Quantum mechanical study of the ring-closing reaction of the hexatriene radical cation

The ring-closing reaction of hexatriene radical cation 1(*)(+) to 1,3-cyclohexadiene radical cation 2(*)(+) was studied computationally at the B3LYP/6-31G* and QCISD(T)/6-311G*//QCISD/6-31G* levels of theory. Both, concerted and stepwise mechanisms were initially considered for this reaction. Upon evaluation at the B3LYP level of theory, three of the possible pathways-a concerted C(2)-symmetric via transition structure 3(*)(+) and stepwise C(1)-symmetric pathways involving three-membered ring intermediate 5(*)(+) and four-membered ring intermediate 6(*)(+)-were rejected due to high-energy stationary points along the reaction pathway. The two remaining pathways were found to be of competing energy. The first proceeds through the asymmetric, concerted transition structure 4(*)(+) with an activation barrier E(a) = 16.2 kcal/mol and an overall exothermicity of -23.8 kcal/mol. The second pathway, beginning from the cis,cis,trans rotamer of 1(*)(+), proceeds by a stepwise pathway to the cyclohexadiene product with an overall exothermicity of -18.6 kcal/mol. The activation energy for the rate-determining step in this process, the formation of the intermediate bicyclo[3.1.0]hex-2-ene via transition structure 9(*)(+), was found to be 20.4 kcal/mol. More rigorous calculations of a smaller subsection of the potential energy hypersurface at the QCISD(T)//QCISD level confirmed these findings and emphasized the importance of conformational control of the reactant.     

Model Calculations on the Squalene Cyclization

As a model for the squalene cyclization the interaction between a methyl cation or a methyl radical and two double bonds has been studied using the CNDO/2 and INDO method. In both cases bond formation between the CH₃-group and one double bond is facilitated by a second one, but not in a concerted way.     

Density functional theory study on a missing piece in understanding of heme chemistry: the reaction mechanism for indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are heme-containing dioxygenases and catalyze oxidative cleavage of the pyrrole ring of L-tryptophan. On the basis of three recent crystal structures of these heme-containing dioxygenases, two new mechanistic pathways were proposed by several groups. Both pathways start with electrophilic addition of the Fe(II)-bound dioxygen concerted with proton transfer (oxygen ene-type reaction), followed by either formation of a dioxetane intermediate or Criegee-type rearrangement. However, density functional theory (DFT) calculations do not support the proposed concerted oxygen ene-type and Criegee-type rearrangement pathways. On the basis of DFT calculations, we propose a new mechanism for dioxygen activation in these heme systems. The mechanism involves (a) direct electrophilic addition of the Fe(II)-bound oxygen to the C2 or C3 position of the indole in a closed-shell singlet state or (b) direct radical addition of the Fe(III)-superoxide to the C2 position of the indole in a triplet (or open-shell singlet) state. Then, a radical-recombination or nearly barrierless charge-recombination step from the resultant diradical or zwitterionic intermediates, respectively, proceeds to afford metastable dioxetane intermediates, followed by ring-opening of the dioxetanes. Alternatively, homolytic O-O bond cleavage from the diradical intermediate followed by oxo attack and facile C2-C3 bond cleavage could compete with the dioxetane formation pathway. Effects of ionization of the imidazole and negatively charged oxyporphyrin complex on the key dioxygen activation process are also studied.     

Substituent effects in pericyclic reactions of radical cations: the ring opening of 3-substituted cyclobutene radical cations

The substituent effects on the ring-opening reaction of cyclobutene radical cations have been studied at the Becke3LYP/6-31G* level of theory. The effect on the reaction energies and activation energies of the concerted and stepwise pathways of electron-donating substituents such as methyl and methoxy as well as electron-withdrawing substituents such as nitrile and carboxaldehyde in the 3-position of the cyclobutene is discussed. The exothermicity of the reaction correlates well with the ability of the substituent to stabilize the 1,3-butadiene radical cation by electron donation or conjugation. The relative stability of the (E) and (Z) isomers of the resulting 1,3-butadiene radical cations depends largely on steric effects. Similarly, steric effects are responsible for the relative energies of the different diastereomeric transition structures. The cyclopropyl carbinyl intermediate of the stepwise pathway resembles the nonclassical carbocation and is stabilized by electron-donating substituents. In the case of electron-donating substituents, this species becomes a minimum on the potential energy hypersurface, whereas unstabilized or destabilized cyclopropyl carbinyl radical cations are not minima on the hypersurface. The stabilization of the cyclopropyl carbinyl radical cation by substituents correlates qualitatively with the Brown-Okamoto substituent parameter sigma+. However, in all cases studied here, the concerted mechanism is the lowest energy pathway.     

