A theoretical study of the N8 cubane to N8 pentalene isomerization reaction

The isomerization reaction of cubic N₈ to the planar bicyclic structure analogous to pentalene has been investigated using multiconfigurational self-consistent field and second-order perturbation theory (CASPT2). Comparative calculations using density functional theory have also been performed. Five local minima on the energy surface have been found, and the transition states between each two consecutive minima have been determined. The results show that all steps in the isomerization process, except one, can proceed via a set of transition states with moderately high energy barriers (10–20 kcal/mol). Received: 9 December 1996 / Accepted: 18 February 1997     

Oxidation mechanism of aromatic peroxy and bicyclic radicals from OH-toluene reactions

Theoretical calculations have been performed to investigate mechanistic features of OH-initiated oxidation reactions of toluene. Aromatic peroxy radicals arising from initial OH and subsequent O(2) additions to the toluene ring are shown to cyclize to form bicyclic radicals rather than undergoing reaction with NO under atmospheric conditions. Isomerization of bicyclic radicals to more stable epoxide radicals possesses significantly higher barriers and, hence, has slower rates than O(2) addition to form bicyclic peroxy radicals. At each OH attachment site, only one isomeric pathway via the bicyclic peroxy radical is accessible to lead to ring cleavage. The study provides thermochemical and kinetic data for quantitative assessment of the photochemical production potential of ozone and formation of toxic products and secondary organic aerosol from toluene oxidation.     

Modeling reaction pathways of low energy particle deposition on polymer surfaces via first principle calculations

The chemical processes that lead to polystyrene surface modification via low energy deposition of C(2)H(+), C(2)F(+), CH(2), CH(2)(+), and H(+) radicals and ions are examined using first principles calculations. Specifically, the reaction mechanisms responsible for products identified in classical molecular dynamics with reactive empirical bond-order potentials are examined using density functional theory. In addition, these calculations consider how the presence of charges on the incident particles changes the result for the CH(2) system through the comparison of barriers, transition states, and final products for CH(2) and CH(2)(+). The structures of the reaction species and energy barriers are determined using the B3LYP hybrid functional. Finally, CCSD/6-31G(d,p) single point energy calculations are carried out to obtain optimized energy barriers. The results indicate that the large variety of reactions occurring on the polystyrene surface are a consequence of complex interactions between the substrate and the deposited particles, which can easily be identified and characterized using advanced computational methodologies, such as first principle calculations.     

Ab initio studies on mechanisms of cycloaddition reaction between dichloro-vinylidene and ethylene

Mechanisms of cycloaddition reaction between singlet dichloro-vinylidene (R1) and ethylene (R2) have been investigated with MP2 and B3LYP /6-31G* methods, including geometry optimization, vibrational analysis, and energy for the involved stationary points on the potential energy surface. CCSD(T)/6-31G* single point calculations are also applied to the geometries from both methods. CCSD(T) relative energies for the stationary points predicted by MP2 and B3LYP are in a very good agreement. Three reaction pathways are located. Along the first one, one intermediate (INT1) is firstly generated, which then rearranges into a three-membered ring compound (P1) via a small barrier of 5.4 kJ/mol; the other two paths share the other intermediate (INT2), which isomerizes into two four-membered ring compounds (P2 and P3) via a chlorine and a hydrogen transfer, respectively. The barriers of the latter two paths are significantly higher by approximately 25 kJ/mol than that of the former (27.2 and 28.8 vs 5.4 kJ/mol), the major reaction is therefore the formation of P1.     

Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.     

霍林河褐煤热解甲烷生成反应类型及动力学的热重-质谱实验与量子化学计算

应用开放体系的热重-质谱联用技术(TG/MS)对未成熟的霍林河褐煤(镜质组最大反射率ROmax为0.33%)进行了热解模拟, 获得了甲烷的在线析出速率曲线. 曲线拟合结果表明, 甲烷生成速率曲线可以分解为5个峰, 结合化学动力学分析, 发现低温阶段甲烷的峰为吸附甲烷析出峰, 其余四个峰为热解甲烷的生成峰, 代表四类不同的化学反应. 将煤的结构特征及量子化学的理论计算相结合, 认为甲烷的生成包括4类反应, 类型1为与氧等杂原子相连的脂碳断裂; 类型2包含了两种反应, 一种是短链脂肪烃类官能团β位断裂, 另一种是所形成的长链脂肪烃类物质二次裂解; 类型3是与芳核直接相连的甲基热解脱落; 类型4为存在于煤结构中脂肪类物质的芳香化.     

