Journal articles: 'Complex Reaction Mechanism'

1

Butuk, N., and J. P. Pemba. "Computing CHEMKIN Sensitivities Using Complex Variables." Journal of Engineering for Gas Turbines and Power 125, no. 3 (July 1, 2003): 854–58. http://dx.doi.org/10.1115/1.1469006.

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This paper discusses an accurate numerical approach based on complex variables for the computation of the Jacobian matrix of complex chemical reaction mechanisms. The Jacobian matrix is required in the calculation of low dimensional manifolds during kinetic chemical mechanism reduction. The approach is suitable for numerical computations of large-scale problems and is more accurate than the finite difference approach of computing Jacobians. The method is demonstrated via a nonlinear reaction mechanism for the synthesis of Bromide acid and a H2/Air mechanism using a modified CHEMKIN package. The Bromide mechanism consisted of five species participating in six elementary chemical reactions and the H2/Air mechanism consisted of 11 species and 23 reactions. In both cases it is shown that the method is superior to the finite difference approach of computing derivatives with an arbitrary computational step size h.

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Хамидуллина, Зульфия Абударовна, Альбина Сабирьяновна Исмагилова, and Семен Израилевич Спивак. "Determination of the basis for nonlinear parametric functions of chemical reactions." Вычислительные технологии, no. 3 (July 15, 2020): 29–34. http://dx.doi.org/10.25743/ict.2020.25.3.004.

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Настоящая работа посвящена математическому и компьютерному моделированию кинетики сложных химических реакций. Сформулирована и доказана теорема о соответствии структуры механизма сложной химической реакции с матрицей связей. Разработан и автоматизирован алгоритм определения базиса нелинейных параметрических функций. Реализована теоретико-графовая интерпретация механизма сложной химической реакции Mathematical and computer modelling of the kinetics of complex chemical reactions is considered in the present study. It was formulated that the structural mechanism of complex chemical reaction corresponds to the matrix of bonds. The appropriate theorem was proved. A graph and theoretical technique that allows determining the functional dependences of kinetic parameters directly from the graph of the reaction mechanism is developed. Based on the proposed algorithm, a program for determining the basis of nonlinear parametric functions of kinetic parameters is proposed. The program implements a graph and theoretic interpretation of the mechanisms of complex chemical reactions for constructing stationary kinetic models of catalytic reactions. An algorithm for determining the basis of nonlinear parametric functions is developed and automated. A graph and theoretical interpretation of the mechanism of a complex chemical reaction is implemented

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3

Simoyi, Reuben H., Patricia Masvikeni, and Angela Sikosana. "Complex kinetics in the bromate-iodide reaction: a clock reaction mechanism." Journal of Physical Chemistry 90, no. 17 (August 1986): 4126–31. http://dx.doi.org/10.1021/j100408a058.

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4

Ratkiewicz, Artur, and Thanh N. Truong. "A canonical form of the complex reaction mechanism." Energy 43, no. 1 (July 2012): 64–72. http://dx.doi.org/10.1016/j.energy.2012.02.029.

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5

Tsona, Narcisse Tchinda, and Lin Du. "A potential source of atmospheric sulfate from O2−-induced SO2 oxidation by ozone." Atmospheric Chemistry and Physics 19, no. 1 (January 17, 2019): 649–61. http://dx.doi.org/10.5194/acp-19-649-2019.

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Abstract. It was formerly demonstrated that O2SOO− forms at collisions rate in the gas phase as a result of SO2 reaction with O2-. Here, we present a theoretical investigation of the chemical fate of O2SOO− by reaction with O3 in the gas phase, based on ab initio calculations. Two main mechanisms were found for the title reaction, with fundamentally different products: (i) formation of a van der Waals complex followed by electron transfer and further decomposition to O2 + SO2 + O3- and (ii) formation of a molecular complex from O2 switching by O3, followed by SO2 oxidation to SO3- within the complex. Both reactions are exergonic, but separated by relatively low energy barriers. The products in the former mechanism would likely initiate other SO2 oxidations as shown in previous studies, whereas the latter mechanism closes a path wherein SO2 is oxidized to SO3-. The latter reaction is atmospherically relevant since it forms the SO3- ion, hereby closing the SO2 oxidation path initiated by O2-. The main atmospheric fate of SO3- is nothing but sulfate formation. Exploration of the reactions kinetics indicates that the path of reaction (ii) is highly facilitated by humidity. For this path, we found an overall rate constant of 4.0×10-11 cm3 molecule−1 s−1 at 298 K and 50 % relative humidity. The title reaction provides a new mechanism for sulfate formation from ion-induced SO2 oxidation in the gas phase and highlights the importance of including such a mechanism in modeling sulfate-based aerosol formation rates.

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Taylor, Annette F. "Mechanism and Phenomenology of an Oscillating Chemical Reaction." Progress in Reaction Kinetics and Mechanism 27, no. 4 (December 2002): 247–326. http://dx.doi.org/10.3184/007967402103165414.

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Chemical reactions, which are far from equilibrium, are capable of displaying oscillations in species concentrations and hence in colour, electrode potential, pH and/or temperature. The oscillations arise from the interplay between positive and negative kinetic feedback. Mechanisms for such reactions are presented, along with the rich phenomenology that these systems exhibit, from complex oscillations and chemical waves, to stationary concentration patterns. This review will focus on the Belousov-Zhabotinksy reaction but reference to other reactions will be made where appropriate.

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7

Back, M. H. "1996 Clara Benson Award Lecture The kinetics of the reaction of carbon with oxygen." Canadian Journal of Chemistry 75, no. 3 (March 1, 1997): 249–57. http://dx.doi.org/10.1139/v97-028.

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The results of studies of the kinetics of the reaction of oxygen with thin films of carbon are described with special emphasis on the role, in the mechanism of the reaction, of the stable complex formed between oxygen and the carbon surface. A key part of the proposed mechanism is the reaction between gaseous oxygen and the stable complex to form the product carbon dioxide. Measurements of the total pressure and the products formed as a function of time of the reaction have allowed estimates of the rate constants for the elementary reactions that make up the mechanism. This in turn has led to the application of computer modelling to the mechanism of the reaction and to the development of a more detailed mechanism involving two types of reactive sites on the carbon surface. Keywords: carbon, oxygen, kinetics, mechanism, computer modelling.

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8

Gromotka, Zoë, Gregory Yablonsky, Nickolay Ostrovskii, and Denis Constales. "Integral Characteristic of Complex Catalytic Reaction Accompanied by Deactivation." Catalysts 12, no. 10 (October 20, 2022): 1283. http://dx.doi.org/10.3390/catal12101283.

