Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.     

Catalysis and mechanistic studies of ruthenium and osmium on synthesis of anthranilic acids

Ruthenium, osmium and ruthenium + osmium catalyzed synthetic methodology was developed for the synthesis of anthranilic acids from indoles in good to excellent yields using bromamine‐B in alkaline acetonitrile–water (1:1) at 313 K. Detailed catalysis studies of ruthenium, osmium and the mixture of both were carried out for the synthetic reactions. The positive synergistic catalytic activity of Ru(III) + Os(VIII) was observed to a large extent with the activity greater than the sum of their separate catalytic activities. Detailed kinetic and mechanistic investigations for each catalyzed reactions were carried out. The kinetic pattern and mechanistic picture of each catalyzed reaction were found to be different for each catalyst and to obey the underlying rate laws: where, x, y < 1. The reactions were studied at different temperatures and the activation parameters were evaluated for each catalyzed reaction. Under the identical set of experimental conditions, the kinetics of all the three catalyzed reactions were compared with uncatalyzed reactions, revealing that the catalyzed reactions were 6‐ to 42‐fold faster. The catalytic efficiency of aforementioned catalysts followed the order: Ru(III) + Os(VIII) > Os(VIII) > Ru(III). This trend may be attributed to the different d‐electronic configuration of the catalysts. The proposed mechanisms and the rigorous kinetic models derived give results that fit well with the experimental data in each catalyzed reaction. Copyright © 2010 John Wiley & Sons, Ltd.     

Kinetics and mechanism of electron transfer reactions in aqueous solutions: Silver(I) catalyzed oxidation of aspartic acid by cerium (IV) in acid perchlorate medium

Silver(I) catalyzed oxidation of aspartic acid by cerium(IV) was studied in acid perchlorate medium. The stoichiometry of the reaction is represented by the eq. (i) Dimeric cerium(IV) species has been indicated and employed in calculations of monomeric cerium(IV) species concentrations. The reaction is second-order and uncatalyzed reaction also simultaneously occurs along with the silver(I) catalyzed reaction conforming to the rate law (ii) where k is an observed second-order rate constant. A probable reaction mechanism is suggested. © 1995 John Wiley & Sons, Inc.     

Experimental versus theoretical evidence for the rate‐limiting steps in uncatalyzed and H+‐ and HO−‐catalyzed hydrolysis of the amide bond

Recent theoretical studies of the alkaline hydrolysis of the amide bond have indicated that the nucleophilic attack of the hydroxide ion at the carbonyl carbon of the amide group is rate limiting. This is shown to be inconsistent with a large amount of experimental observations where the expulsion of the leaving group has been shown to be rate limiting. A kinetic approach has been described, which allows us to diagnose whether the pH‐independent/uncatalyzed hydrolysis of amides involves (a) both the uncatalyzed water reaction (k_w) and H⁺‐ (k_H) and HO^?‐catalyzed (k_OH) water reaction, (b) only the k_w reaction, or (c) only the k + k_OH reaction. The analysis described in this critical review does not favor the recent theoretical claims of the absence of the water reaction in the pH‐independent/uncatalyzed hydrolysis of formamide and urea. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 599–611, 2009     

The kinetics of secondary reactions in the iodination of monogermane. The effect of iodine substitution on the Ge?H bond dissociation energy

A study has been made both of secondary reactions occurring during the reaction of I₂ with GeH₄, and of the direct reaction between I₂ and GeH₃I. Both these studies show that the abstraction reaction occurs about 30 times faster than the reaction in the temperature range of 425–446 K. This information is used to show that iodine substitution weakens Ge–H bonds by 14.4 ± 2.5 kJ/mol and that D(H₂IGe? H) = 332 ± 10 kJ/mol (79.3 kcal/mol). Possible reasons for the effects of halogen substituents on Ge? H and Si? H bond strengths are discussed.     