Domino carbocationic rearrangement of aryl-2-(1-N-methyl/benzyl-3-indolyl)cyclopropyl ketones: a serendipitous route to 1H-cyclopenta[c]carbazole framework

Aryl-2-(N-methyl/benzyl-3-indolyl)cyclopropyl ketones 2a-m are shown to undergo a novel unexpected domino carbocationic rearrangement in the presence of SnCl(4)/CH(3)NO(2) yielding 2-aroyl-3-aryl-1H-cyclopenta[c]carbazoles 3a-m in good yields. The possible mechanistic pathway for this interesting transformation involves a series of cascade events, (a) electrophilic ring opening of cyclopropyl ketone, (b) intermolecular enol capture of the resulting zwitterionic intermediate, (c) electrophilic dimerization of indole moieties to give tetrahydrocarbazole intermediate and its subsequent aromatization by elimination of an indole moiety and dehydrogenation, and (d) intramolecular aldol condensation of the side chain to give a cyclopentene ring. The overall transformation involves formation of three carbon-carbon bonds along with a fused benzene and a substituted cyclopentene ring in one-pot operation from simple indole precursors.     

Theoretical Study on the Mechanism of the Cycloaddition Reaction between Alkylidene Carbene and Ethylene

The mechanism of cycloaddition reaction between singlet alkylidene carbene and ethylene has been investigated with second-order Moller-Plesset perturbation theory (MP2). By using 6-31 G^* basis, geometry optimization, vibrational analysis and energetics have been calculated for the involved stationary points on the potential energy surface. The results show that the title reaction has two major competition channels. An energy-rich intermediate (INT) is firstly formed between alkylidene carbene and ethylene through a barrier-free exothermic reaction of 63.62 kJ/mol, and the intermediate then isomerizes to a three-membered ring product (P 1) and a four-memberd ring product (P2) via transition state TS1 and TS2, in which energy barriers are 47.00 and 51.02 kJ/mol, respectively. P1 is the main product.     

Copper(II) catalyzed aromatization of tetrahydrocarbazole: An unprecedented protocol and its utility towards the synthesis of carbazole alkaloids

An efficient protocol for the aromatization of tetrahydrocarbazole is described by using catalytic copper(II) chloride dihydrate in DMSO. This newly established methodology has utilized towards the synthesis of naturally occurring carbazole alkaloids, namely 3-methylcarbazole, 3-formyl carbazole, glycozoline, glycozolicine and clauszoline-K. In addition, the protocol is generalized for the aromatization of N-substituted tetrahydrocarbazole, 1,2,3,4-tetrahydroquinoline, 1,2,3,4-tetrahydroisoquinoline and 1,2,3,4-tetrahydro β-carboline to give the corresponding heteroaromatic compounds from very good to excellent yield. Moreover, this method has been proven to be tolerant to a broad range of functional groups with excellent yields.     

Quantum chemical study of mechanisms for oxidative dehydrogenation of propane on vanadium oxide

We have carried out a hybrid density functional study of mechanisms for oxidative dehydrogenation of propane on the (010) surface of V2O5. The surface was modeled using both vanadium oxide clusters and a periodic slab. We have investigated a Mars-van Krevelen mechanism that involves stepwise adsorption of the propane at an oxygen site followed by desorption of a water molecule and propene, and subsequent adsorption of an oxygen molecule to complete the catalytic cycle. The potential energy surface is found to have large barriers, which are lowered somewhat when the possibility of a triplet state is considered. The barriers for propane adsorption and propene elimination are 45-60 kcal/mol. The highest energy on the potential energy surface at the B3LYP/6-31G* level of theory is about 80 kcal/mol above the energy of the reactants and corresponds to formation of an oxygen vacancy after water elimination. Subsequent addition of an oxygen molecule to fill the vacancy is predicted to be energetically downhill. The reactions of propane at a bridging oxygen site and at a vanadyl site have similar energetics. The key results of the cluster calculations are confirmed by periodic calculations. Factors that may lower the barriers on the potential energy surface, including the interaction of vanadium oxide clusters with a support material and a concerted reaction with O2, are discussed.     

