClCH2Cl were also calculated with PCM using the united atom (UA0) cavity model and, in general, results similar to the gas phase were obtained. An optimized structure for the trans-1,2-dibromo product was also found at all levels of theory both in gas phase and in solution, but no transition state leading to the trans-1,2-dibromo product was obtained.     

异硫氰酸与甲亚胺环加成反应机理的理论研究

对异硫氰酸与甲亚胺形成四元或六元环产物的环加成反应进行了理论研究,结果表明,一分子异硫氰酸与一分子甲亚胺形成四元环(1:1)产物P1的反应(1)为经过一个两性离子中间体的分步反应,其中第二步为速控步骤,其活化热垒为107.86kJ/mol.此外,反应(1)的中间体还可与另一甲亚胺或异硫氰酸分子继续反应形成两个不同的六元环(1:2或2:1)产物P2或P3;这两个反应均为协同反应,其活化势垒分别为15.88和21.82kJ/mol.这些结果与当异硫氰酸酯与亚胺发生环加成反应时,只有类似于P2和P3的两种六元环产物生成的实验事实一致。     

Transition state structure and energetics of the N(2)O + X (X = Cl,Br) reactions

The structural and vibrational properties of the transition state of the N(2)O + X (X = Cl,Br) reactions have been characterized by ab initio methods using density functional theory. We have employed Becke's hybrid functional (B3LYP), and transition state optimizations were performed with 6-31G(d), 6-311G(2d,2p), 6-311+G(3d,2p), and 6-311+G(3df,2p) basis sets. For the chlorine atom reaction the coupled-cluster method (CCSD(T)) with 6-31G(d) basis set was also used. All calculations resulted in transition state structures with a planar cis arrangement of atoms for both reactions. The geometrical parameters of transition states at B3LYP are very similar, and the reaction coordinates involve mainly the breaking of the N-O bond. At CCSD(T)/6-31G(d) level a contribution of the O-Cl forming bond is also observed in the reaction coordinate. In addition, several highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction energetics. All model chemistries predict exothermic reactions. The G3 and G2 methods result in the smallest deviations from experiment, 1.8 and 0 kcal mol(-1), for the enthalpies of reaction for N(2)O reaction with chlorine and bromine, respectively. The G3//B3LYP and G1 methods perform best among the composite methods in predicting energies of the transition state, with a deviation of 1.9 and 3.0 kcal mol(-1), respectively, in the activation energies for the above processes. However, the B3LYP/6-311+G(3df,2p) method gives smaller deviations of 0.4 and -1.0 kcal mol(-1), respectively. The performance of the methodologies applied in predicting transition state energies was analyzed.     

Dispersion corrections essential for the study of chemical reactivity in fullerenes

In a previous paper (J. Phys. Chem. A2009, 113, 9721), we analyzed theoretically the Diels-Alder cycloaddition between cyclopentadiene and C(60) for which experimental results on energy barriers and reaction energies are known. One of the main conclusions reached was that the two-layered ONIOM2(B3LYP/6-31G(d):SVWN/STO-3G) method provides results very close to the full B3LYP/6-31G(d) ones. Unfortunately, however, both the exothermicity of the reaction and the energy barrier were clearly overestimated by these two methods. In the present work, we analyze the effect of the inclusion of Grimme's dispersion corrections in the energy profile of this reaction. Our results show that these corrections are essential to get results close to the experimental values. In addition, we have performed calculations both with and without dispersion corrections for the Diels-Alder reaction of C(60) and several dienes and for the Diels-Alder cycloaddition of a (5,5) single-walled carbon nanotube and 1,3-cis-butadiene. The results obtained indicate that inclusion of dispersion corrections is compulsory for the study of the chemical reactivity of fullerenes and nanotubes.     

New insights into the bromination reaction for a series of alkenes--a computational study

Ab initio calculations were carried out for the reaction of Br2 with ethene, propene, isobutene, fluoroethene, chloroethene, (E)-1,2-difluoroethene, and (E)-1,2-dichloroethene. For ethene the calculations were also carried out for the reaction with 2Br2. Geometries were optimized at the HF, MP2, and B3LYP levels using the 6-31G(d) and 6-31+G(d) basis sets where for Br both the standard 6-31G and the Binning-Curtiss bromine basis sets were used. Energies were also calculated at the G3MP2 and G3MP2B3 levels. For a single Br2 one mechanism involves a perpendicular attack by Br2 to the C=C bond, and a second mechanism consists of sidewise attack by Br2. Alkenes can react with 2Br2 via several mechanisms, all leading to the dibromo product. The most likely pathway for the reaction of ethene and 2Br2 involves a trans addition of a Br atom from Br3- to one of the bromonium ion carbons. Activation energies, free energies, and enthalpies of activation along with thermodynamic properties (DeltaE, DeltaH, and DeltaG) for each reaction were calculated. We have found that the reaction of ethene with 2Br2 is favored over reaction with only Br2. There is excellent agreement between the calculated free energies of activation for the reaction of ethene and 2Br2 and experimental values in nonpolar aprotic solvents. However, the free energies of activation for the reaction with a single Br2 agrees well with the experimental results for polar protic solvents only when the reaction is mediated by a solvent molecule. A kinetic expression is proposed that accounts for the difference between bromination of alkenes in protic and nonprotic solvents. Some previously unknown heats of formation are reported.     