The gas-phase kinetics of the reaction of 1,1-difluoroiodoethane with hydrogen iodide: The C–I bond dissociation energy in 1,1-difluoroiodoethane

The kinetics of gas-phase reaction of CH₃CF₂I with HI were studied from 496 to 549K and have been shown to be consistent with the following mechanism: A least squares treatment of the data gave where θ = 2.303 RT kcal/mole. The observed activation energy E₁ was combined with E₂ = 0 ± 1 kcal/mole to yield The result, combined with data for several C? I bond dissociation energies, leads us to conclude that the C(sp³)? I bond is relatively insensitive to F for H substitution and that the C(sp²)–I bond has considerable double-bond character.     

The kinetics of the thermal bromination of CF3I. Determination of the bond dissociation energy D(CF3−I)

The kinetics of the thermal bromination reaction have been studied in the range of 173–321°C. For the step we obtain where θ=2.303RT cal/mole. From the activation energy for reaction (11), we calculate that This is compared with previously published values of D(CF₃?I). The relevance of the result to published work on k_c for a combination of CF₃ radicals is discussed.     

Thermal decomposition of 3,4-dimethylpentene-1, 2,3,3-trimethylpentane, 3,3-dimethylpentane,and isobutylbenzene in a single pulse shock tube

Several hydrocarbons have been pyrolyzed in a single pulse shock tube. Rate parameters for the main bond breaking step have been found to be In combination with similar studies carried out earlier and through application of the well-established experimental rule (k(AB)/k_r(AA)k_r(BB))^1/2 ～ 2 where A and B are radicals and the rate constants are for the combination of these radicals, rate parameters for the thermal decomposition of all the hydrocarbons formed from any pair of the following radicals: methyl, ethyl, isopropyl, t-butyl, t-amyl, allyl, methylallyl, and benzyl have been calculated. The available calculated and experimental values of the decomposition rate constants are in excellent agreement. It appears that, with the possible exception of reactions involving the ejection of methyl radicals, the frequency factors per bond are nearly constant, depending only upon the type of carbon–carbon bond that is being broken. These values are all lower than those expected from the radical recombination rates. Heats of formation of ethyl, t-amyl, benzyl, methylallyl, n-propyl, s-butyl, isobutyl, neopentyl, and 3-pentyl radicals have been derived. Rate parameters for the decomposition of some simple ketones and ethers have also been estimated.     

Kinetics of the gas-phase reaction CH3F + I2 ⇆ CH2FI + HI: The C?H bond dissociation energy in methyl and methylene fluorides

The kinetics of the gas-phase reaction of CH₃F with I₂ have been studied spectrophotometrically from 629 to 710 K, and were determined to be consistent with the following mechanism: (1) A least-squares analysis of the kinetic data taken in the initial stages of reaction resulted in where θ = 4.575T/1000 kcal/mol. The errors represent one standard deviation. The experimental activation energy E₄ = 30.8 ± 0.2 kcal/mol was combined with the assumption E₃ = 1 ± 1 kcal/mol and estimated heat capacities to obtain The enthalpy change at 298 K was combined with selected thermochemical data to derive The kinetic studies of ?HF₂ and CH₂F₂ have been reevaluated to yield These results are combined with literature data to yield the C? H, C? F, and C? Cl bond dissociation energies in their respective fluoromethanes, and the effect of α-fluorine substitution is discussed.     

The kinetics of the gas phase decomposition reactions of the hexafluoro-t-butoxy radical

Hexafluoro-t-butoxy radicals have been generated by reacting fluorine with hexafluoro-2-methyl isopropanol: Over the temperature range of 406–600 K the hexafluoro-t-butoxy radical decomposes exclusively by loss of a CF₃ radical [reaction (-2)] rather than by loss of a CH₃ radical [reaction (-1)]: (1) The limits of detectability of the product CF₃COCF₃, by gas-chromatographic analysis, place a lower limit on the ratio k_?2/k_-1 of ～80. The implications of this finding in relation to the reverse radical addition reactions to the carbonyl group are briefly discussed. A thermochemical kinetic calculation reveals a discrepancy in the kinetics and thermodynamics of the decomposition and formation reactions of the related t-butoxy radical:      

Kinetics of the gas-phase reaction between iodine and monogermane and the bond dissociation energy D(H3Ge?H)

