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.     

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     

二氟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单重态二氟亚烷基卡宾与甲醛发生的环加成反应机理,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.结果表明,单重态二氟亚烷基卡宾与甲醛的环加成反应主要有两种反应通道,通道1中,两个反应物经a,b和c三条反应途径生成三元环构型的产物P1,其中途径c是主反应途径,该途径有两步组成:(Ⅰ)二氟亚烷基卡宾与甲醛生成了1个富能中间体(INT1c),是无势垒放热反应,放出能量为219.18kJ/mol;(Ⅱ)中间体(INT1c)异构化为产物二氟亚烷基环氧乙烷,其势垒为134.71kJ/mol.通道2的反应途径由三步组成:(Ⅰ)反应物首先生成了1个富能中间体(INT1b),为无势垒的放热反应,放出的能量142.77kJ/mol;(Ⅱ)中间体(INT1b)异构化成另一中间体(INT2),其势垒为22.31kJ/mol;(Ⅲ)中间体(INT2)异构化成四元环构型产物P2,其势垒为11.98kJ/mol.     

Theoretical studies of mechanism of cycloaddition reaction between germylidene and formaldehyde

Mechanism of the cycloadditional reaction between singlet germylidene (R1) and formaldehyde (R2) 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, it can be predicted that the dominant reaction pathway of the cycloadditional reaction between singlet germylidene and formaldehyde is reaction (4) , which consists of three steps: the two reactants (R1, R2) first form an intermediate INT1b through a barrier‐free exothermic reaction of 28.1 kJ/mol; this intermediate reacts further with formaldehyde (R2) to give an intermediate INT4, which is also a barrier‐free exothermic reaction of 37.2 kJ/mol; subsequently, the intermediate INT4 isomerizes to a heteropolycyclic germanic compound P4 via a transition state TS4, for which the barrier is 18.6 kJ/mol. The dominant reaction has an excellent selectivity and differs considerably from its competitive reactions in thermodynamic property and reaction rate. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

碳酸二甲酯法制备1,5-萘二氨基甲酸甲酯中间产物的结构表征

研究发现,由碳酸二甲酯与1,5-萘二胺合成1,5-萘二氨基甲酸甲酯的反应是一个经过中间产物的串联反应。关于这个中间产物,在目前现有的各种文献中未见报道。本文利用萃取、结晶等分离手段提纯出了该中间产物,并通过质谱、元素分析、红外光谱以及核磁共振谱等分析方法对其组成和结构进行了测定,结果表明该中间产物的分子量为216,组成为C12H12N2O2,结构为5-氨基-萘基-1-氨基甲酸甲酯。     

Control of the evolution of iron peroxide intermediate in superoxide reductase from Desulfoarculus baarsii. Involvement of lysine 48 in protonation

Superoxide reductase is a nonheme iron metalloenzyme that detoxifies superoxide anion radicals O(2)(?-) in some microorganisms. Its catalytic mechanism was previously proposed to involve a single ferric iron (hydro)peroxo intermediate, which is protonated to form the reaction product H(2)O(2). Here, we show by pulse radiolysis that the mutation of the well-conserved lysine 48 into isoleucine in the SOR from Desulfoarculus baarsii dramatically affects its reaction with O(2)(?-). Although the first reaction intermediate and its decay are not affected by the mutation, H(2)O(2) is no longer the reaction product. In addition, in contrast to the wild-type SOR, the lysine mutant catalyzes a two-electron oxidation of an olefin into epoxide in the presence of H(2)O(2), suggesting the formation of iron-oxo intermediate species in this mutant. In agreement with the recent X-ray structures of the peroxide intermediates trapped in a SOR crystal, these data support the involvement of lysine 48 in the specific protonation of the proximal oxygen of the peroxide intermediate to generate H(2)O(2), thus avoiding formation of iron-oxo species, as is observed in cytochrome P450. In addition, we proposed that the first reaction intermediate observed by pulse radiolysis is a ferrous-iron superoxo species, in agreement with TD-DFT calculations of the absorption spectrum of this intermediate. A new reaction scheme for the catalytical mechanism of SOR with O(2)(?-) is presented in which ferrous iron-superoxo and ferric hydroperoxide species are reaction intermediates, and the lysine 48 plays a key role in the control of the evolution of iron peroxide intermediate to form H(2)O(2).     

