Kinetic Isotope Effect For Oxidation Research Articles

Reagent or catalyst? – FeS as activator for persulfate in water

FeS was evaluated as heterogeneous activator for peroxydisulfate (PS) with trichloroethene (TCE) chosen as model substance representing organic water pollutants prone to fast oxidation by sulfate radicals. The TCE degradation followed in most cases pseudo-first-order kinetics with a FeS-normalized maximum rate constant of k’TCE = 140 M−1min−1 (with cFeS,0 = 0.28 mM and cPS,0 = 5 mM).Sulfate radicals were determined as predominant radical species formed during PS activation by FeS by evaluation of the kinetic isotope effect for oxidation of cyclohexanes C6H12 vs. C6D12 (kC6H12: kC6D12 = 2.22). Monitoring of sulfur and iron species during the course of the reaction revealed that sulfide is rapidly oxidized, whereas Fe(II)solid is rather stable over time.The present study describes in detail the influence of the pH value on the reaction and the long-term performance of FeS as activator for PS with an optimum pH value of 5. On the basis of the radical yield from PS of 1.6 mols SO4− per mol S2O82− and the activation energy of EA = (31 ± 1) kJ mol−1 for the heterogeneous radical generation, a surface-assisted homolytic bond cleavage without simultaneous electron transfer is proposed as activation mechanism, which is contrary to the currently prevailing opinion.

Mechanistic studies of reactions catalysed by diamine oxidase using isotope effects

Diamine oxidase (DAO), the enzyme that is responsible for amine biodegradation in animals, plants and humans, catalyses the biotransformation of amines such as histamine (HA), putrescine, 1-phenylethylamine, tyrosine, tryptamine, serotonine and spermine. The kinetic and solvent isotope effects (SIEs) were applied to study the mechanism of the biotransformation using HA and its methylderivatives. The SIE for the biotransformation of HA, Nτ-methylhistamine and Nπ-methylhistamine was found to be 3.58, 2.22 and 5.70 on Vmax, and 1.58, 1.06 and 1.14 on Vmax/KM, respectively. On the other hand, the kinetic isotope effect for oxidation of stereospecifically deuterium-labelled [(α R)-2H]-Nτ-methylhistamine and [(α R)-2H]-Nπ-methylhistamine was 0.69 and 0.62 on Vmax, and 15.06 and 7.50 on Vmax/KM, respectively. These results demonstrate that DAO catalyses amine biotransformation by stereospecifically cleaving the αC\\bond H bond in the pro-S position. Moreover, the oxidation of amine to aldehyde involves several transition states, including hybridisation change from sp3 (Schiff base) to sp2 (imine), then back again to sp3 to give a final product with hybridisation sp2 (aldehyde).

Quantitative Production of Compound I from a Cytochrome P450 Enzyme at Low Temperatures. Kinetics, Activation Parameters, and Kinetic Isotope Effects for Oxidation of Benzyl Alcohol

Cytochrome P450 enzymes are commonly thought to oxidize substrates via an iron(IV)-oxo porphyrin radical cation transient termed Compound I, but kinetic studies of P450 Compounds I are essentially nonexistent. We report production of Compound I from cytochrome P450 119 (CYP119) in high conversion from the corresponding Compound II species at low temperatures in buffer mixtures containing 50% glycerol by photolysis with 365 nm light from a pulsed lamp. Compound I was studied as a reagent in oxidations of benzyl alcohol and its benzylic mono- and dideuterio isotopomers. Pseudo-first-order rate constants obtained at -50 degrees C with concentrations of substrates between 1.0 and 6.0 mM displayed saturation kinetics that gave binding constants for the substrate in the Compound I species (K(bind)) and first-order rate constants for the oxidation reactions (k(ox)). Representative results are K(bind) = 214 M(-1) and k(ox) = 0.48 s(-1) for oxidation of benzyl alcohol. For the dideuterated substrate C(6)H(5)CD(2)OH, kinetics were studied between -50 and -25 degrees C, and a van't Hoff plot for complexation and an Arrhenius plot for the oxidation reaction were constructed. The H/D kinetic isotope effects (KIEs) at -50 degrees C were resolved into a large primary KIE (P = 11.9) and a small, inverse secondary KIE (S = 0.96). Comparison of values extrapolated to 22 degrees C of both the rate constant for oxidation of C(6)H(5)CD(2)OH and the KIE for the nondeuterated and dideuterated substrates to values obtained previously in laser flash photolysis experiments suggested that tunneling could be a significant component of the total rate constant at -50 degrees C.

