Theoretical study on the mechanism of extraction reaction between silylene carbene and its derivatives and thiirane

The mechanism of the sulfur extraction reaction between singlet silylene carbine and its derivatives and thiirane has been investigated with density functional theory (DFT), 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 B3LYP/6-311G(d, p) method. From the potential energy profile, it can be predicted that the reaction pathway of this kind consists in two steps: (1) the two reactants firstly form an intermediate through a barrier-free exothermic reaction; (2) the intermediate then isomerizes to a product via a transition state. This kind of reactions has similar mechanism: when the silylene carbene and its derivatives [X₂Si=C: (X = H, F, Cl, CH₃)] and thiirane approach each other, the shift of 3p lone electron pair of S in thiirane to the 2p unoccupied orbital of C in X₂Si=C: gives a p → p donor-acceptor bond, thereby leading to the formation of intermediate (INT). As the p → p donor-acceptor bond continues to strengthen (that is the C-S bond continues to shorten), the intermediate (INT) generates product (P + C₂H₄) via transition state (TS). It is the substituent electronegativity that mainly affect the extraction reactions. When the substituent electronegativity is greater, the energy barrier is lower, and the reaction rate is greater.     

The form of the rate constant for elementary reactions at equilibrium from MD: framework and proposals for thermokinetics

The rates of formation and concentration distributions of a dimer reaction showing hysteresis behavior are examined in an ab initio chemical reaction designed as elementary and where the hysteresis structure precludes the formation of transition states (TS) with pre-equilibrium and internal sub-reactions. It was discovered that the the reactivity coefficients, defined as a measure of departure from the zero density rate constant for the forward and backward steps had a ratio that was equal to the activity coefficient ratio for the product and reactant species. This surprising result, never formally incorporated in elementary rate expressions over approximately one and a half centuries of quantitative chemical kinetics measurement and calculation is accepted axiomatically and leads to an outline of a theory for the form of the rate constant, in any one given substrate—here the vacuum state. A major deduction is that the long-standing definition of the rate constant for elementary reactions is not complete and is nonlinear, where previous works almost always implicitly refer to the zero density limit for strictly irreducible elementary reactions without any attending concatenation of side-reactions. This is shown directly from MD simulation, where for specially designed elementary reactions without any transition states, density dependence of reactants and products always feature, in contrast to current practice of writing rate equations. It is argued that the rate constant expression without reactant and product dependence is due to historical conventions used for strictly elementary reactions. From the above observations, a theory is developed with the aid of some proven elementary theorems in thermodynamics, and expressions under different state conditions are derived whereby a feasible experimental and computational method for determining the activity coefficients from the rate constants may be obtained under various approximations and conditions. Elementary relations for subspecies equilibria and its relation to the bulk activity coefficient are discussed. From one choice of reaction conditions, estimates of activity coefficients are given which are in at least semi-quantitative agreement with the data for non-reacting Lennard-Jones (LJ) particles for the atomic component. The theory developed is applied to ionic reactions where the standard Brönsted-Bjerrum rate equation and exceptions to this are rationalized.     

Kinetic parameters and geometry of the transition state of acyl radical decarbonylation

Experimental data on acyl radical decomposition reactions (RC^·O → R^· + CO, where R = alkyl or aryl) are analyzed in terms of the intersecting parabolas method. Kinetic parameters characterizing these reactions are calculated. The transition state of methyl radical addition to CO at the C atoms is calculated using the DFT method. A semiempirical algorithm is constructed for calculating the transition state geometry for the decomposition of acyl radicals and for the reverse reactions of R^· addition to CO. Kinetic parameters (activation energy and rate constant) and geometry (interatomic distances in the transition state) are calculated for 18 decomposition reactions of structurally different acyl radicals. A linear correlation between the interatomic distance r ^#(C…C) (or r ^#(C…O)) in the transition state the enthalpy of the reaction (δH _e) is established for acyl decomposition reactions (at br _e = const). A comparative analysis of the enthalpies, activation energies, and interatomic distances in the transition state is carried out for the decomposition and formation of acyl, carboxyl, and formyl radicals.     