Pd掺杂Fe催化剂上愈创木酚加氢脱氧理论研究

通过密度泛函理论(DFT)计算研究了愈创木酚在Fe(211)表面上的吸附活化行为和加氢脱氧(HDO)反应性能.讨论了Pd的掺杂和H_2O~*的参与对Fe催化剂活性和选择性的影响.计算结果表明,通过苯环水平吸附在催化剂表面的愈创木酚的稳定性高于仅通过羟基的垂直吸附构型,这有利于苯环, C_(Ar)-OCH_3键和O-CH_3键的活化.在Fe(211)表面上,愈创木酚通过脱甲基再加氢生成邻苯二酚在动力学上比通过脱甲氧基生成苯酚和通过脱羟基生成苯甲醚更有利. Pd掺杂对愈创木酚的吸附稳定性影响较小(0.05 eV),但增加了其加氢脱氧反应的活化能垒,抑制了C_(Ar)-OCH_3, O-CH_3和C_(Ar)-OH键的断裂以及随后加氢生成苯酚,邻苯二酚和苯甲醚的反应过程.在Fe(211)表面上, H_2O~*通过与-CH_3形成氢键作用(H-bonding机理)对反应产生影响,从而降低了愈创木酚脱甲基和脱甲氧基反应的活化能垒.在Fe(211)-1Pd表面上, H_2O~*通过H转移参与反应(H-shuttling机理),促进了愈创木酚向邻苯二酚和苯酚产物的转化,并提高了加氢脱氧反应对苯酚的选择性.     

Solid-phase synthesis of substituted 3-amino-3′-carboxy-tetrahydrocarbazoles

Two related solid-phase synthesis routes have been developed allowing the synthesis of 3-amino-3′-carboxy substituted tetrahydrocarbazole derivatives. Diversity can be introduced at the amino and carboxy functionalities and at the nitrogen and the aromatic ring of the tetrahydrocarbazole moiety. Both routes rely on Fmoc-protected 1-amino-4-oxocyclohexanone carboxylic acid as central core element. Derivatization of the carboxy function is achieved with amines, derivatization of the amino functionality is possible by reaction with alkyl halides, isocyanates, activated alcohols, sulfonic acid chlorides or carboxylic acids. The tetrahydrocarbazole scaffold is generated by Fischer indole cyclization with phenyl hydrazine derivatives, thereby introducing diversity in the aromatic moiety. N-Alkylation at the indole nitrogen with alkyl halides delivers N-substituted derivatives.     

Reaction Mechanisms and Kinetics of the Melt Transesterification of Bisphenol‐A and Diphenyl Carbonate

The catalyzed and uncatalyzed reaction mechanisms of the melt transesterification process of bisphenol‐A and diphenyl carbonate are proposed based on nucleophilic substitution at the carbonyl group of the reactants. The reaction paths and energy barriers of the melt transesterification reaction were predicted and identified via density functional theory (DFT) calculations. The calculations reveal that the different oligomers with only one repeating unit are formed through different thermal processes. The theoretical evaluation further indicates that the basic hydroxide catalysts can reduce the energy barrier for the transesterification reaction, which allows subsequent nucleophilic attack to easily occur. Furthermore, the reaction kinetics of transesterification using tetraethyl ammonium hydroxide as a catalyst were investigated experimentally over a temperature range of 155–175°C. The reaction rate constants and equilibrium constants were determined based on the functional group model, and the equilibrium constants decreased with increasing reaction temperature. A detailed molecular species model with a specific repeating unit (n = 3) was developed and applied to predict the change in the reactants, oligomers, and phenol, and the experimental data and model calculation agree quite well. The standard curves of the oligomer were reversely derived, which provide intuitive insight into the concentration change of each oligomer. Both the DFT calculations and experimental results indicate that the C1 oligomer is first formed, and some of which are then converted to other types or higher molecular weight oligomers.     

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.     

Stairway to the conical intersection: a computational study of the retinal isomerization

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order M?ller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.     

Cycloaddition isomerizations of adsorbed 1,3-cyclohexadiene on Si(100)-2x1 surface: first neighbor interactions

The initial and subsequent surface reaction mechanisms of 1,3-cyclohexadiene on the Si(100)-2x1 surface were theoretically explored, focusing on the possible first-neighbor interactions. Five different initial reaction channels leading to nine different surface products were identified, confirming previous experimental reports of inter-dimer structures. Among the nine identified products, five of these surface products are new species that have not previously been reported. Potential energy surface studies reveal that the net reaction barriers within a given channel are very small, indicating that the final product distributions within that channel are determined by thermodynamics. On the other hand, thermal isomerizations between different channels are not expected to occur easily. Therefore, the surface product distributions among the five different channels are more likely to be determined by kinetics. As a result, understanding the relationships among the available reaction channels both kinetically and thermodynamically is essential for properly interpreting the experimental results. The current study shows that the subsequent surface chemical reactions of unsaturated initial surface products are strongly coupled with the first-neighbor interactions.     