Effect of amine nature on reaction mechanism: aminolyses of o-4-nitrophenyl thionobenzoate with primary and secondary amines

Pseudo-first-order rate constants (k(obs)) have been measured spectrophotometrically for reactions of O-4-nitrophenyl thionobenzoate (2) with a series of primary and acyclic secondary amines. The plots of k(obs) vs amine concentration are linear for the reaction of 2 with primary amines. The slope of the Br?nsted-type plot for the reaction of 2 with primary amines decreases from 0.77 to 0.17 as the amine basicity increases, indicating that the reaction proceeds through a zwitterionic addition intermediate in which the rate-determining step changes from the breakdown of the intermediate to the reaction products to the formation of the intermediate as the amine basicity increases. On the other hand, for reactions with all the acyclic secondary amines studied, the plot of k(obs) vs amine concentration exhibits an upward curvature, suggesting that the reaction proceeds through two intermediates, e.g., a zwitterionic addition intermediate and an anionic intermediate. The microscopic rate constants (k(1), k(-)(1), k(2), and k(3) where available) have been determined for the reactions of 2 with all the primary and secondary amines studied. The k(1) value is larger for the reaction with the primary amine than for the reaction with the isobasic acyclic secondary amines, while the k(-)(1) value is much larger for the latter reaction than for the former reaction. The k(3) value for the reaction with secondary amine is independent of the amine basicity. The small k(2)/k(-)(1) ratio is proposed to be responsible for the deprotonation process observed in aminolyses of carbonyl or thiocarbonyl derivatives.     

Mechanisms of Staudinger reactions within density functional theory

The Staudinger reactions of substituted phosphanes and azides have been investigated by using density functional theory. Four different initial reaction mechanisms have been found. All systems studied go through a cis-transition state rather than a trans-transition state or a one-step transition state. The one-step pathway of the phosphorus atom attacking the substituted nitrogen atom is always unfavorable energetically. Depending on the substituents on the azide and the phosphane, the reaction mechanism with the lowest initial reaction barrier can be classified into three categories: (1). like the parent reaction, PH(3) + N(3)H, the reaction goes through a cis-transition state, approaches a cis-intermediate, overcomes a PN-bond-shifting transition state, reaches a four-membered ring intermediate, dissociates N(2) by overcoming a small barrier, and results in the final products: N(2) and a phosphazene; (2). once reaching the cis-intermediate, the reaction goes through the N(2)-eliminating transition state and produces the final products; (3). the reaction has a concerted initial cis-transition state, in which the phosphorus atom attacks the first and the third nitrogen atoms of the azide simultaneously and reaches an intermediate, and then the reaction goes through similar steps of the first reaction mechanism. In contrast to the previous predictions on the relative stability of the unsubstituted cis-configured phosphazide intermediate and the unsubstituted trans-configured phosphazide intermediate, the total energy of the substituted trans-configured phosphazide intermediate is close to that of the substituted cis-configured phosphazide intermediate. The preference of the initial cis-transition state reaction pathway is thoroughly discussed. The relative stability of the cis- and the trans-intermediates is explored and analyzed with the aid of molecular orbitals. The effects of substituents and solvent effects on the reaction mechanisms of the Staudinger reactions are discussed in detail.     

Theoretical Studies on the Mechanism of Photocycloaddition Reaction Between 6 Azauracil and Acetone

The mechanism of photocycloaddition reaction between 6-azauracll and acetone was studied by using semiemptrical SCFMO AMI method. It was found that this reaction is not a concerted one. The calculated results are as follows:(1) A T1 state exciplex is on the T1 state energy surface; (2) T exciplex as a reactant will proceed along the energy surface of T1 state to form a diradical intermediate. The energy barrier of this reaction step is 63. 6 kJ/mol; (3) The T1 state diradical intermediate happens to be close in energy to the ground state intermediate with a similar geometry. Such a situation turns out to be very favorable for an intersystem crossing (jump from the T, state to the ground state) ; (4) The final product will be formed from the ground S0 state intermediate via an energy barrier 88. 2 kJ/mol.     