Interpretation paradoxes in unimolecular heterolysis kinetics

The rate constant of the first-order rate equation w = k[RX] that is derived from the variation of the reaction product concentration or determined by the verdazyl method characterizes the lifetime of the transition state or that of the solvent-separated ion pair rather than the heterolysis rate. The diffusion rate constant is equal to the dissociation rate constant of the contact ion pair and to the reverse of the lifetime of the solvent-separated ion pair: k _D ≈ k = 1/τ ≈ 10¹⁰ s⁻¹.     

CH2XH→CH3X (X＝O, S, Se)异构化的量子拓扑研究

利用从头算和量子拓扑方法讨论了CH₂XH→CH₃X (X＝O, S, Se)异构化过程的反应机理. 着重从电子密度拓扑分析计算了反应进程中的各点, 讨论了反应进程中键的断裂和生成, 上述反应都经历了三元环过渡结构, 找到了这类反应的"能量过渡态"和"结构过渡态", 且结构过渡态均在能量过渡态之后出现. 三元结构过渡态结构出现的范围与反应热成正比.     

The Reactivity of Ambident Nucleophiles: Marcus Theory or Hard and Soft Acids and Bases Principle?

The model reactions CH₃X + (NH—CH=O)M ➔ CH₃—NH—NH═O or NH═CH—O—CH₃ + MX (M = none, Li, Na, K, Ag, Cu; X = F, Cl, Br) are investigated to demonstrate the feasibility of Marcus theory and the hard and soft acids and bases (HSAB) principle in predicting the reactivity of ambident nucleophiles. The delocalization indices (DI) are defined in the framework of the quantum theory of atoms in molecules (QT-AIM), and are used as the scale of softness in the HSAB principle. To react with the ambident nucleophile NH═CH—O⁻, the carbocation H₃C⁺ from CH₃X (F, Cl, Br) is actually a borderline acid according to the DI values of the forming C…N and C…O bonds in the transition states (between 0.25 and 0.49), while the counter ions are divided into three groups according to the DI values of weak interactions involving M (M…X, M…N, and M…O): group I (M = none, and Me₄N) basically show zero DI values; group II species (M = Li, Na, and K) have noticeable DI values but the magnitudes are usually less than 0.15; and group III species (M = Ag and Cu(I)) have significant DI values (0.30–0.61). On a relative basis, H₃C⁺ is a soft acid with respect to group I and group II counter ions, and a hard acid with respect to group III counter ions. Therefore, N-regioselectivity is found in the presence of group I and group II counter ions (M = Me₄N, Li, Na, K), while O-regioselectivity is observed in the presence of the group III counter ions (M = Ag, and Cu(I)). The hardness of atoms, groups, and molecules is also calculated with new functions that depend on ionization potential (I) and electron affinity (A) and use the atomic charges obtained from localization indices (LI), so that the regioselectivity is explained by the atomic hardness of reactive nitrogen atoms in the transition states according to the maximum hardness principle (MHP). The exact Marcus equation is derived from the simple harmonic potential energy parabola, so that the concepts of activation free energy, intrinsic activation barrier, and reaction energy are completely connected. The required intrinsic activation barriers can be either estimated from ab initio calculations on reactant, transition state, and product of the model reactions, or calculated from identity reactions. The counter ions stabilize the reactant through bridging N- and O-site of reactant of identity reactions, so that the intrinsic barriers for the salts are higher than those for free ambident anions, which is explained by the increased reorganization parameter Δr. The proper application of Marcus theory should quantitatively consider all three terms of Marcus equation, and reliably represent the results with potential energy parabolas for reactants and all products. For the model reactions, both Marcus theory and HSAB principle/MHP principle predict the N-regioselectivity when M = none, Me₄N, Li, Na, K, and the O-regioselectivity when M = Ag and Cu(I). © 2019 Wiley Periodicals, Inc.     

Radical addition reactions: factors determining the transition-state geometry

Interatomic distances in the reaction centers of the addition reactions of (i) H^· to the C=C, C=O, N≡C, and C≡C bonds, (ii) ^·CH₃ radical to the C=C, C=O, and C≡C bonds, and (iii) alkyl, aminyl, and alkoxyl radicals to olefin C=C bonds were determined using a new semiempirical method for calculating transition-state geometries of radical reactions. For all reactions of the type X^· + Y=Z → X— Y—Z^· the r ^# _X...Y distance in the transition state is a linear function of the enthalpy of reaction. Parameters of this dependence were determined for seventeen classes of radical addition reactions. The bond elongation, Δr ^# _X...Y, in the transition state decreases as the triplet repulsion, electronegativity difference between the atoms X and Y in the reaction center, and the force constant of the attacked multiple bond increase. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 894–902, April, 2005.     