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New theoretical relationships for a complex catalytic reaction accompanied by deactivation are obtained, using as an example the two-step catalytic mechanism (Temkin–Boudart mechanism) with irreversible reactions and irreversible deactivation. In the domain of small concentrations, Alim=NSk1CAkd, where Alim is the limit of the integral consumption of the gas substance, NS is the number of active sites per unit of catalyst surface; k1 and kd, are kinetic coefficients which relate to two reactions which compete for the free active site Z. CA is the gas concentration. One reaction belongs to the catalytic cycle. The other reaction with kinetic coefficient kd is irreversible deactivation. The catalyst lifetime, τcat=1CZ′1kd, where CZ′ is the dimensionless steady-state concentration of free active sites. The main conclusion was formulated as follows: the catalyst lifetime can be enhanced by decreasing the steady-state (quasi-steady-state) concentration of free active sites. In some domains of parameters, it can also be achieved by increasing the steady-state (quasi-steady-state) reaction rate of the fresh catalyst. We can express this conclusion as follows: under some conditions, an elevated fresh catalyst activity protects the catalyst from deactivation. These theoretical results are illustrated with the use of computer simulations.

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9

Parker, Vernon D. "Is the single transition-state model appropriate for the fundamental reactions of organic chemistry?" Pure and Applied Chemistry 77, no. 11 (January 1, 2005): 1823–33. http://dx.doi.org/10.1351/pac200577111823.

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In recent years, we have reported that a number of organic reactions generally believed to follow simple second-order kinetics actually follow a more complex mechanism. This mechanism, the reversible consecutive second-order mechanism, involves the reversible formation of a kinetically significant reactant complex intermediate followed by irreversible product formation. The mechanism is illustrated for the general reaction between reactant and excess reagent under pseudo-first-order conditions in eq. i where kf' is the pseudo-first-order rate constant equal to kf[Excess Reagent].Reactant + Excess reagent = Reactant complex = Products (i)The mechanisms are determined for the various systems, and the kinetics of the complex mechanisms are resolved by our "non-steady-state kinetic data analysis". The basis for the non-steady-state kinetic method will be presented along with examples. The problems encountered in attempting to identify intermediates formed in low concentration will be discussed.

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10

Tsutsui, Minoru. "π-COMPLEX MECHANISM OF CATALYSIS: THE ARYL-COUPLING REACTION." Annals of the New York Academy of Sciences 93, no. 4 (December 15, 2006): 135–46. http://dx.doi.org/10.1111/j.1749-6632.1961.tb30517.x.

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11

Chandrawat, Uttra, Aditya Prakash, and Raj N. Mehrotra. "Kinetics and mechanism of the oxidation of the sulphite ion by the Mn(III)–cydta complex ion." Canadian Journal of Chemistry 73, no. 9 (September 1, 1995): 1531–37. http://dx.doi.org/10.1139/v95-190.

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The reinvestigated oxidation of S(IV), HSO3−/SO32−ions, by [Mn(cydta)(OH)]− confirmed that S(IV) is oxidized in two parallel paths; the order with respect to [S(IV)] is one in one of the paths and two in the other. The nature of the dependence of the rate on [H+] is also confirmed. However, the rapid scan of the reaction mixture and measurement of the initial absorbance of the reaction mixture at different wavelengths at the beginning of the reaction suggest an outer-sphere mechanism. The rate parameters are of the same order as obtained in known reactions of an outer-sphere mechanism and this mechanism is further supported by the Marcus cross relation. Keywords: kinetics, outer-sphere mechanism, [Mn(cydta)]−, SO32−.

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12

Sbirrazzuoli, Nicolas. "Advanced Isoconversional Kinetic Analysis for the Elucidation of Complex Reaction Mechanisms: A New Method for the Identification of Rate-Limiting Steps." Molecules 24, no. 9 (April 30, 2019): 1683. http://dx.doi.org/10.3390/molecules24091683.

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Two complex cure mechanisms were simulated. Isoconversional kinetic analysis was applied to the resulting data. The study highlighted correlations between the reaction rate, activation energy dependency, rate constants for the chemically controlled part of the reaction and the diffusion-controlled part, activation energy and pre-exponential factors of the individual steps and change in rate-limiting steps. It was shown how some parameters computed using Friedman’s method can help to identify change in the rate-limiting steps of the overall polymerization mechanism as measured by thermoanalytical techniques. It was concluded that the assumption of the validity of a single-step equation when restricted to a given α value holds for complex reactions. The method is not limited to chemical reactions, but can be applied to any complex chemical or physical transformation.

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13

Liu, Zhenfeng, and Jianyong Liu. "DFT investigation on mechanism of dirhodium tetracarboxylate-catalyzed O-H insertion of diazo compounds with H2O." Open Chemistry 8, no. 1 (February 1, 2010): 223–28. http://dx.doi.org/10.2478/s11532-009-0118-8.

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AbstractThe mechanism of the dirhodium tetracarboxylate-catalyzed O-H insertion reaction of diazomethane and methyl diazoacetate with H2O has been studied in detail using DFT calculations. The rhodium catalyst and a diazo compound couple to form a rhodiumcarbene complex. Of two reaction pathways of the Rh(II)-carbene complex with H2O, the stepwise pathway is more preferable than the concerted one. Formation of a Rh(II) complex-associated oxonium ylide is an exothermal process, and direct decomposition of the ylide gives a very high barrier. The high barriers for the 1,2-H shift of Rh(II) complex-associated oxonium ylides make the ylides become stable intermediates in both reactions, especially for the reactions in solution. Difficulty in formation of a free oxonium ylide supports experimental results, indicating that the Rh(II) complex-catalyzed nucleophilic addition of a diazo compound proceeds via a Rh(II) complex-associated oxonium ylide rather than via a free oxonium ylide.

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14

Masters, Andrew P., and Ted S. Sorensen. "Pentacarbonylmanganese enolate and dienolate complexes. Preparative and mechanistic considerations." Canadian Journal of Chemistry 68, no. 3 (March 1, 1990): 492–501. http://dx.doi.org/10.1139/v90-076.

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Reactions of pentacarbonyl manganate anion with 4-halocrotonate esters or 2-halocarboxylate esters result in a complex set of inorganic and organic products, usually including the expected dienolate (or enolate) complexes. The reaction variables include the counterion, solvent, and halo group. The mechanism of the reaction has been investigated by conducting a thorough characterization of the reaction products under various conditions and also by carrying out model reactions. One can rationalize most of the non-organometallic products using either a radical or carbanion mechanism, but the latter seems to fit the available data better. Experimental procedures for optimizing the yield of the organometallic dienolate or enolate complexes have been worked out. Keywords: pentacarbonyl manganate, metalate nucleophilicity, enolate complex, nucleophilic substitution, 55Mn NMR spectroscopy.

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15

Naik, R. M., B. Kumar J. Rai, R. Rastogi, and S. B. S. Yadav. "Kinetics and Mechanism of Oxidation of Hexamethylenediaminetetraacetatocobaltate(II) Complex by Periodate Ion in Aqueous Medium." E-Journal of Chemistry 7, s1 (2010): S391—S399. http://dx.doi.org/10.1155/2010/180576.