Promotion of phosphaalkyne cyclooligomerisation by a Sb(v) to Sb(iii) redox process

A high yield of the tetraphosphaladderene, anti-tetraphosphatricyclo[4.2.0.0(2,5)]octa-3,7-diene, is obtained from reaction of the zirconocene 1,3-diphosphabicyclo[1.1.0]butane with Ph(2)SbCl(3) in THF or CH(2)Cl(2). Exploration of the reaction pathway using density functional theory suggests that an envelope-type adduct of Ph(2)SbCl and 1,3-diphosphabicyclo[1.1.0]butane plays a pivotal role in the reaction. The zwitterionic character of this intermediate species allows it to act simultaneously as both an ene and an eneophile, and a symmetry-allowed bimolecular reaction leads to the tetraphosphaladderene species via a spirocyclic intermediate.     

Quantum molecular dynamics study of the reaction of O2 with HOCO

The reaction of O2 with HOCO has been studied by using an ab initio direct dynamics method based on the UB3PW91 density functional theory. Results show that the reaction can occur via two mechanisms: direct hydrogen abstraction and an addition reaction through a short-lived HOC(O)O2 intermediate. The lifetime of the intermediate is predicted to be 660 +/- 30 fs. Although it is an activated reaction, the activation energy is only 0.71 kcal/mol. At room temperature, the obtained thermal rate coefficient is 2.1 x 10(-12) cm3 molecule(-1) s(-1), which is in good agreement with the experimental results.     

Ab initio study on the mechanism of forming a silapolycyclic compound between silylidene and formaldehyde

The mechanism of the cycloaddition reaction of forming a silapolycyclic compound between singlet silylidene 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, it can be predicted that the cycloaddition reaction process of forming the silapolycyclic compound (P₂) for this reaction consists of four steps: (I) the two reactants first form a semi-cyclic intermediate INT1a through a barrier-free exothermic reaction of 32.5 kJ mol⁻¹; (II) this intermediate then isomerizes to an active four-membered ring intermediate INT1 via a transition state TS1a with an energy barrier of 30.8 kJ mol⁻¹; (III) INT1 further reacts with formaldehyde to form an intermediate INT2, which is also a barrier-free exothermic reaction of 30.1 kJ mol⁻¹; (IV) INT2 isomerizes to a silapolycyclic compound P₂ via a transition state TS2 with a barrier of 50.6 kJ mol⁻¹. Comparing this reaction path with other competitive reaction paths, we can see that this cycloaddition reaction has an excellent selectivity.     

Theoretical studies on the mechanism of formation of a heteropolycyclic germanic compound between dimethyl‐germylidene and ethylene

Mechanism of the cycloadditional reaction between singlet dimethyl‐germylidene (R1) and ethylene (R2) 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, it can be predicted that the dominant reaction pathway of the cycloadditional reaction of forming a heteropolycyclic germanic compound between singlet dimethyl‐germylidene and ethylene consists of three steps: (1) the two reactants (R1, R2) first form a three‐membered intermediate (INT1) through a barrier‐free exothermic reaction of 39.6 kJ/mol. (2) Three‐membered intermediate (INT1) isomerizes to an active four‐membered intermediate (INT2) via a transition state (TS2), for which the barrier is 50.1 kJ/mol. (3) Four‐membered intermediate (INT2) reacts further with ethylene (R2) to form a heteropolycyclic germanic compound (P3), which is also a barrier‐free exothermic reaction of 87.7 kJ/mol. This dominant reaction has an excellent selectivity and differs considerably from its competitive reactions in thermodynamic property and reaction rate. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