Multipath variational transition state theory: rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical

We propose a new formulation of variational transition state theory called multipath variational transition state theory (MP-VTST). We employ this new formulation to calculate the forward and reverse thermal rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical in the gas phase. First, we find and optimize all the local-minimum-energy structures of the reaction, product, and transition state. Then, for the lowest-energy transition state structures, we calculate the reaction path by using multiconfiguration Shepard interpolation (MSCI) method to represent the potential energy surface, and, from this representation, we also calculate the ground-state vibrationally adiabatic potential energy curve, the reaction-path curvature vector, and the generalized free energy of activation profile. With this information, the path-averaged generalized transmission coefficients <γ> are evaluated. Then, thermal rate constant containing the multiple-structure anharmonicity and torsional anharmonicity effects is calculated using multistructural transition state theory (MS-TST). The final MP-VTST thermal rate constant is obtained by multiplying k(MS-T)(MS-TST) by <γ>. In these calculations, the M06 density functional is utilized to compute the energy, gradient, and Hessian at the Shepard points, and the M06-2X density functional is used to obtain the structures (conformers) of the reactant, product, and the saddle point for computing the multistructural anharmonicity factors.     

On the Apparent Compensation Effect Found for Two Consecutive Reactions

A critical analysis of the use of an overall single rate reaction equation instead of the true rate equation corresponding to a complex process consisting in two consecutive reactions is presented. In accordance with this approximation, often used in the kinetic analysis of the system in which several reactions take place, the overall process is described by the apparent activation parameters (the apparent activation energy, E _ap, and the apparent pre-exponential factor, A _ap) and the apparent conversion function. The theoretical isotherms (α=α(t), where a is the conversion degree and t is the time) have been simulated for a system in which two consecutive reactions occur. In this case, the apparent activation parameters depends on: (a) the considered range of the temperature; (b) the temperature, for a given conversion degree. It is shown that the apparent activation parameters are corrrelated by the compensation effect relationship: lnA _ap=α*+β*E _ap where α* and β* are the parameters of the linear regression. The possibility of using the apparent kinetic parameters to predict the isotherms α=α(t) for temperatures lower than those for which these parameters were evaluated, is discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

F+NCO反应的机理和动力学

利用Ｇ２（ＭＰ２）理论研究Ｆ（＾２Ｐ）与ＮＣＯ（Ｘ＾２ＩＩ）在三重激发态（ａ＾３Ａ＂）势能面上的反应机理揭示了生成ＮＦ）Ｘ＾３Σ＾－）的两种反应途径,即顺式和反式加成－消除,其中顺式反应途径的势垒较低（２０．０ｋｊ．ｍｏｌ＾－１）,。动力学计算显示,在室温 上,Ｆ与ＮＣＯ反应于三重态势能面上只能较缓慢地生成ＮＦ（Ｘ＾３Σ＾－）自由基。预测ＦＣ（Ｎ）Ｏ是另一可能的反应产物     

“Inversion substitution” reactions with participation of molecular oxygen: ZH<Subscript>3</Subscript>I + O<Subscript>2</Subscript> → O<Subscript>2</Subscript>ZH<Subscript>3</Subscript> + I (Z = C,Si). The potential energy surface and rate constants

A new class of reactions of molecular oxygen O₂ + ZH₃I → O₂ZH₃ + I (Z = C, Si) proceeding by the mechanism of “inversion substitution” was investigated by quantum chemistry methods and the transition state theory (TST). The profiles of the potential energy surfaces (PES) along the reaction coordinate and the characteristics of transition states were calculated using the DFT approach with the B3LYP hybrid functional and the DZVP basis set. The characteristics of the transition states were then used for TST calculations of the rate constants for the direct and reverse “inversion substitution” reactions and their temperature dependences in the temperature interval 273–2000 K. The activation barriers to the substitution reactions under study were found to be substantially lower than the barriers to the abstraction reactions O₂ + ZH₃I → ZH₂I + HO₂ (by 16.3 kcal mol⁻¹ for Z = C and by 7.2 kcal mol⁻¹ for Z = Si). The results obtained show that the “inversion substitution” reactions dominate over the abstraction reactions in the interaction of molecular oxygen with carbon- and silicon-centered iodides as well as (probably) many other substrates. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1803–1807, September, 2008.     