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The kinetics and mechanism of oxidation of [CoIIHDTA]4-(Where HDTA=Hexamethylenediamine tetraacetic acid} by periodate ion has been studied in aqueous acidic medium. The reactions has been investigated spectrophotometrically at λmax= 580 nm under pseudo- first -order condition by taking large excess of oxidant [IO4] at pH = 4.0±0.02, I = 0.1 M (CH3COONa + NaNO3).and temperature = 30± 0.1°C The electron transfer reaction between [CoIIHDTA]4-and [IO4-] obeys inner sphere reaction pathway through the formation of long-lived intermediate complex which finally get converted into a corresponding [CoIIIHDTA]3-complex as final reaction product. The experimental observations have shown that the reaction obey first- order dependence in [CoIIHDTA]4--. The variation of pseudo-first-order rate constants (kobs) with[IO4-], keeping other reaction variables fixed at constant value was found to obey the rate law: kobs=a[IO4-]2/b+c[IO4-], which is consistent with a three step mechanistic scheme. The values of kobsare almost constant with increasing pH, which can be attributed to the reaction of deprotonated form of [CoIIIHDTA]4-complex only, in the entire pH region. Eyring’s equation has been used to calculate the thermal or activation parameters and found to be, ΔH#= 28.69 kJ mole–1; ΔS#= – 481.13 J K-1mole–1respectively and support the proposed mechanistic scheme.

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16

Shallangwa, Gideon A., Adamu Uzairu, Victor O. Ajibola, and Hamza Abba. "MNDO and DFT Computational Study on the Mechanism of the Oxidation of 1,2-Diphenylhydrazine by Iodine." ISRN Physical Chemistry 2014 (March 27, 2014): 1–8. http://dx.doi.org/10.1155/2014/592850.

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The reaction mechanisms of the oxidation of 1,2-diphenylhydrazine by iodine have been examined using semiempirical and density functional theory methods, the oxidation proceeded via two independent pathways that can be separately monitored. One pathway involved the chain multistep mechanism. The other pathway occurred via a one-step mechanism in which a “cyclic” activated complex was formed which on disproportionation gave the products. The one-step “cyclic” activated complex mechanism proceeds more rapidly than the chain multistep mechanism. The results were explained by analyses based on computational energetics of the optimised reactants, intermediates, transition states, and products of the reaction of iodine with 1,2-diphenylhydrazine.

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17

Nguyen, Hue Minh Thi, and Trong Nghia Nguyen. "Calculations on the complex mechanism of the HCNO+OH reaction." Chemical Physics Letters 599 (April 2014): 15–22. http://dx.doi.org/10.1016/j.cplett.2014.03.001.

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18

Iwasaki, Takanori, Asuka Fukuoka, Wataru Yokoyama, Xin Min, Ichiro Hisaki, Tao Yang, Masahiro Ehara, Hitoshi Kuniyasu, and Nobuaki Kambe. "Nickel-catalyzed coupling reaction of alkyl halides with aryl Grignard reagents in the presence of 1,3-butadiene: mechanistic studies of four-component coupling and competing cross-coupling reactions." Chemical Science 9, no. 8 (2018): 2195–211. http://dx.doi.org/10.1039/c7sc04675h.

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19

Jambrina, P. G., M. Menéndez, and F. J. Aoiz. "The dynamics of the Hg + Br2 reaction: elucidation of the reaction mechanism for the Br exchange reaction." Physical Chemistry Chemical Physics 19, no. 25 (2017): 16433–45. http://dx.doi.org/10.1039/c7cp01871a.

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20

Proulx, Grant, Frederick J. Hollander, and Robert G. Bergman. "Reaction of Cp2(CH3)Ta=CH2 with Ru3(CO)12: deoxygenative coupling of carbon monoxide and methylene units to give a heteronuclear cluster-bound 4-cumulene ligand." Canadian Journal of Chemistry 73, no. 7 (July 1, 1995): 1111–15. http://dx.doi.org/10.1139/v95-137.

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The mechanisms of reactions that deoxygenate carbon monoxide (CO) and convert it into longer-chain hydrocarbons are not well understood. A reaction is reported between an early metal methylidene complex and a late transition metal carbonyl species that results in CO deoxygenation along with coupling of the CO carbon to methylidene groups and other CO carbons. The Schrock tantalum-methylene complex (η5-C5H5)Ta(=CH2)(CH3) reacts with the trinuclear metal carbonyl species Ru3(CO)12 to yield the cluster complex Cp2(CH3)Ta(µ-O)Ru3(C4H4)(CO)9. This material contains a 4-cumulene ligand that bridges the three late-metal centers. Also formed in this reaction is the unstable free tantalum oxo species, (η5-C5H5)Ta(=O)(CH3). A crystal structure of the TaRu3 cluster is reported along with a proposed mechanism for this unusual carbon–carbon bond-forming reaction. Keywords: deoxygenation, carbon monoxide, alkylidene, coupling, cluster.

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21

Wu, Iuan Yuan, Jian Hua Tsai, Bor Chen Huang, Shinn Chi Chen, and Ying Chih Lin. "Annulation reaction of (triphenylmethyl)allene on a cationic metal complex and the reaction mechanism." Organometallics 12, no. 10 (October 1993): 3971–78. http://dx.doi.org/10.1021/om00034a032.

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22

Hirst, Judy. "Towards the molecular mechanism of respiratory complex I." Biochemical Journal 425, no. 2 (December 23, 2009): 327–39. http://dx.doi.org/10.1042/bj20091382.

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Complex I (NADH:quinone oxidoreductase) is crucial to respiration in many aerobic organisms. In mitochondria, it oxidizes NADH (to regenerate NAD+ for the tricarboxylic acid cycle and fatty-acid oxidation), reduces ubiquinone (the electrons are ultimately used to reduce oxygen to water) and transports protons across the mitochondrial inner membrane (to produce and sustain the protonmotive force that supports ATP synthesis and transport processes). Complex I is also a major contributor to reactive oxygen species production in the cell. Understanding the mechanisms of energy transduction and reactive oxygen species production by complex I is not only a significant intellectual challenge, but also a prerequisite for understanding the roles of complex I in disease, and for the development of effective therapies. One approach to defining a complicated reaction mechanism is to break it down into manageable parts that can be tackled individually, before being recombined and integrated to produce the complete picture. Thus energy transduction by complex I comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer from the flavin to bound quinone along a chain of iron–sulfur clusters, quinone reduction and proton translocation. More simply, molecular oxygen is reduced by the flavin, to form the reactive oxygen species superoxide and hydrogen peroxide. The present review summarizes and evaluates experimental data that pertain to the reaction mechanisms of complex I, and describes and discusses contemporary mechanistic hypotheses, proposals and models.

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23

Sugishima, Masakazu, Kei Wada, and Keiichi Fukuyama. "Recent Advances in the Understanding of the Reaction Chemistries of the Heme Catabolizing Enzymes HO and BVR Based on High Resolution Protein Structures." Current Medicinal Chemistry 27, no. 21 (June 15, 2020): 3499–518. http://dx.doi.org/10.2174/0929867326666181217142715.