Mechanism insights of ethane C-H bond activations by bare [Fe(III)═O]+: explicit electronic structure analysis

Alkane C-H bond activation by various catalysts and enzymes has attracted considerable attention recently, but many issues are still unanswered. The conversion of ethane to ethanol and ethene by bare [Fe(III)═O](+) has been explored using density functional theory and coupled-cluster method comprehensively. Two possible reaction mechanisms are available for the entire reaction, the direct H-abstraction mechanism and the concerted mechanism. First, in the direct H-abstraction mechanism, a direct H-abstraction is encountered in the initial step, going through a collinear transition state C···H···O-Fe and then leading to the generation of an intermediate Fe-OH bound to the alkyl radical weakly. The final product of the direct H-abstraction mechanism is ethanol, which is produced by the hydroxyl group back transfer to the carbon radical. Second, in the concerted reaction mechanism, the H-abstraction process is characterized via overcoming four/five-centered transition states (6/4)TSH_c5 or (4)TSH_c4. The second step of the concerted mechanism can lead to either product ethanol or ethene. Moreover, the major product ethene can be obtained through two different pathways, the one-step pathway and the stepwise pathway. It is the first report that the former pathway starting from (6/4)IM_c to the product can be better described as a proton-coupled electron transfer (PCET). It plays an important role in the product ethene generation according to the CCSD(T) results. The spin-orbital coupling (SOC) calculations demonstrate that the title reaction should proceed via a two-state reactivity (TSR) pattern and that the spin-forbidden transition could slightly lower the rate-determining energy barrier height. This thorough theoretical study, especially the explicit electronic structure analysis, may provide important clues for understanding and studying the C-H bond activation promoted by iron-based artificial catalysts.     

顺-8-三甲基锡烷基-6-辛烯醛分子内环化反应立体选择性的理论研究

用密度泛函方法在B3LYP/6-31G^*水平上研究了顺-8-三甲基锡烷基-6-辛烯醛分子内环化反应的机理,通过振动分析和内禀反应坐标对过渡态进行了确认,解析了三种反应途径.结果表明,反应具有很强的立体选择性,虽然-OSn(CH₃)₃和-C₂H₃基团均处于环的平伏位,是最稳定的产物构型,但是主要产物是经过活化能最低,且具有两个六元环椅式构象的过渡态形成的,主要产物中-OSn(CH₃)₃基团处于环的直立位.该结果与实验事实一致.     

氧杂环丁烷热解机理的量子化学研究

本文利用半经验分子轨道理论研究了氧杂环丁烷热解为甲醛和乙烯的反应机理计算是采用半经验方法AM1进行的, 各种驻点全部运用Berny梯度方法优化. 同时, 对过渡态的结构进行了振动分析的确证. 计算表明: 1)不存在协同的同面-同面反应途径的过渡态, 其驻点只是一个二级鞍点; 2) 协同的同面-异面反应途径需要经过一个能量很高的过渡态; 3)有利的反应途径是包含了双自由基中间体的分步过程。     

Carbon-carbon bond activation of 2,2,6,6-tetramethyl-piperidine-1-oxyl by a Rh(II) metalloradical: a combined experimental and theoretical study

Competitive major carbon-carbon bond activation (CCA) and minor carbon-hydrogen bond activation (CHA) channels are identified in the reaction between rhodium(II) meso-tetramesitylporphyrin [Rh(II)(tmp)] (1) and 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO) (2). The CCA and CHA pathways lead to formation of [Rh(III)(tmp)Me] (3) and [Rh(III)(tmp)H] (5), respectively. In the presence of excess TEMPO, [Rh(II)(tmp)] is regenerated from [Rh(III)(tmp)H] with formation of 2,2,6,6-tetramethyl-piperidine-1-ol (TEMPOH) (4) via a subsequent hydrogen atom abstraction pathway. The yield of the CCA product [Rh(III)(tmp)Me] increased with higher temperature at the cost of the CHA product TEMPOH in the temperature range 50-80 degrees C. Both the CCA and CHA pathways follow second-order kinetics. The mechanism of the TEMPO carbon-carbon bond activation was studied by means of kinetic investigations and DFT calculations. Broken symmetry, unrestricted b3-lyp calculations along the open-shell singlet surface reveal a low-energy transition state (TS1) for direct TEMPO methyl radical abstraction by the Rh(II) radical (SH2 type mechanism). An alternative ionic pathway, with a somewhat higher barrier, was identified along the closed-shell singlet surface. This ionic pathway proceeds in two sequential steps: Electron transfer from TEMPO to [Rh(II)(por)] producing the [TEMPO]+ [RhI(por)]- cation-anion pair, followed by net CH3+ transfer from TEMPO+ to Rh(I) with formation of [Rh(III)(por)Me] and (DMPO-like) 2,2,6-trimethyl-2,3,4,5-tetrahydro-1-pyridiniumolate. The transition state for this process (TS2) is best described as an SN2-like nucleophilic substitution involving attack of the d(z)2 orbital of [Rh(I)(por)]- at one of the C(Me)-C(ring) sigma* orbitals of [TEMPO]+. Although the calculated barrier of the open-shell radical pathway is somewhat lower than the barrier for the ionic pathway, R-DFT and U-DFT are not likely comparatively accurate enough to reliably distinguish between these possible pathways. Both the radical (SH2) and the ionic (SN2) pathway have barriers which are low enough to explain the experimental kinetic data.     