硅苯与HX (X=F,OH, NH2)的1,2-及1,4-加成反应

采用密度泛函理论方法在B3LYP/6-311++G(d,p)水平上, 研究了硅苯与HX (X=F, OH, NH₂)的1,2-及1,4-加成反应的微观机理和势能剖面, 考察了Si 原子上的取代基及四氢呋喃溶剂对反应势能剖面的影响. 研究结果表明, 标题反应有两种可能的机理: (1) 硅苯与一个HX (X=F, OH, NH₂)分子先形成中间复合物, 然后经过四元环过渡态(机理1)生成最终产物; (2) 硅苯与两个HX分子先形成中间复合物, 然后经过六元环过渡态(机理2)生成另一中间复合物, 该中间复合物脱去一个HX分子形成最终产物. 机理2 在动力学上远较机理1 有利. 1,2-及1,4-加成产物哪种优先形成由动力学控制且与X基团的种类有关. HX在气相中参与加成反应从易到难的次序为: HF>H₂O>NH₃. Si 原子上具有较强供电子和吸电子性质的取代基, 在热力学和动力学上均有利于反应的进行, 但具有较大体积的2,4,6-三甲基苯基取代基对反应反而不利. 四氢呋喃溶剂在热力学上不利于硅苯与HX的1,2-及1,4-加成反应, 在动力学上对HF或H₂O作为加成试剂的反应也不利, 但对NH3作为加成试剂的反应反而有利.     

Physical factors determining the activation energy of alkyl radical addition to unsaturated compounds

A parabolic model of the transition state is used for the analysis of experimental data (rate constants and activation energies) for reactions of addition of alkyl and phenyl radicals to multiple bonds of unsaturated compounds. The parameters describing the activation energy as a function of the enthalpy of the reactions were calculated from the experimental data. The activation energy depends also on the strength of the forming C−C bond, the presence of π-bonds in the α-position near the attacked C=C bond and the presence of polar groups in the monomer and radical. The empirical dependence of the activation energy of a thermoneutral addition reactionE _e0 on the dissociation energyD _e of the forming C−C bond was obtained:E _e0=(5.95±0.06)·10⁻⁴ D _e ² kJ mol⁻¹, indicating the important role of triplet repulsion in the formation of the transition state of radical addition. The contribution of the polar interaction to the activation energy of addition of polar radicals to polar monomers was calculated. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 445–450, March, 1999.     

Mechanism of the hydrolysis of α-(<Emphasis Type="Italic">p</Emphasis>-nitrophenyl)cinnamonitrile derivatives

The rate constant hydrolysis of α-(p-nitrophenyl)cinnamonitrile(NCPN) and its derivatives have been determined at various pH, and the rate equation which can be applied over a wide pH range is obtained. On the basis of the rate equation, hydrolysis product, general base, and substituent effects, a plausible mechanism of hydrolysis has been proposed: At pH < 4.0, the hydrolysis was initiated by the addition of water to β-carbon of the carbon-carbon double bond. At pH > 8.5, the addition of hydroxide ion to the double bond was rate controlling. In the range of pH 4.0–8.5, these two reactions occurred competitively. Published in Russian in Kinetika i Kataliz, 2007, Vol. 48, No. 5, pp. 670–676. This article was submitted by the authors in English.     

Estimation of rate constants as a function of temperature for the reactions W + XYZ = WX + YZ,where W,X, Y,and Z are H or O atoms

Rate constants have been estimated as a function of temperature for seven reactions of the type W + XYZ = WX + YZ, where W, X, Y, and Z are H and O atoms. From transition state theory and estimates of the heat capacities of activation, where int k is the rate constant per transferable atom for the forward and reverse reactions in the exothermic direction, and where ΔH°_≠298 is in kcal/mol. Values of ΔS°_≠298 and ΔH°_≠298 were obtained from the above equation and previously measured and evaluated rate constants at 298°K. The results are summarized in a table. Rate constants were calculated at temperature from 250 to 2000 K. The estimated rate constants were compared with recommended values. The results for ΔH°_≠298 for reactions (15), (16), (17), and (19), in which a stable intermediate may precede the transition state, together with similar results previously found for reactions X + YZ = XY + Z, suggests that many such reactions may have values of ΔH°_≠298 that are close to zero. The result for the reaction O + O₃ = O₂ + O₂ is however, an exception to the foregoing perhaps because it is the reaction of a singlet with a triplet.ΔS°_≠298 for the same reaction is unexpectedly low.     