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In mammals, catabolism of the heme group is indispensable for life. Heme is first cleaved by the enzyme Heme Oxygenase (HO) to the linear tetrapyrrole Biliverdin IXα (BV), and BV is then converted into bilirubin by Biliverdin Reductase (BVR). HO utilizes three Oxygen molecules (O2) and seven electrons supplied by NADPH-cytochrome P450 oxidoreductase (CPR) to open the heme ring and BVR reduces BV through the use of NAD(P)H. Structural studies of HOs, including substrate-bound, reaction intermediate-bound, and several specific inhibitor-bound forms, reveal details explaining substrate binding to HO and mechanisms underlying-specific HO reaction progression. Cryo-trapped structures and a time-resolved spectroscopic study examining photolysis of the bond between the distal ligand and heme iron demonstrate how CO, produced during the HO reaction, dissociates from the reaction site with a corresponding conformational change in HO. The complex structure containing HO and CPR provides details of how electrons are transferred to the heme-HO complex. Although the tertiary structure of BVR and its complex with NAD+ was determined more than 10 years ago, the catalytic residues and the reaction mechanism of BVR remain unknown. A recent crystallographic study examining cyanobacterial BVR in complex with NADP+ and substrate BV provided some clarification regarding these issues. Two BV molecules are bound to BVR in a stacked manner, and one BV may assist in the reductive catalysis of the other BV. In this review, recent advances illustrated by biochemical, spectroscopic, and crystallographic studies detailing the chemistry underlying the molecular mechanism of HO and BVR reactions are presented.

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24

Elliott, L., D. B. Ingham, A. G. Kyne, N. S. Mera, M. Pourkashanian, and C. W. Wilson. "A Novel Approach to Mechanism Reduction Optimization for an Aviation Fuel/Air Reaction Mechanism Using a Genetic Algorithm." Journal of Engineering for Gas Turbines and Power 128, no. 2 (March 1, 2004): 255–63. http://dx.doi.org/10.1115/1.2131887.

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This study presents a novel multiobjective genetic-algorithm approach to produce a new reduced chemical kinetic reaction mechanism to simulate aviation fuel combustion under various operating conditions. The mechanism is used to predict the flame structure of an aviation fuel/O2∕N2 flame in both spatially homogeneous and one-dimensional premixed combustion. Complex hydrocarbon fuels, such as aviation fuel, involve large numbers of reaction steps with many species. As all the reaction rate data are not well known, there is a high degree of uncertainty in the results obtained using these large detailed reaction mechanisms. In this study a genetic algorithm approach is employed for determining new reaction rate parameters for a reduced reaction mechanism for the combustion of aviation fuel-air mixtures. The genetic algorithm employed incorporates both perfectly stirred reactor and laminar premixed flame data in the inversion process, thus producing an efficient reaction mechanism. This study provides an optimized reduced aviation fuel-air reaction scheme whose performance in predicting experimental major species profiles and ignition delay times is not only an improvement on the starting reduced mechanism but also on the full mechanism.

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Whitehouse, L. E., A. S. Tomlin, and M. J. Pilling. "Systematic lumping of complex tropospheric chemical mechanisms using a time-scale based approach." Atmospheric Chemistry and Physics Discussions 4, no. 4 (July 8, 2004): 3785–834. http://dx.doi.org/10.5194/acpd-4-3785-2004.

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Abstract. This paper presents a formal method of species lumping that can be applied automatically to intermediate compounds within detailed and complex tropospheric chemical reaction schemes. The method is based on grouping species with reference to their chemical lifetimes and reactivity structures. A method for determining the forward and reverse transformations between individual and lumped compounds is developed. Preliminary application to the Leeds Master Chemical Mechanism (MCMv2.0) has led to the removal of 734 species and 1777 reactions from the scheme, with minimal degradation of accuracy across a wide range of test trajectories relevant to polluted tropospheric conditions. The lumped groups are seen to relate to groups of peroxy acyl nitrates, nitrates, carbonates, oxepins, substituted phenols, oxeacids and peracids with similar lifetimes and reaction rates with OH. In combination with other reduction techniques, such as sensitivity analysis and the application of the quasi-steady state approximation (QSSA), a reduced mechanism has been developed that contains 35% of the number of species and 40% of the number of reactions compared to the full mechanism. This has led to a speed up of a factor of 8 in terms of computer calculation time within box model simulations.

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Rao, Pradeep Kumar, and Hari Ji Singh. "Kinetics and mechanism of gas-phase reaction of CF3OCH2CH3 (HFE-263) with the OH radical — a theoretical study." Canadian Journal of Chemistry 93, no. 3 (March 2015): 303–10. http://dx.doi.org/10.1139/cjc-2014-0400.

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In the present study, the density functional method with recently developed M06 functionals has been used to study the reaction of CF3OCH2CH3 with the OH radical. All possible hydrogen abstraction and displacement reaction channels have been modeled. The minimum energy path on the respective potential energy surface and energetics were calculated at the M06-2X/6-311++G(d,p) level of theory. Two different reaction mechanisms were considered: (i) reactant and product complexes called the complex mechanism and (ii) the direct mechanism (reactant → transition state → product). Tunneling corrections were made using the Eckart unsymmetrical potential. The overall rate constant calculated by the complex mechanism (keff = 1.8 × 10−13 cm3 molecule−1 s−1) has been found to be in good agreement with the experimentally determined value (1.5 ± 0.25 × 10−13 cm3 molecule−1 s−1), while the rate constant calculated by the direct mechanism (kD = 7.6 × 10−14 cm3 molecule−1 s−1) is about two times lower than the experimental value. The theoretical studies show that hydrogen atom abstraction from the –CH2– site is the most favorable reaction pathway and the reaction involves prereactive and product complexes before leading to stable product formation.

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27

Speranza, Giovanna, Wolfgang Buckel, and Bernard T. Golding. "CoenzymeB12-dependent enzymatic dehydration of 1,2-diols: simple reaction, complex mechanism!" Journal of Porphyrins and Phthalocyanines 08, no. 03 (March 2004): 290–300. http://dx.doi.org/10.1142/s1088424604000271.

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The conversion of glycerol to acrolein is an undesirable event in whisky production, caused by infection of the broth with Klebsiella pneumoniae. This organism uses glycerol dehydratase to transform glycerol into 3-hydroxypropanal, which affords acrolein on distillation. The enzyme requires adenosylcobalamin (coenzyme B12) as cofactor and a monovalent cation (e.g. K+). Diol dehydratase is a similar enzyme that converts 1,2-diols ( C2- C4) including glycerol into an aldehyde and water. The subtle stereochemical features of these enzymes are exemplified by propane-1,2-diol: both enantiomers are substrates but different hydrogen and oxygen atoms are abstracted. The mechanism of action of the dehydratases has been elucidated by protein crystallography and ab initio molecular orbital calculations, aided by stereochemical and model studies. The 5'-deoxyadenosyl (adenosyl) radical from homolysis of the coenzyme's Co - C σ-bond abstracts a specific hydrogen atom from C -1 of diol substrate giving a substrate radical that rearranges to a product radical by 1,2-shift of hydroxyl from C -2 to C -1. The rearrangement mechanism involves an acid-base 'push-pull' in which migration of OH is facilitated by partial protonation by Hisα143, synergistically assisted by partial deprotonation of the non-migrating ( C -1) OH by the carboxylate of Gluα170. The active site K+ion holds the two hydroxyl groups in the correct conformation, whilst not significantly contributing to catalysis. Recently, diol dehydratases not dependent on coenzyme B12have been discovered. These enzymes utilize the same kind of diol radical chemistry as the coenzyme B12-dependent enzymes and they also use the adenosyl radical as initiator, but this is generated from S-adenosylmethionine.