Direct detection of products from the pyrolysis of 2-phenethyl phenyl ether

The pyrolysis of 2-phenethyl phenyl ether (PPE, C(6)H(5)C(2)H(4)OC(6)H(5)) in a hyperthermal nozzle (300-1350 °C) was studied to determine the importance of concerted and homolytic unimolecular decomposition pathways. Short residence times (<100 μs) and low concentrations in this reactor allowed the direct detection of the initial reaction products from thermolysis. Reactants, radicals, and most products were detected with photoionization (10.5 eV) time-of-flight mass spectrometry (PIMS). Detection of phenoxy radical, cyclopentadienyl radical, benzyl radical, and benzene suggest the formation of product by the homolytic scission of the C(6)H(5)C(2)H(4)-OC(6)H(5) and C(6)H(5)CH(2)-CH(2)OC(6)H(5) bonds. The detection of phenol and styrene suggests decomposition by a concerted reaction mechanism. Phenyl ethyl ether (PEE, C(6)H(5)OC(2)H(5)) pyrolysis was also studied using PIMS and using cryogenic matrix-isolated infrared spectroscopy (matrix-IR). The results for PEE also indicate the presence of both homolytic bond breaking and concerted decomposition reactions. Quantum mechanical calculations using CBS-QB3 were conducted, and the results were used with transition state theory (TST) to estimate the rate constants for the different reaction pathways. The results are consistent with the experimental measurements and suggest that the concerted retro-ene and Maccoll reactions are dominant at low temperatures (below 1000 °C), whereas the contribution of the C(6)H(5)C(2)H(4)-OC(6)H(5) homolytic bond scission reaction increases at higher temperatures (above 1000 °C).     

An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.     

过渡金属参与C―H键切断模式的理论研究进展

过渡金属催化活化C―H键来构建新共价键因具有原子经济和合成简捷的特点,已成为合成化学中最为有效策略之一。本文中,我们总结了过渡金属参与的C―H键切断的理论研究进展,并系统性提出了C―H键切断的相关模式,包括:C―H键对金属的氧化加成、碱协助的去质子化、σ-复分解、Friedel-Crafts型亲电芳香取代、α-或β-氢消除以及夺氢活化等。理论计算表明,当使用还原性较强的零价金属催化剂时,反应可按照氧化加成模式进行。当使用金属羧酸盐作为催化剂时,通常以协同金属化-去质子化机理模式实现C―H键切断。当使用阳离子金属催化剂,富电子芳烃比缺电子芳烃优先反应时,C―H键切断则会经历碱协助的内部亲电取代模式。σ-复分解是协同金属化-去质子化机理的另一种模式。如果亲电体对芳烃进行加成时,则可按照Friedel-Crafts型亲电芳香取代方式活化C―H键。α-或β-氢消除也是比较常见的活化C―H键模式。此外,夺氢活化可通过自由基过程实现C―H键活化。本文通过对过渡金属参与的C―H键活化模式的论述旨在为实验提供理论指导。     

Theoretical calculations on the cycloreversion of oxetane radical cations

The molecular mechanism for the cycloreversion of oxetane radical cations has been studied at the UB3LYP/6-31G* level. Calculations support that the cycloreversion takes place via a concerted but asynchronous process, where C-C bond breaking at the transition state is more advanced than O-C breaking. This allows a favorable rearrangement of the spin electron density from the oxetane radical cation (with the spin density located mainly on the oxygen atom) to the alkene radical cation which is one of the final products. Inclusion of solvent effects does not modify the gas-phase results.     