DFT study of the active intermediate in the Fenton reaction

Density functional theory has been used to investigate the nature of the oxidizing agent in the Fenton reaction. Starting from the primary intermediate [FeII(H2O)5H2O2]2+, we show that the oxygen-oxygen bond breaking mechanism has a small activation energy and could therefore demonstrate the catalytic effect of the metal complex. The O-O bond cleavage of the coordinated H2O2, however, does not lead to a free hydroxyl radical. Instead, the leaving hydroxyl radical abstracts a hydrogen from an adjacent coordinated water leading to the formation of a second Fe-OH bond and of a water molecule. Along this reaction path the primary intermediate transforms into the [FeIV(H2O)4(OH)2]2+ complex and in a second step into a more stable high valent ferryl-oxo complex [FeIV(H2O)5O]2+. We show that the energy profile along the reaction path is strongly affected by the presence of an extra water molecule located near the iron complex. The alternative intermediate [FeII(H2O)4(OOH-)(H3O+)]2+ suggested in the literature has been also investigated, but it is found to be unstable against the primary intermediate. Our results support a picture in which an FeIV-oxo complex is the most likely candidate as the active intermediate in the Fenton reaction, as indeed first proposed by Bray and Gorin already in 1932.     

Theoretical study on the mechanism of cycloaddition reaction between dimethyl germylidene and formaldehyde

The cycloaddition mechanism of the reaction between singlet dimethyl germylidene 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 with CCSD (T)//MP2/6-31G* method. From the potential energy profile, we predict that the cycloaddition reaction between singlet dimethyl germylidene and formaldehyde has two dominant reaction pathways. First dominant reaction pathway consists of three steps: (1) the two reactants (R1, R2) firstly form an intermediate INT1a through a barrier-free exothermic reaction of 43.0 kJ/mol; (2) INT1a then isomerizes to a four-membered ring compound P1 via a transition state TS1a with an energy barrier of 24.5 kJ/mol; (3) P1 further reacts with formaldehyde(R2) to form a germanic heterocyclic compound INT3, which is also a barrier-free exothermic reaction of 52.7 kJ/mol; Second dominant reaction pathway is as following: (1) the two reactants (R1, R2) firstly form a planar four-membered ring intermediate INT1b through a barrier-free exothermic reaction of 50.8 kJ/mol; (2) INT1b then isomerizes to a twist four-membered ring intermediate INT1.1b via a transition state TS1b with an energy barrier of 4.3 kJ/mol; (3) INT1.1b further reacts with formaldehyde(R2) to form an intermediate INT4, which is also a barrier-free exothermic reaction of 46.9 kJ/mol; (4) INT4 isomerizes to a germanic bis-heterocyclic product P4 via a transition state TS4 with an energy barrier of 54.1 kJ/mol.     

Decomposition of reaction networks: the initial phase of the permanganate/oxalic acid reaction

The determination of all chemical reaction networks composed of elementary reactions for a given net chemical reaction is one of the fundamental problems in chemistry, since the decomposition elucidates the reaction mechanism. It is essential in a wide range of applications: from the derivation of rate laws in physical chemistry to the design of large-scale reactors in process engineering where presence of unexpected side products can disturb operation. As an example we consider the well-known permanganate/oxalic acid reaction. We characterize all intermediate substances that can in principle act (auto-)catalytic, list all possible additional intermediate substances that would suffice to start the reaction without assuming presence of any autocatalyst. In particular, we propose for the first time a minimal network in which the well-known autocatalyst Mn²⁺ is produced. To derive our results we present an automatic method to determine whether a net chemical reaction can be explained by some reaction network with a given list of intermediate substances, how to generate all such networks, and how to suggest more intermediate substances if no network with the initially given substances exists.     

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     

Solvent-dependent changes in the ene reaction of RTAD with alkenes: the cyclopropyl group as a mechanistic probe

[reaction: see text] The vinylcyclopropyl moiety was used as an efficient probe to test mechanistic possibilities of the triazolinedione-alkene ene reaction. In non-hydroxylic solvents, this reaction afforded only the ene adducts via a closed three-membered aziridinium imide (AI) intermediate, whereas in hydroxylic solvents a dipolar intermediate is favored and trapped by the cyclopropyl moiety to form the corresponding cyclopropyl-rearranged solvent-trapped adducts.     

Characterization of a Thiolato Iron(III) Peroxy Dianion Complex

Nucleophilic oxidant: The reaction between a thiolato iron(II) complex 1 and superoxide in aprotic solvent at -90?°C yields a novel thiolato iron(III) peroxide intermediate 2, which exhibits unusually high nucleophilic reactivity. Compound 2 is an isomer of the thiolato iron(II) superoxide intermediate that is invoked in the reaction between superoxide reductase and superoxide.     

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P_2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P₃ via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007