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28

Hindson, V. John, and William V. Shaw. "Random-Order Ternary Complex Reaction Mechanism of Serine Acetyltransferase fromEscherichia coli." Biochemistry 42, no. 10 (March 2003): 3113–19. http://dx.doi.org/10.1021/bi0267893.

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29

Barragan, Angela M., Alexander V. Soudackov, Zaida Luthey-Schulten, Klaus Schulten, Sharon Hammes-Schiffer, and Ilia Solov'yov. "Unveiling the Rate-Limiting Step of the Bc1 Complex Reaction Mechanism." Biophysical Journal 116, no. 3 (February 2019): 419a. http://dx.doi.org/10.1016/j.bpj.2018.11.2257.

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30

Teixido, Francisco, Dolores De Arriaga, Félix Busto, and Joaquin Soler. "Cytoplasmic malate dehydrogenase from Phycomyces blakesleeanus: Kinetics and mechanism." Canadian Journal of Biochemistry and Cell Biology 63, no. 10 (October 1, 1985): 1097–105. http://dx.doi.org/10.1139/o85-137.

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The kinetics and reaction mechanism of cytoplasmic malate dehydrogenase (L-malate:NAD+ oxidoreductase, EC 1.1.1.37) from mycelium of Phycomyces blakesleeanus NRRL 1555 (−) in 0.1 M potassium phosphate buffer (pH 7.5) at 30 °C have been investigated. The initial rate and product inhibition studies were consistent with an ordered bi-bi mechanism that involved more than one kinetically significant ternary complex and also with the coenzyme binding first. The dissociation of the coenzyme from the enzyme–coenzyme complex appeared to be the slowest step in either direction of the reaction. The kinetic and rate constants for the individual steps of the reaction were determined.

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Khademzadeh, Ashraf, Morteza Vahedpour, and Fereshte Karami. "Prediction of Tetraoxygen Reaction Mechanism with Sulfur Atom on the Singlet Potential Energy Surface." Scientific World Journal 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/912391.

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The mechanism of S+O4(D2h) reaction has been investigated at the B3LYP/6-311+G(3df) and CCSD levels on the singlet potential energy surface. One stable complex has been found for the S+O4(D2h) reaction, IN1, on the singlet potential energy surface. For the title reaction, we obtained four kinds of products at the B3LYP level, which have enough thermodynamic stability. The results reveal that the product P3 is spontaneous and exothermic with −188.042 and −179.147 kcal/mol in Gibbs free energy and enthalpy of reaction, respectively. Because P1 adduct is produced after passing two low energy level transition states, kinetically, it is the most favorable adduct in the1S+1O4(D2h) atmospheric reactions.

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SAEED, Noor Hazim Mohammed Thalji, and Ahmed Majed ABBAS. "KINETICS AND MECHANISM OF TETRAHYDROFURAN OXIDATION BY CHLORAMINET IN ACIDIC MEDIA." Periódico Tchê Química 17, no. 35 (July 20, 2020): 449–61. http://dx.doi.org/10.52571/ptq.v17.n35.2020.39_saeed_pgs_449_461.pdf.

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The kinetics of tetrahydrofuran oxidation by sodium N-chloro-p-toluene sulfonamide in the hydrochloric acid medium was studied in this work at 308 K. The reaction rate shows a first-order dependence on [CAT] and fractional-order dependence each on [THF] and [H+]. The derivative rate law, which suitable for experimental results, is Equation 24. The first-order rate constant has been evaluated from the relationship of the plot of Log [CAT] versus Time. The variation of the ionic strength by the addition of sodium perchlorate (NaClO4) and chloride ion on the medium showed no significant effect on the reaction. The reaction rate raised with decreasing dielectric constant (D), while the addition of p-toluene sulfonamide retards the rate of reaction. The oxidation reaction of tetrahydrofuran have been studied at a different temperature, The equilibrium constants for the formation of hypochlorous acid, protonated hydrochlorous acid and protonated hydrochlorous acid–THF complex and its decomposition constant have been estimated. Also, the rate constant for the slow (rate-determining step) and the activation parameter have been calculated. A suitable mechanism for the oxidation reaction of tetrahydrofuran was proposed based on the experimental finding. The mechanism includes the reaction of active species (H2OCl) of the oxidizing agent with the tetrahydrofuran in a fast step to give the complex(X). This complex will then transformed into complex (X̅ ) in slow step then to γ-butyrolactone in another fast step.

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Giri, Binod R., Aamir Farooq, Milán Szőri, and John M. Roscoe. "The kinetics of the reactions of Br atoms with the xylenes: an experimental and theoretical study." Physical Chemistry Chemical Physics 24, no. 8 (2022): 4843–58. http://dx.doi.org/10.1039/d1cp03740d.

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The reactions of Br atoms with xylenes were investigated experimentally and theoretically. It was found that the reaction proceeds via a complex forming mechanism. The experimental and theoretical and rate coefficients matched remarkably well.

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Fu, Kaiwei, Bei Liu, Xiaopeng Chen, Zhiyu Chen, Jiezhen Liang, Zhongyao Zhang, and Linlin Wang. "Investigation of a Complex Reaction Pathway Network of Isobutane/2-Butene Alkylation by CGC–FID and CGC-MS-DS." Molecules 27, no. 20 (October 13, 2022): 6866. http://dx.doi.org/10.3390/molecules27206866.

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The mechanism of reaction in isobutane/2-butene alkylation systems is extremely complicated, accompanied by numerous side reactions. Therefore, a comprehensive understanding of the reaction pathways in this system is essential for an in-depth discussion of the reaction mechanism and for improving the selectivity of the major products (clean fuel blend components). The alkylation of isobutane/2-butene was studied using a self-made intermittent reaction device with a metering, cooling, reaction, vacuum and analysis system. The alkylates were qualitatively and quantitatively analyzed using a capillary gas chromatography-mass spectrometry-data system (CGC-MS-DS) and capillary gas chromatography with flame ionization detection (CCGC-FID), respectively, and the precision and recovery of the quantitative analytical methods were verified. The results showed that the relative standard deviation (RSD) of the standard sample was below 0.78%, and the recoveries were from 98.53% to 102.85%. Under the specified reaction conditions, 79 volatile substances were identified from the alkylates, and the selectivity of C8 and trimethylpentanes (TMPs) reached 63.63% and 53.81%, respectively. The changes of the main chemical components in the alkylation reaction with time were tracked and analyzed, based on which reaction pathways were determined, and a complex reaction network containing the main products’ and the by-products’ generation pathway was constructed.