A computational study of the cycloaddition of thiobenzophenone S-methylide to thiobenzophenone

The cycloaddition of thiobenzophenone S-methylide to thiobenzophenone, an experimentally well-known reaction, was studied, using (U)HF/3-21G* for finding stationary points and (U)B3LYP/6-31G*//(U)HF/3-21G* single-point calculations for energies. Some optimizations were performed by (U)B3LYP/ 6-31G* to check the reliability of the calculations. The comparison of the concerted pathways and stepwise reactions via C,C-biradicals and C,S-zwitterions showed that the formation of a tetraphenyl-substituted C,C-biradical and its ring closure to 4,4,5,5-tetraphenyl-1,3-dithiolane constitutes the energetically most probable pathway of product formation, despite the fact that the regioisomeric 2,2,4,4-tetraphenyl-substituted product is more favorable by 17 kcal mol(-1). Model calculations on bond dissociation energies showed that (U)B3LYP with various basis sets overestimates radical stabilization, whereas CBS-QB3 closely reproduced experimental values. Results with the BLYP functional are similar to those with B3LYP. The consequences of the overestimation of radical stability for the cycloaddition mechanism involving biradicals are discussed. Thiobenzophenone S-methylide, if not captured by a dipolarophile, dimerizes to 2,2,3,3-tetraphenyl-1,4-dithiane. Calculation disclosed likewise a tetraphenyl-substituted C,C-biradical as intermediate.     

Large Nonstatistical Branching Ratio in the Dissociation of Pentane-2,4-dione Radical Cation: An Ab Initio Direct Classical Trajectory Study

The dissociation of pentane-2,4-dione radical cation has been studied by ab initio direct classical trajectory calculations at the MP2/6-31G(d) level of theory. A bond additivity correction has been used to improve the MP2 potential energy surface (BAC-MP2). A microcanonical ensemble was constructed using quasiclassical normal-mode sampling by distributing 10 kcal/mol of excess energy above ZPE for the transition state for the tautomerization of the enol with a terminal double bond, 4-hydroxypent-4-en-2-one radical cation, to the diketo form. A total of 244 trajectories were run starting from this transition state, yielding pentane-2,4-dione radical cation and depositing energy in the terminal CC bond. As a result, the branching ratio for dissociation of the terminal CC bond versus the interior CC bonds is significantly larger than expected from RRKM theory. The branching ratio for the dissociation of the two interior CC bonds is ～20:1, with the one closest to the activated methyl breaking more often. Since the two interior bonds are equivalent and should dissociate with equal probability, this branching ratio represents a very large deviation from statistical behavior. A simple kinetic scheme has been constructed to model the dissociation rates. The nonstatistical behavior is seen because the rate of energy flow within the molecule is comparable to or less than the rates of dissociation for the activated system. In addition to the expected dissociation products, some of the trajectories also lead to the formation of an ester-like product, prop-1-en-2-yl acetate radical cation.     

Energy-variable collision-induced dissociation study of 1,3,5-trisubstituted 2-pyrazolines by electrospray mass spectrometry

The pathways of the ([M+H](+)) ions generated from electrosprayed solutions of nine 1,3,5-trisubstituted 2-pyrazoline derivatives were studied using energy-variable collision-induced dissociation (CID) and pseudo-MS(3) (in-source CID combined with MS/MS) methods. It was shown that under CID conditions several structurally important product ions such as the 2,4-substituted azete and 1,2-substituted aziridine ions were formed. The compositions of the product ions were unambiguously supported by accurate mass measurement (mass accuracy was within +/- 8 ppm). The fragmentation pathways of 1,3,5-trisubstituted 2-pyrazolines were established by means of pseudo-MS(3). It was found that a substituent at the N-1 position greatly affects the fragmentation pathways of the 2-pyrazoline derivatives. The 1-acetyl- and 1-propionyl-2-pyrazoline derivatives dissociate mainly through formation of a pyrazolium cation, while in the case of 1-phenyl-2-pyrazoline derivatives product ions arising from the consecutive fragmentation of 2,4-substituted azete and 1,2-substituted aziridine ions dominate. Another interesting finding is the formation of a radical cation from the 2,4-substituted azete by loss of a methyl radical. The fragmentation yield as a function of the collision energy for each of the 1,3,5-trisubstituted 2-pyrazolines was determined. Based on the fragmentation yield versus collision energy curves the relative fragmentation stabilities for the 1,3,5-trisubstituted 2-pyrazoline derivatives were also evaluated.     