Mechanisms for the reaction of thiophene and methylthiophene with singlet and triplet molecular oxygen

Mechanisms for the reaction of thiophene and 2-methylthiophene with molecular oxygen on both the triplet and singlet potential energy surfaces (PESs) have been investigated using ab initio methods. Geometries of various stationary points involved in the complex reaction routes are optimized at the MP2/6-311++G(d, p) level. The barriers and energies of reaction for all product channels were refined using single-point calculations at the G4MP2 level of theory. For thiophene, CCSD(T) single point energies were also determined for comparison with the G4MP2 energies. Thiophene and 2-methylthiophene were shown to react with O(2) via two types of mechanisms, namely, direct hydrogen abstraction and addition/elimination. The barriers for reaction with triplet oxygen are all significantly large (i.e., >30 kcal mol(-1)), indicating that the direct oxidation of thiophene by ground state oxygen might be important only in high temperature processes. Reaction of thiophene with singlet oxygen via a 2 + 4 cycloaddition leading to endoperoxides is the most favorable channel. Moreover, it was found that alkylation of the thiophene ring (i.e., methyl-substituted thiophene) is capable of lowering the barrier height for the addition pathway. The implication of the current theoretical results may shed new light on the initiation mechanisms for combustion of asphaltenes.     

二氯硅烯与乙烯和甲醛环加成反应机理的理论研究

用RHF/6-31G^*解析梯度方法研究了单重态二氯硅烯与乙烯和甲醛环加成反应的机理,并用二级微扰方法对各构型能量进行了相关能校正.结果表明,两反应历程均由两步组成:(1)二氯硅烯与乙烯和甲醛分别生成了中间配合物,是无势垒的放热反应;(2)中间配合物异构化成产物二氯硅杂环丙烷和二氯硅杂环氧甲烷,其势垒经零点能校正分别为97.43和103.29kJ/mol(MP₂/6-31G^*//6-31G^*).     

Ab initio study on the mechanism of forming a germanic hetero-polycyclic compound between alkylidenegermylene and ethylene

The mechanism of the cycloaddition reaction of forming a germanic hetero-polycyclic compound between singlet alkylidenegermylene and ethylene 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 surface energy profile, it can be predicted that the dominant reaction pathway for this reaction consists of three steps: the two reactants first form a three-membered ring intermediate INT1 through a barrier-free exothermic reaction of 35.4 kJ/mol; this intermediate then isomerizes to an active four-membered ring product P2.1 via a transition-state TS2.1 with a barrier of 57.6 kJ/mol; finally, P2.1 further reacts with ethylene to form the germanic hetero-polycyclic compound P3, for which the barrier is only 0.8 kJ/mol. The rate of this reaction path considerably differs from other competitive reaction paths, indicating that the cycloaddition reaction has an excellent selectivity.     

Substituent effects on the rate of formation of azomethine ylides. A computational investigation

The effect of substituents on the rate of conrotatory thermal cleavage of aziridine has been studied at the MP2(Full)/6-311++G(d,p)//MP2(Full)/6-31+G(d) level and also using SCS-MP2 methodology. While the parent compound has a high free energy of activation (194.6 kJ mol(-1)), this value could be drastically lowered by substituent effects. Anionic species were found to be particularly effective in increasing the calculated reaction rate. The potential utility of this approach in 1,3-dipolar cycloaddition is discussed.     

Transition structures and exo/endo stereoselectivities of concerted [6 + 4] cycloadditions with density functional theory

Density functional theory transition structures were located for three concerted [6 + 4] cycloaddition reactions involving cis-hexatriene and butadiene, cyclopentadiene and cycloheptatriene, and cyclopentadiene and tropone. Geometries, energies, and entropies were computed at the Becke3LYP/6-31G* level. The activation energy of the concerted [6 + 4] cycloaddition of hexatriene and butadiene is 33.3 kcal/mol, about 8 kcal/mol above the activation energy of the butadiene plus ethylene [4 + 2] cycloaddition. The endo concerted [6 + 4] transition state is 1.1 kcal/mol higher than the exo. The [6 + 4] reaction of cyclopentadiene and cycloheptatriene has a barrier of 25.9 kcal/mol, while the cyclopentadiene–tropone barrier drops to 20.7 kcal/mol. Received: 3 December 1998 / Accepted: 18 February 1999 / Published online: 7 June 1999     

Pericyclic versus pseudopericyclic reactions. What the Laplacian of the charge density, inverted Delta2rho(r), has to say about it? The case of cycloaddition reactions

The pseudopericyclic character of a group of cycloaddition reactions is theoretically investigated with the quantum theory of atoms in molecules of Bader at B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory. The analysis of the topology of the Laplacian of the charge density, inverted Delta2rho(r), along the reaction coordinate sets out a clear cut between pericyclic and pseudopericyclic processes and also allows one to account for intermediate cases.