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Meadows, Margaret K., Xiaolong Sun, Igor V. Kolesnichenko, Caroline M. Hinson, Kenneth A. Johnson, and Eric V. Anslyn. "Mechanistic studies of a “Declick” reaction." Chemical Science 10, no. 38 (2019): 8817–24. http://dx.doi.org/10.1039/c9sc00690g.

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Damen, R., P. J. Nieuwenhuizen, J. G. Haasnoot, J. Reedijk, S. M. Couchman, J. Jeffery, and J. A. McCleverty. "Homogeneous Zinc (II) Catalysis in Accelerated Vulcanization: V. The Prevailing Mechanism of Crosslink Formation in Mercaptobenzothiazole Systems." Rubber Chemistry and Technology 76, no. 1 (March 1, 2003): 82–100. http://dx.doi.org/10.5254/1.3547742.

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Abstract This paper reports a detailed investigation of the molecular mechanism of crosslink formation in sulfur vulcanization accelerated by mercaptobenzothiazole accelerators, such as bis(mercaptobenzothiazolato)zinc(II) (ZMBT), mercaptobenzothiazole disulfide (MBTS) and N-cyclohexyl-2-benzothiazole sulfenamide (CBS). First, the current state of knowledge regarding the mechanism of crosslink formation in these systems is briefly reviewed. Subsequently, Reaction-Stage Modeling experiments are reported with the model-crosslink precursor (2,3-dimethyl-2-butene-1-yl)(mercaptobenthiazolato)sulfide (dmb-S2-Bt). These experiments reveal that in the presence of bis(cyclohexylamine)bis(mercapto benzo-thiazolato)zinc(II) (ZMBT·(H2NC6H11)) the precursor dmb-S2-Bt is transformed into a disulfidic crosslink and MBTS via symmetric disproportionation reactions. Also sulfuration and isomerization reactions, leading to a hitherto unknown type of pendent group, namely 2-(2,3-dimethyl-2-buten-1-yl)-1,2-benzisothioazolin-3-thione, were shown to occur. The zinc-amine complex was found to have a pronounced catalytic effect on the crosslink reaction; in its absence, hardly any crosslinks are formed. Reactions performed in the presence of additional MBTS showed an inhibitory effect on crosslink formation, suggesting that the disproportionation reaction is in fact an equilibrium reaction. Indeed, it appeared possible to transform disulfidic model crosslinks into crosslink precursors in the presence of both MBTS and the ZMBT-amine complex. These results have lead to determine the prevailing mechanism by which crosslinks are formed during mercaptobenzothiazole vulcanization, namely through an equilibrated, ZMBT-catalyzed disproportionation reaction of crosslinks precursors. This mechanism not only explains the observations in the present model study, but is also in line with results obtained earlier in real rubber experiments.

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Trishch, Vitaliy, Yurii Beznosyk, Gregory S. Yablonsky, and Denis Constales. "Conservatively perturbed equilibrium phenomenon in multi-route catalytic systems." Proceedings of the NTUU “Igor Sikorsky KPI”. Series: Chemical engineering, ecology and resource saving, no. 3 (September 30, 2022): 39–55. http://dx.doi.org/10.20535/2617-9741.3.2022.265360.

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Increasing the intensity of a complex catalytic reaction is an obvious task of chemical technology, and one of the important problems is obtaining the over-equilibrium kinetic characteristics (rate, concentration, yield, selectivity) in the transient non-steady-state regime. As known, for a closed system or an open system of infinite length, the chemical equilibrium is the final state of the chemical reaction, simple or complex. The fundamental properties of the equilibrium composition are its uniqueness and stability. For the closed chemical system, it means that at fixed amounts of chemical elements and at the given temperature, the system reaches the same chemical composition starting from any initial state, and the equilibrium chemical composition is unique and stable. The calculation of the equilibrium composition has become the basis for solving many problems of chemical and biochemical engineering. Such calculations are made based on a list of reactions with known equilibrium constants, or using a list of components with known chemical potentials and minimizing the Gibbs energy of chemical system. In this phenomenon, some initial concentrations of components are replaced by corresponding equilibrium concentrations. The temperature of the system and the total amount of any given chemical element in the system are assumed to be constant. In this paper, the phenomenon of conservatively perturbed-equilibrium (CPE) in multi-route complex catalytic reactions was studied. The computational phenomenon of the CPE is carried out as follows: The values of equilibrium concentrations of all components are determined. Some components are selected so that their initial concentrations differ from the equilibrium concentrations. At least one component is selected so that its initial concentration is equal to the equilibrium value. Perturbations referred above (see item 2) shall comply with all conservation laws of chemical elements which are applicable to this reaction system. The evolution of all concentrations is observed when they tend to the final chemical equilibrium. The following multi-route catalytic mechanisms have been studied: the two-route mechanism with the single common intermediate; the multi-route mechanisms with common steps. The kinetic model of plug-flow reactor (PFR) was chosen. The phenomenon of CPE was demonstrated for all indicated mechanisms. At given rate constants, the mechanism with a single common intermediate exhibited a CPE‑effect which is more pronounced than for the mechanism with common steps. In comparing the kinetic characteristics of non-catalytic and catalytic reactions, a special computer experiment shows that the absolute values of extreme concentrations at the CPE-point are almost the same. It was assumed that non-catalytic and catalytic reaction have the same the overall reaction with same equilibrium constants. This fact makes it possible to estimate the CPE value of the concentrations of complex catalytic reactions based on similar characteristics of the corresponding simple reactions.

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Trisovic, T., Lj Gajic-Krstajic, N. Krstajic, and M. Vojnovic. "On the kinetics of the hydrogen evolution reaction on zinc in sulfate solutions." Journal of the Serbian Chemical Society 66, no. 11-12 (2001): 811–23. http://dx.doi.org/10.2298/jsc0112811t.

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The kinetics and mechanism of the hydrogen evolution reaction (her) were studied on zinc in 1.0 mol dm-3 Na2SO4 at 298 K, in the pH range 4.4 - 10. It was found that a combination of classical potentiostatic steady-state voltammetry (PSV) and electrochemical impedance spectroscopy (EIS) can help to elucidate dilemmas concerning the mechanism of this reaction. Thus, over the whole potential region, the reaction path of the her on zinc cannot be presented by the classical Volmer-Tafel-Heyrovsky route. It was found that the very complex S-shape of the polarization curves could be explained by two parallel reaction mechanisms for the her. The first reaction mechanism is a consecutive combination of three steps, in which the surface zinc oxide plays an active role in the her, and second reaction mechanism is a consecutive combination of a Volmer step, followed by a Heyrovsky step. The second mechanism is dominant in the more negative potential region where the active sites for the her are metallic zinc.

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Gong, Wanqi, and Lihua Kang. "BNPd single-atom catalysts for selective hydrogenation of acetylene to ethylene: a density functional theory study." Royal Society Open Science 5, no. 7 (July 2018): 171598. http://dx.doi.org/10.1098/rsos.171598.