DFT Study on the Recovery of Hoveyda–Grubbs‐Type Catalyst Precursors in Enyne and Diene Ring‐Closing Metathesis

DFT (B3LYP‐D) calculations have been used to better understand the origin of the recovered Hoveyda–Grubbs derivative catalysts after ring‐closing diene or enyne metathesis reactions. For that, we have considered the activation process of five different Hoveyda–Grubbs precursors in the reaction with models of usual diene and enyne reactants as well as the potential precursor regeneration through the release/return mechanism. The results show that, regardless of the nature of the initial precursor, the activation process needs to overcome relatively high energy barriers, which is in agreement with a relatively slow process. The precursor regeneration process is in all cases exergonic and it presents low energy barriers, particularly when compared to those of the activation process. This indicates that the precursor regeneration should always be feasible, unlike the moderate recoveries sometimes observed experimentally, which suggests that other competitive processes that hinder recovery should take place. Indeed, calculations presented in this work show that the reactions between the more abundant olefinic products and the active carbenes usually require lower energy barriers than those that regenerate the initial precatalyst, which could prevent precursor regeneration. On the other hand, varying the precursor concentration with time obtained from the computed energy barriers shows that, under the reaction conditions, the precursor activation is incomplete, thereby suggesting that the origin of the recovered catalyst probably arises from incomplete precursor activation.     

The reaction of n- and i-C4H5 radicals with acetylene

In this article, we discuss the reactions of i-C4H5 and n-C4H5 with acetylene. Both have been proposed as possible cyclization steps, forming benzene or fulvene, in rich flames burning aliphatic fuels. The relevant parts of the potential energy surface were determined from rQCISD(T) calculations extrapolated to the infinite-basis-set limit. Using this information in a Rice-Ramsperger-Kassel-Marcus-based master equation, we have calculated thermal rate coefficients and product distributions for both reactions as a function of temperature and pressure. The results are cast in forms that can be used in modeling, and the implications of the results for flame chemistry are discussed.     

Excited biradical states in oxirane ring opening

The mechanism of oxirane ring opening was studied by ab initio [RHF, ROHF, GVB/DH, RHF/SBK(p, d)] calculations. The strained structure of oxiranes and their complexes with aliphatic alcohols and amines is characterized by low-lying biradical states whose thermal population leads to the ring opening. The examined oxirane ring opening reacitons have low activation energy (<10 kcal mol-¹) and are catalyzed by labile hydrogen atoms in hydroxy and amino groups of the reaction complex.     

Reactivity of the 4d transition metals toward N hydrogenation and NH dissociation: a DFT-based HSAB analysis

The density functional theory (DFT) based hard-soft acid-base (HSAB) reactivity indices, including the electrophilicity index, have been successfully applied to many areas of molecular chemistry. In this work we test the applicability of such an approach to fundamental surface chemistry. We have considered, as prototypical surface reactions, both the hydrogenation of atomic nitrogen and the dissociative adsorption of the NH molecular radical. By use of a DFT methodology, the minimum energy reaction pathways, and corresponding reaction barriers, of the above reactions over Zr(001), Nb(110), Mo(110), Tc(001), Ru(001), Rh(111), and Pd(111) have been determined. By consideration of the chemical potential and chemical hardness of the surface metal atoms, and the principle of electronegativity equalization, it is found that the charge transferred to the NH radical during the process of dissociative adsorption correlates very well with that determined by Mulliken population analysis. Furthermore, it is found that the stability of the NH/surface transition state complex relates directly to this charge transfer and that the trend in transition state stability predicted by a HSAB treatment correlates very strongly with that determined by DFT calculations. With regards to N hydrogenation, we find that during the course of the reaction, H loses cohesion to the surface, as it must migrate from a 3-fold hollow site to either a bridge or top site, to react with N. Partial density of states (PDOS) and Mulliken population analysis reveal that this loss of bonding is accompanied by charge transfer from H to the surface metal atoms. Moreover, by simple modeling, we show that the reaction barriers are directly proportional to this mandatory charge transfer. Indeed, it is found that the reaction barriers correlate very well with the electrophilicity index of the metal atoms.