Experimental and theoretical studies of the dimerizations of imidoylketenes

Reaction conditions are presented that, for the first time, allow the generation and dimerization of N-alkylimidoylketenes, e.g.,1d, while avoiding the intramolecular rearrangements observed under conventional conditions. The dimer of 1d (22a) is the result of [4 + 2] cycloaddition across the C=C bond of one ketene. In contrast, the N-H imidoylketene 1c dimerizes across the C=O bond to form 24b. Furthermore, N-methylbenzoimidoylketene (5b), in equilibrium with the more stable benzoazetidinone 14b, gives the formal [4 + 4] dimer 8b. B3LYP/6-31G(d) transition structure calculations on these three modes of dimerization reproduce and offer explanations for these divergent regiochemistries. Both [4 + 2] dimerizations have planar, pseudopericyclic transition structures (25a and 29b). Five transition structures were found for the formation of 8b. A unique pseudopericyclic dimerization of 5b with an orthogonal [4 + 4] geometry (31) has a barrier of only 0.7 kcal/mol. However, the overall lowest energy pathway involves concerted addition of 5b across a sigma bond in 14b via 35.     

Intermolecular Hydroamination of Vinylarenes by Iminoanilide Alkaline‐Earth Catalysts: A Computational Scrutiny of Mechanistic Pathways

A thorough computational exploration of the mechanistic intricacies of the intermolecular hydroamination (HA) of vinylarenes by a recently reported class of kinetically stabilised iminoanilide [{N^N}Ae{N(SiMe₃)₂} ? (THF)_n] alkaline‐earth amido compounds (Ae=Ca, Sr, Ba) is presented. Two distinct mechanistic pathways for catalytic HA mediated by alkaline‐earth and rare‐earth compounds have emerged over the years that account equally well for the specific features of the process. On one hand, a concerted proton‐assisted pathway to deliver the amine product in a single step can be invoked and, on the other, a stepwise σ‐insertive pathway that comprises a rapid, reversible migratory olefin insertion step linked to a less facile, irreversible Ae?C alkyl bond aminolysis. The results of the study presented herein, which employed a heavily benchmarked and reliable DFT methodology, supports a stepwise σ‐insertive pathway that involves fast and reversible migratory C?C bond insertion into the polar Ae?N pyrrolido σ bond. This proceeds with strict 2,1 regioselectivity via a highly polarised four‐centre transition state (TS) structure, linked to irreversible intramolecular Ae?C bond aminolysis of the alkaline‐earth alkyl intermediate as the energetically favourable mechanism. Turnover‐limiting aminolysis is consistent with the significant KIE measured; the DFT‐derived effective barrier matches the Eyring parameter empirically determined for the best‐performing {N^N}Ba(NR₂) catalyst gratifyingly well. It also predicts the observed trend in reactivity (Ca<Sr<Ba) correctly and the computationally estimated primary KIE is close to the observed values. Non‐competitive kinetic demands militate against the operation of the alternative concerted proton‐assisted pathway, which describes N?C bond formation triggered by concomitant amino proton transfer at the C?C linkage via a multi‐centre TS structure. A detailed comparison of {N^N}Ae(NR₂) catalysts revealed that the variation in the Ae?pyrrolido bond strength together with the degree of protection of the alkaline earth by a sterically encumbering iminoanilide ligand scaffold not only profoundly influences the performance in HA catalysis, but also the likelihood of traversing rival mechanistic pathways.     

"Concerted" transition state, stepwise mechanism. Dynamics effects in C2-C6 enyne allene cyclizations

The C2-C6 (Schmittel)/ene cyclization of enyne-allenes is studied by a combination of kinetic isotope effects, theoretical calculations, and dynamics trajectories. For the cyclization of allenol acetate 9, the isotope effect (k(CH3)/k(CD3) is approximately 1.43. The isotope effect is interpreted in terms of a highly asynchronous transition state near the concerted/stepwise boundary. This is supported by density functional theory calculations that locate a highly asynchronous transition structure for the concerted ene reaction. However, calculations of both the experimental system and a model reaction were unable to locate a transition structure for formation of the diradical intermediate of a stepwise mechanism. The stepwise mechanism and the asynchronous concerted mechanism start out geometrically similar, and the two pathways appear to have merged as far as the initial transition structure. For the model reaction, quasiclassical direct dynamics trajectories emanating from the initial transition structure afforded the diradical intermediate in 29 out of 101 trajectories. A large portion of the remaining trajectories completes hydrogen transfer before carbon-carbon bond formation, despite the advanced carbon-carbon bond formation in the asynchronous transition structure. Overall, the single minimum-energy path from starting material to product is inadequate to describe the reaction, and a consideration of dynamic effects is necessary to understand the mechanism. The implications of these observations toward questions of concert in other reactions are discussed.