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The mechanisms of selective hydrogenation of acetylene to ethylene on B 11 N 12 Pd single-atom catalyst were investigated through the density functional theory by using the 6-31++G** basis set. We studied the adsorption characteristics of H 2 and C 2 H 2 , and simulated the reaction mechanism. We discovered that H 2 underwent absolute dissociative chemisorption on single-atom Pd, forming the B 11 N 12 Pd(2H) dihydride complex, and then the hydrogenation reaction with C 2 H 2 proceeded. The hydrogenation reaction of acetylene on the B 11 N 12 Pd complex complies with the Horiuti–Polanyi mechanism, and the energy barrier was as low as 26.55 kcal mol −1 . Meanwhile, it also has a higher selectivity than many bimetallic alloy single-atom catalysts.

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Burmistrov, Vladimir A., Irina P. Trifonova, Alexandr V. Zakharov, and Oscar I. Koifman. "Kinetics and mechanism of ligands substitution in the chromium(III) complex of tetraphenylporphin." Journal of Porphyrins and Phthalocyanines 17, no. 11 (November 2013): 1064–72. http://dx.doi.org/10.1142/s108842461350079x.

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The reaction of axial coordination of imidazole derivatives by (X)CrTPP in amphiprotic media was studied. The reaction includes two stages: consecutive substitution of the two alcohols molecules, first in the outer coordination sphere, and then in the inner sphere. For the reaction of the intrasphere substitution the solvolytic associative-dissociative mechanism has been found. The molecule of (chloro)chromium(III) porphyrin and its derivatives have been studied by density functional theory (DFT) computations utilizing the B3LYP hybrid method.

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Whitehouse, L. E., A. S. Tomlin, and M. J. Pilling. "Systematic reduction of complex tropospheric chemical mechanisms, Part II: Lumping using a time-scale based approach." Atmospheric Chemistry and Physics 4, no. 7 (October 5, 2004): 2057–81. http://dx.doi.org/10.5194/acp-4-2057-2004.

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Abstract. This paper presents a formal method of species lumping that can be applied automatically to intermediate compounds within detailed and complex tropospheric chemical reaction schemes. The method is based on grouping species with reference to their chemical lifetimes and reactivity structures. A method for determining the forward and reverse transformations between individual and lumped compounds is developed. Preliminary application to the Leeds Master Chemical Mechanism (MCMv2.0) has led to the removal of 734 species and 1777 reactions from the scheme, with minimal degradation of accuracy across a wide range of test trajectories relevant to polluted tropospheric conditions. The lumped groups are seen to relate to groups of peroxy acyl nitrates, nitrates, carbonates, oxepins, substituted phenols, oxeacids and peracids with similar lifetimes and reaction rates with OH. In combination with other reduction techniques, such as sensitivity analysis and the application of the quasi-steady state approximation (QSSA), a reduced mechanism has been developed that contains 35% of the number of species and 40% of the number of reactions compared to the full mechanism. This has led to a speed up of a factor of 8 in terms of computer calculation time within box model simulations.

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Freindorf, Marek, and Elfi Kraka. "URVA and Local Mode Analysis of an Iridium Pincer Complex Efficiently Catalyzing the Hydrogenation of Carbon Dioxide." Inorganics 10, no. 12 (December 1, 2022): 234. http://dx.doi.org/10.3390/inorganics10120234.

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The catalytic effects of iridium pincer complexes for the hydrogenation of carbon dioxide were investigated with the Unified Reaction Valley Approach (URVA), exploring the reaction mechanism along the reaction path traced out by the reacting species on the potential energy surface. Further details were obtained with the Local Mode Analysis performed at all stationary points, complemented by the Natural Bond Orbital and Bader’s Quantum Atoms in Molecules analyses. Each of the five reaction paths forming the catalytic cycle were calculated at the DFT level complemented with DLPNO-CCSD(T) single point calculations at the stationary points. For comparison, the non-catalytic reaction was also investigated. URVA curvature profiles identified all important chemical events taking place in the non-catalyzed reaction and in the five reactions forming the catalytic cycle, and their contribution to the activation energy was disclosed. The non-catalytic reaction has a large unfavorable activation energy of 76.3 kcal/mol, predominately caused by HH bond cleave in the H2 reactant. As shown by our study, the main function of the iridium pincer catalyst is to split up the one–step non-catalytic reaction into an energy efficient multistep cycle, where HH bond cleavage is replaced by the cleavage of a weaker IrH bond with a small contribution to the activation energy. The dissociation of the final product from the catalyst requires the cleavage of an IrO bond, which is also weak, and contributes only to a minor extent to the activation energy. This, in summary, leads to the substantial lowering of the overall activation barrier by about 50 kcal/mol for the catalyzed reaction. We hope that this study inspires the community to add URVA to their repertoire for the investigation of catalysis reactions.

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Kozyrev, Yuriy N., Andrey S. Mendkovich, Vladimir A. Kokorekin, Victor B. Luzhkov, and Alexander I. Rusakov. "Integrated Study of the Thiocyanate Anion Electrooxidation by Electroanalytical and Computational Methods." Journal of The Electrochemical Society 168, no. 12 (December 1, 2021): 125501. http://dx.doi.org/10.1149/1945-7111/ac39d4.

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The mechanism of the electrochemical oxidation of thiocyanate anion in acetonitrile was studied by cyclic voltammetry, chronoamperometry, electrolysis, digital simulations and quantum chemical calculations. The experimental data indicated complex character of the reaction mechanism, which includes reactions of thiocyanate anion with the products of its oxidation, thiocyanate radical and thiocyanogen. It was proposed that the last reaction takes place in the reduction of thiocyanogen as well. The DFT PCM-SMD M06–2X/aug-CC-pVQZ calculations show that the reaction of thiocyanate anion with thiocyanate radical and disproportionation of thiocyanogen anion radical are thermodynamically favorable. The effects of the mentioned reactions on the shape of the curves of cyclic voltammetry and chronoamperometry as well as that of the mass transfer regime are discussed.

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Balbo, Paul B., and Andrew Bohm. "Proton transfer in the mechanism of polyadenylate polymerase." Biochemical Journal 420, no. 2 (May 13, 2009): 229–42. http://dx.doi.org/10.1042/bj20082019.

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PAP (polyadenylate polymerase) is the template-independent RNA polymerase responsible for synthesis of the 3′ poly(A) tails of mRNA. To investigate the role of proton transfer in the catalytic mechanism of PAP, the pH dependence of the steady-state kinetic parameters of yeast PAP were determined for the forward (adenyl transfer) and reverse (pyrophosphorolysis) reactions. The results indicate that productive formation of an enzyme–RNA–MgATP complex is pH independent over a broad pH range, but that formation of an active enzyme–RNA–MgPPi complex is strongly pH dependent, consistent with the production of a proton on the enzyme in the forward reaction. The pH dependence of the maximum velocity of the forward reaction suggests two protonic species are involved in enzyme catalysis. Optimal enzyme activity requires one species to be protonated and the other deprotonated. The deuterium solvent isotope effect on Vmax is also consistent with proton transfer involved in catalysis of a rate-determining step. Finally, pKa calculations of PAP were performed by the MCCE (multiconformational continuum electrostatic) method. Together, the data support that the protonation of residues Lys215 and Tyr224 exhibit co-operativity that is important for MgATP2− and MgPPi2− binding/dissociation, and suggest these residues function in electrostatic, but not in general acid, catalysis.