The title reaction has been investigated in the temperature range of 403–446 K. Monoiodogermane and di-iodogermane together with hydrogen iodide were the main products, although at high conversions at least one other product was formed. GeH₃I is clearly the primary product. Initial rates were found to obey the rate law over a wide range of initial iodine and monogermane pressures. Secondary reactions (of GeH₃I with I₂) affect the subsequent kinetics, although at sufficiently high initial reactant ratios ([GeH₄]₀/[I₂]₀ ≥ 100) an integrated rate equation fits the data with the same rate constants as the initial rate expression. The observed kinetics are consistent with an iodine atom abstraction chain mechanism, and for the step log k₁ (dm³/mol·s) = (11.03 ± 0.13) – (52.3 ± 1.0 kJ/mol)/RT ln 10 has been deduced. From this the bond dissociation energy D(GeH₃? H) = 346 ± 10 kJ/mol (82.5 kcal/mol) is obtained. The significance of this value, together with derived values for Ge–Ge and Ge–C bond strengths, is discussed.     

Unexpectedly rapid vapor-phase reaction between bromine and methyl iodide

The overall reaction (1) occurs readily in the gas phase, even at room temperature in the dark. The reaction is much faster than the corresponding process and does not involve the normal bromination mechanism for gas phase reactions. Reaction (1) is probably heterogeneous although other mechanisms cannot be excluded. The overall reactions (1) (2) proceed, for all practical purposes, completely to the right-hand side in the vapor phase. The expected mechanism is (3) (4) (5) (6) (7) where reaction (3) is initiated thermally or photochemically. Reaction (4) is of interest because little kinetic data are available on reactions involving abstraction of halogen by halogen and also because an accurate determination of the activation energy E₄ would prmit us to calculate an acccurate value of the bond dissociation energy D(CH₃? I).     

Mechanism for acetic acid-catalyzed ester aminolysis

A computational study is described to elucidate the mechanism for acetic acid-catalyzed ester aminolysis to produce amides. A concerted acyl substitution mechanism is proposed to involve concurrent acyl-O bond cleavage and acyl-N bond formation where acetic acid acts as a bifunctional catalyst connecting to both the alkoxide and the amino moieties. This mechanism does not involve the intermediacy of a tetraheral adduct nor the rehybridization of acyl carbon, in sharp contrast to classic stepwise acyl substitution mechanism.     

Kinetics of the gas-phase reaction between iodine and trifluorosilane and the bond dissociation energy D(F3Si?H)

The title reaction has been investigated in the temperature range 667–715K. The only reaction products were trifluorosilyl iodide and hydrogen iodide. The rate law was obeyed over a wide range of iodine and trifluorosilane pressures. This expression is consistent with an iodine atom abstraction mechanism and for the step log k₁(dm³/mol·sec) = (11.54 ± 0.17) ? (130.5 ± 2.2 kJ/mol)/RT In 10 has been deduced. From this the bond dissociation energy D(F₃Si? H) = (419 ± 5) kJ/mol (100.1 kcal/mol) is obtained. The kinetic andthermochemical implications of this value are discussed.     

The reaction of trifluoromethyl radicals with ammonia

The reaction of trifluoromethyl radicals with ammonia in the gas phase has been studied in the temperature range 30-352°. Product formation is not explicable simply in terms of the reactions: and curvature of the Arrhenius plot at high and low temperatures suggests that there are additional sources of fluoroform.     

Thermal stability of intermediate sized acetylenic compounds and the heats of formation of propargyl radicals

4-Methylhexyne-1, 5-methylhexyne-1, hexyne-1, and 6-methylheptyne-2 have been decomposed in comparative-rate single-pulse shock-tube experiments. Rate expressions for the initial decomposition reactions at 1100°K and from 2 to 6 atm pressure are In combination with previous results, rate expressions for propargyl C? C bond cleavage are related to that for the alkanes by the expression These results yield a propargyl resonance energy of D(nC₃H₇-H) – D(C₃H₃-H) = 36 ± 2 kJ, in excellent agreement with a previous shock-tube study. They also lead to D(CH₃C≡CCH₂-H) – D(C₃H₃-H) = 0.6 ± 3 kJ, D(sC₄H₉-H) – D(iC₃H₇-H) = 0 ± 3 kJ, D(iC₄H₉-H) – D(nC₃H₇-H) = 2 ± 3 kJ, and D(nC₃H₇-H) – D(iC₃H₇-H) = 13.9 ± 3 kJ (all values are for 300°K). The systematics of the molecular decomposition process are explored.     