Structure and isomerization of cyclotrimetallenes

The substituent migration on the X₂Y rings (X, Y=C, Si, Ge) was studied by theoretical method with silyl and hydrogen substituents and it was found that all the reactions (with the exception of cyclopropene) proceed in a two-step mechanism via a stable intermediate. The rate determining step of the reaction is the first step. The barrier of the second step is small and the energy of the intermediate is close to that of the reactant. Both the first transition state (T1) and the intermediate (I) are of monobridge structures of different types. Since the intermediate bridge structure is almost as stable as the product, it may be observed in the substituent migration reactions.     

A Semi-Empirical Model of the Energy Barrier of Proton Transfer Reactions

The energy barrier in proton transfer reactions is described by a Johnston-type equation (1) (n = order of bond to be broken). The barrier model is discussed in terms of free energies. The V_i values are free energies of ionic cleavage in aqueous solution of the X? H and Y? H bonds; they are computed from eqns. (4c) and (4d). The values of p₁ and p₂ affect curvature (absence or presence of maximum) and symmetry of the barrier. It is postulated that pi is a typical constant of the reacting bond and can be transferred from one transition state to another. With the aid of eqn. (1) and its first derivative, values of pi and n_m (bond order at maximum of barrier) can be based on quantities determined experimentally, Δ≠ and ΔG. For O? H bonds, pi ≈ 1.0. For C? H bonds pi is larger than 1.0 and depends on the structure of the carbanionic moiety (influence of resonance and inductive effects). As there cannot be a maximum if p₁ = p₂ = 1.0, the suggested model of the barrier leads to a better understanding why proton transfer must be ‘fast’ in some reactions and ‘slow’ in others. The computed values of n_m may be utilized to gain some insight into the nature of the transition states; they supply a basis for the discussion of primary hydrogen isotope effects.     

正碳离子样的过渡态类似物研究进展

综述了应用酶催化过渡态理论设计的几类正碳离子样的过渡态类似物作为酶的抑制剂的研究进展。其中包括类异戊二烯的正离子过渡态类似物,唾液酸转移酶的过渡态类似物,3-脱氧-D-甘露糖-2-辛酮糖酸酯-8-磷酸酯(KDO8P) 合成酶的过渡态类似物,尿苷二磷酸酯葡糖醛酸基转移酶(UGT) 的过渡态类似物。     

Studies on the Mechanism for the Bimolecular Metathesis Reaction CH3 + HCI ⇔︁ CH4 + CI

The geometry optimization of the transition state, the precursor complex and the successor complex was performed at the 6–311G* basis set level. From the analysis of the vibrational frequency of the precursor complex, transition state, successor complex and the isolated state, the reaction mechanism was derived which was complicated with the bond‐rupture electron transfer theory. The atom H in molecule HCI attacks the atom C, forming a transition state via the precursor complex and the electron‐transfer happens in precursor complex. And the active energy, electronic coupling matrix element, the reorganization energy, and the reaction rate are obtained.     

Stereoisomeric effects on mass spectra—I. A Review

The unimolecular reactions that give rise to mass spectra are controlled by spatial relationships and energy considerations. In molecules that contain a heteroatom, elimination reactions, involving bond-making as well as breaking, are often prominent, e.g. loss of water from alcohols. The ease of such reactions depends on spatial relationships in the molecule, and the resultant ion intensities in the spectra of geometric isomers can consequently be correlated with differences in geometry and hence furnish a basis for assigning structures. Processes that do not involve bond-making do not have such rigorous geometric requirements, but depend rather on attainment of a transition state defined in terms of a minimum energy content. Common product ions from stereoisomeric hydrocarbons seem often to arise via a common transition state. When this condition holds, the difference between the enthalpies of the isomers is reflected in the relative appearance potentials and–though the cause-and-effect relationship here is less direct and more readily obscured by other factors–relative intensities of the common product derived from the isomers. In both classes of processes, the spectra of stereoisomers can be simplified and made more distinctive by lowering source temperature and ionizing voltage.