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Sasaki, Kenta, Hitomi Yamate, Haruka Yoshino, Hiroki Miura, Yuushi Shimoda, Kiyoshi Miyata, Ken Onda, Ryo Ohtani, and Masaaki Ohba. "Vapor switching of the luminescence mechanism in a Re(v) complex." Chemical Communications 56, no. 85 (2020): 12961–64. http://dx.doi.org/10.1039/d0cc05462c.

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WANG, JIANYI, and SHUHUA LI. "THEORETICAL STUDY TOWARD UNDERSTANDING THE CATALYTIC MECHANISM OF PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX E1 COMPONENT." Journal of Theoretical and Computational Chemistry 05, spec01 (January 2006): 447–59. http://dx.doi.org/10.1142/s0219633606002386.

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Density functional calculations are employed to investigate the mechanisms of all elementary reaction steps involved in the catalytic reaction of pyruvate dehydrogenase multienzyme complex E1 (PDHc E1). We have obtained the free energy profiles for all reaction steps, and have demonstrated the importance of some key residues (Glu571, Glu522, His640 and a water molecule) near the active center in each individual step. Glu571 plays an essential role in the ylide formation, the addition of pyruvate, and the release of acetaldehyde. Glu522 helps to orientate the carboxyl of pyruvate in favor of the addition reaction of pyruvate. The protonation of the enamine is found to proceed through a concerted double proton transfer transition state involving His640 and a water molecule. All reaction steps are calculated to be thermodynamically favorable, except for the release of acetaldehyde which is slightly endothermic. The protonation of the enamine is a rate-limiting step with a barrier of 24.5 kcal/mol in the protein environment. Comparing the energetics of the catalytic reaction in PDHc E1 with that in PDC, we find that the relative orientation of some conserved residues and the conformation of the cofactor ThDP have a significant impact on the reaction rates of individual steps.

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47

Pettersson, G. "Mechanistic origin of the sigmoidal rate behaviour of glucokinase." Biochemical Journal 233, no. 2 (January 15, 1986): 347–50. http://dx.doi.org/10.1042/bj2330347.

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Model studies are presented which demonstrate that reactions proceeding by a random ternary-complex mechanism may exhibit most pronounced deviations from Michaelis-Menten kinetics even if the reaction is effectively ordered with respect to net reaction flow. In particular, the kinetic properties and reaction flow characteristics of glucokinase can be accounted for in such terms. It is concluded that insufficient evidence has been presented to support the idea that glucokinase operates by a ‘mnemonical’ type of mechanism involving glucose binding to distinct conformational states of free enzyme. The sigmoidal rate behaviour of glucokinase can presently be more simply explained in terms of glucose binding to differently ligated states of the enzyme.

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Kampjut, Domen, and Leonid A. Sazanov. "The coupling mechanism of mammalian respiratory complex I." Science 370, no. 6516 (September 24, 2020): eabc4209. http://dx.doi.org/10.1126/science.abc4209.

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Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo–electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.

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ZHAO, FENG, JIAN ZHANG, and MASAO KANEKO. "Electron transfer in the redox reaction of cobalt tetraphenylporphyrin incorporated in a Nafion film." Journal of Porphyrins and Phthalocyanines 04, no. 02 (March 2000): 158–67. http://dx.doi.org/10.1002/(sici)1099-1409(200003)4:2<158::aid-jpp156>3.0.co;2-n.

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Potential step chronoamperospectrometry (PSCAS) was carried out to analyze electron transfer in the redox reaction processes of 5,10,15,20-tetraphenylporphyrinatocobalt(II) ( Co II TPP (-2)) incorporated in a Nafion film. The reactions of Co II TPP (-2) to [ Co III TPP (-2)]+ and of [ Co III TPP (-2)]+ to Co II TPP (-2) took place through a diffusion mechanism, as confirmed by the first-order initial reaction rate with respect to the complex concentration in the matrix. However, the reaction of [ Co III TPP (-2)]+ to [ Co III TPP (-1)]2+ occurred by an electron-hopping mechanism, as confirmed by the second-order initial reaction rate with respect to the complex concentration. The fraction of electroactive complex (Rct) increased with the sample time after the potential step until it reached saturation. In the reactions of Co II TPP (-2) to [ Co III TPP (-2)]+ and of [ Co III TPP (-2)]+ to Co II TPP (-2), Rct approached 1.0, while in the reaction of [ Co III TPP (-2)]+ to [ Co III TPP (-1)]2+, only about 0.3 was reached. The apparent diffusion coefficient (Dapp) decreased in the order of [ Co III TPP (-2)]+ to Co II TPP (-2) > Co II TPP (-2) to [ Co III TPP (-2)]+>[ Co III TPP (-2)]+ to [ Co III TPP (-1)]2+. The different behavior of these redox reactions was ascribed to the microenvironment of the redox species in the matrix, interaction of the redox centers, especially the product with the framework, and counter ion migration.

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SHARPE, Martyn A., and Chris E. COOPER. "Reactions of nitric oxide with mitochondrial cytochrome c: a novel mechanism for the formation of nitroxyl anion and peroxynitrite." Biochemical Journal 332, no. 1 (May 15, 1998): 9–19. http://dx.doi.org/10.1042/bj3320009.

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The aerobic reactions of nitric oxide with cytochrome c were analysed. Nitric oxide (NO) reacts with ferrocytochrome c at a rate of 200 M-1 s-1 to form ferricytochrome cand nitroxyl anion (NO-). Ferricytochrome c was detected by optical spectroscopy; NO- was detected by trapping with metmyoglobin (Mb3+) to form the EPR-detectable Mb–nitrosyl complex, and by the formation of dimers in yeast ferrocytochrome cvia cross-linking of the free cysteine residue. The NO- formed subsequently reacted with oxygen to form peroxynitrite, as measured by the oxidation of dihydrorhodamine 123. NO binds to ferricytochrome c to form the ferricytochrome c-NO complex. The on-rate for this reaction is 1.3±0.4×103 M-1·s-1, and the off-rate is 0.087±0.054 s-1. The dissociation constant (Kd)of the complex is 22±7 µM. These reactions of NO with cytochrome c are likely to be relevant to mitochondrial metabolism of NO. Ferricytochrome c can act as a reversible sink for excess NO in the mitochondria. The reduction of NO to NO- by ferrocytochrome cmay play a role in the irreversible inhibition of mitochondrial oxygen consumption by peroxynitrite. It is generally assumed that peroxynitrite would be formed in mitochondria via the reaction of NO with superoxide. The finding that NO- is formed from the reaction of NO and ferrocytochrome c provides a means of producing peroxynitrite in the absence of superoxide, via the reaction of NO- with oxygen.

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Journal articles on the topic 'Complex Reaction Mechanism'

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