Kinetic investigation of the bromate–ascorbic acid–malonic acid system

According to our experiments the bromide ion concentration exhibits in the bromate–ascorbic acid–malonic acid–perchloric acid system three extrema as a function of time. To describe this peculiar phenomenon, the kinetics of four component reactions have been studied separately. The following rate equations were obtained: Bromate–ascorbic acid reaction: Bromate–bromide ion reaction: Bromide–ascorbic acid reaction: Bromine–malonic acid reaction: k₄ = 6 × 10^?3 s^?1, k_-4 ≥ 1.7 × 10³ s^?1, k₅ ≥ 1 × 10⁷M^?1 · s^?1 Taking into account the stoichiometry of the component reactions and using these rate equations, the concentration versus time curves of the composite system were calculated. Although the agreement is not as good as in the case of the component reactions, it is remarkable that this kinetic structure exhibits the three extrema found.     

Kinetics of the gas-phase reaction between iodine and monosilane and the bond dissociation energy D(H3Si?H)

The title reaction has been investigated in the temperature range of 494–545 K. During the early stages of reaction the only observed products were silyl iodide and hydrogen iodide. Initial rates were found to obey the rate law over a wide range of initial iodine and monosilane pressures. Secondary reactions, most probably of SiH₃I with I₂, became more important as the reaction progressed. However, provided [SiH₄]₀/[I₂]₀ > 20, these secondary processes had a negligible effect on the kinetics, and an integrated rate expression could be used. These kinetics are consistent with an iodine atom abstraction chain mechanism, and for the step has been deduced. From this the bond dissociation energy D(SiH₃? H) = 378 ± 5 kJ/mol (90 kcal/mol) is obtained. The kinetic and thermochemical implications of this value, especially to the pyrolysis of monosilane, are discussed.     

A kinetic study of the thermal elimination of hydrogen fluoride from 1,2-difluoroethane. Determination of the bond dissociation energies D(CH2F?CH2F) and D(CH2F?H).

The kinetics of the thermal elimination of HF from 1,2-difluoroethane have been studied in a static system over the temperature range 734–820°K. The reaction was shown to be first order and homogeneous, with a rate constant of where θ = 2.303RT in kcal/mole. The A-factor falls within the normal range for such reactions and is in line with transition state theory; the activation energy is similarly consistent with an estimate based on data for the analogous reactions of ethyl fluoride and other alkyl halides. The above activation energy has been compared with values of the critical energy calculated from data on the decomposition of chemically activated 1,2-difluoroethane by the RRKM theory and the bond dissociation energy, D(CH₂F? CH₂F) = 88 ± 2 kcal/mole, derived. It follows from thermochemistry that ΔH_f⁰(CH₂F) = -7.8 and D(CH₂F? H) = 101 ± 2 kcal/mole. Bond dissociation energies in fluoromethanes and fluoroethanes are discussed.     

A concerted hydrogen-transfer reaction in the gas phase

The kinetics of the thermal reaction of mixtures of ethylene and cyclopentene has been examined for the occurrence of a concerted hydrogen-transfer reaction, . The main products of the reaction were ethane and cyclopentadiene, and the rate of formation of ethane was first order in each reactant over a 2500-fold change in the ratio of concentrations of the reactants. An increased surface-to-volume ratio of the reaction vessel or additions of oxygen and nitric oxide had little effect on the rate of formation of ethane, and it was concluded that the dominant reaction in the system was the concerted hydrogen-transfer process. The rate constant for the reaction, measured over the temperature range of 325–505°C, was represented as