Use of pH and Kinetic Isotope Effects To Establish Chemistry as Rate-Limiting in Oxidation of a Peptide Substrate by LSD1

The mechanism of oxidation of a peptide substrate by the flavoprotein lysine-specific demethylase (LSD1) has been examined using the effects of pH and isotopic substitution on steady-state and rapid-reaction kinetic parameters. The substrate contained the 21 N-terminal residues of histone H3, with a dimethylated lysyl residue at position 4. At pH 7.5, the rate constant for flavin reduction, k(red), equals k(cat), establishing the reductive half-reaction as rate-limiting at physiological pH. Deuteration of the lysyl methyls results in identical kinetic isotope effects of 3.1 +/- 0.2 on the k(red), k(cat), and k(cat)/K(m) values for the peptide, establishing C-H bond cleavage as rate-limiting with this substrate. No intermediates between oxidized and reduced flavin can be detected by stopped-flow spectroscopy, consistent with the expectation for a direct hydride transfer mechanism. The k(cat)/K(m) value for the peptide is bell-shaped, consistent with a requirement that the nitrogen at the site of oxidation be uncharged and that at least one of the other lysyl residues be charged for catalysis. The (D)(k(cat)/K(m)) value for the peptide is pH-independent, suggesting that the observed value is the intrinsic deuterium kinetic isotope effect for oxidation of this substrate.

Laser Flash Photolysis Generation and Kinetic Studies of Porphyrin−Manganese−Oxo Intermediates. Rate Constants for Oxidations Effected by Porphyrin−MnV−Oxo Species and Apparent Disproportionation Equilibrium Constants for Porphyrin−MnIV−Oxo Species

Porphyrin-manganese(V)-oxo and porphyrin-manganese(IV)-oxo species were produced in organic solvents by laser flash photolysis (LFP) of the corresponding porphyrin-manganese(III) perchlorate and chlorate complexes, respectively, permitting direct kinetic studies. The porphyrin systems studied were 5,10,15,20-tetraphenylporphyrin (TPP), 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin (TPFPP), and 5,10,15,20-tetrakis(4-methylpyridinium)porphyrin (TMPyP). The order of reactivity for (porphyrin)Mn(V)(O) derivatives in self-decay reactions in acetonitrile and in oxidations of substrates was (TPFPP) > (TMPyP) > (TPP). Representative rate constants for reaction of (TPFPP)Mn(V)(O) in acetonitrile are k = 6.1 x 10(5) M(-1) s(-1) for cis-stilbene and k = 1.4 x 10(5) M(-1) s(-1) for diphenylmethane, and the kinetic isotope effect in oxidation of ethylbenzene and ethylbenzene-d(10) is k(H)/k(D) = 2.3. Competitive oxidation reactions conducted under catalytic conditions display approximately the same relative rate constants as were found in the LFP studies of (porphyrin)Mn(V)(O) derivatives. The apparent rate constants for reactions of (porphyrin)Mn(IV)(O) species show inverted reactivity order with (TPFPP) < (TMPyP) < (TPP) in reactions with cis-stilbene, triphenylamine, and triphenylphosphine. The inverted reactivity results because (porphyrin)Mn(IV)(O) disproportionates to (porphyrin)Mn(III)X and (porphyrin)Mn(V)(O), which is the primary oxidant, and the equilibrium constants for disproportionation of (porphyrin)Mn(IV)(O) are in the order (TPFPP) < (TMPyP) < (TPP). The fast comproportionation reaction of (TPFPP)Mn(V)(O) with (TPFPP)Mn(III)Cl to give (TPFPP)Mn(IV)(O) (k = 5 x 10(8) M(-1) s(-1)) and disproportionation reaction of (TPP)Mn(IV)(O) to give (TPP)Mn(V)(O) and (TPP)Mn(III)X (k approximately 2.5 x 10(9) M(-1) s(-1)) were observed. The relative populations of (porphyrin)Mn(V)(O) and (porphyrin)Mn(IV)(O) were determined from the ratios of observed rate constants for self-decay reactions in acetonitrile and oxidation reactions of cis-stilbene by the two oxo derivatives, and apparent disproportionation equilibrium constants for the three systems in acetonitrile were estimated. A model for oxidations under catalytic conditions is presented.

Oxidation of C-H bonds by [(bpy)2(py)RuIVO]2+ occurs by hydrogen atom abstraction.

Anaerobic oxidations of 9,10-dihydroanthracene (DHA), xanthene, and fluorene by [(bpy)(2)(py)Ru(IV)O](2+) in acetonitrile solution give mixtures of products including oxygenated and non-oxygenated compounds. The products include those formed by organic radical dimerization, such as 9,9'-bixanthene, as well as by oxygen-atom transfer (e.g., xanthone). The kinetics of these reactions have been measured. The kinetic isotope effect for oxidation of DHA vs DHA-d(4) gives k(H)/k(D) > or = 35 +/- 1. The data indicate a mechanism of initial hydrogen-atom abstraction forming radicals that dimerize, disproportionate and are trapped by the oxidant. This mechanism also appears to apply to the oxidations of toluene, ethylbenzene, cumene, indene, and cyclohexene. The rate constants for H-atom abstraction from these substrates correlate well with the strength of the C-H bond that is cleaved. Rate constants for abstraction from DHA and toluene also correlate with those for oxygen radicals and other oxidants. The rate constant for H-atom transfer from toluene to [(bpy)(2)(py)Ru(IV)O](2+) appears to be close to that predicted by the Marcus cross relation, using a tentative rate constant for hydrogen atom self-exchange between [(bpy)(2)(py)Ru(III)OH](2+) and [(bpy)(2)(py)Ru(IV)O](2+).

Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase

We present a theoretical framework for the calculation of rate constants of enzyme-catalyzed reactions that combines variational optimization of the dynamical bottleneck for overbarrier reactive events and multidimensional quantum mechanical tunneling dynamics for through-barrier reactive events, both in the presence of the protein environment. The theory features a two-zone, three-stage procedure called ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) with the transmission coefficient based on the equilibrium secondary-zone (ESZ) approximation for including the effects of the protein on a catalytic reaction center, called the primary zone. The dynamics is calculated by canonical variational theory with optimized multidimensional tunneling contributions, and the formalism allows for Boltzmann averaging over an ensemble of reactant and transition state conformations. In the first stage of the calculations, we assume that the generalized transition states can be well described by a single progress coordinate expressed in primary-zone internal coordinates; in subsequent steps, the transmission coefficient is averaged over a set of primary-zone reaction paths that depend on the protein configuration, and each reaction path has its own reaction coordinate and optimized tunneling path. We also present a simpler approximation to the transmission coefficient that is called the static secondary-zone (SSZ) approximation. We illustrate both versions of this method by carrying out calculations of the reaction rate constants and kinetic isotope effects for oxidation of benzyl alcoholate to benzaldehyde by horse liver alcohol dehydrogenase. The potential energy surface is modeled by a combined generalized hybrid orbital/quantum mechanical/molecular mechanical/semiempirical valence bond (GHO-QM/MM/SEVB) method. The multidimensional tunneling calculations are microcanonically optimized by employing both the small-curvature tunneling approximation and version 4 of the large-curvature tunneling approximation. We find that the variation of the protein mean force as a function of reaction coordinate is quantitatively significant, but it does not change the qualitative conclusions for the present reaction. We obtain good agreement with experiment for both kinetic isotope effects and Swain−Schaad exponents.

Kinetics and mechanism of oxidation of N,N′-dimethyl-9,9′-biacridanyl by some π acceptors and a one-electron oxidant

Oxidation of N,N′-dimethyl-9,9′-biacridanyl (DD) has been investigated as a model for single electron transfer (SET)-initiated oxidation of NADH coenzyme models such as N-methylacridan (DH). Oxidants investigated cover a 1010-fold range of reactivity in acetonitrile and include the π acceptors 1,4-benzoquinone (BQ), 2,6-dichloro-1,4-benzoquinone (DCIBQ), p-chloranil (CA), 2,3-dicyanobenzoquinone (DCBQ), 2,3-dicyano-1,4-naphthoquinone (DCNQ), 2,3-dicyano-5-nitro-1,4-naphthoquinone (DCNNQ), 9-dicyanomethylene-2,4,7-trinitrofluorene (DCMTNF), 9-dicyanomethylene-2,4,5,7-tetranitrofluorene (DCMTENF), 7,7,8,8-tetracyanoquinodimethane (TCNQ), and tetracyanoethylene (TCNE), and the one-electron oxidant tris(2,2′-bipyridyl)cobalt(III), [Formula: see text] The oxidation product is, in every case, N-methylacridinium ion (D+). A mechanism involving a rate-determining electron transfer with simultaneous fragmentation to D+ and N-methyl-9-acridanyl radical (D•) is proposed. This mechanism is supported by the observed dependence of the rate on oxidant reduction potential, by spin-trapping experiments, by kinetic isotope effects in oxidation of 9,9′-dideuterio-DD, and by substituent effects in oxidation of 2,2′- and 3,3′-dimethoxy-DD. The rate of oxidation of DD relative to that of DH is 3.4 × 102 with [Formula: see text] and with the π acceptors varies from ea. 0.3 (BQ) to 8.1 × 104 (DCMTENF). The results rule out a SET-initiated mechanism for oxidation of DH by all of the oxidants studied except TCNQ and DCMTENF.

Acid and Base Catalysis in the Oxidation of 6,7,8-Trimethyllumazine. II. Kinetics and Mechanism

The kinetics of the oxidation of 6,7,8-trimethyllumazine, 1, by permanganate in aqueous solution is examined. The pH–rate plot shows a minimum at pH 3.5 and there is catalysis by buffers. Above pH 3.5 the 7-keto compound, 5, is produced by a general base catalyzed route the rate of which is identical to that of the reaction that causes exchange at the 7-methyl group. The kinetic isotope effect for oxidation of the 7-CD3 compound is 6.89 at 31.4°.Below pH 3.5 scission of the pyrazine ring occurs, there is a small isotope effect, and the rate is somewhat faster than that observed for exchange of the 7-methyl group. There appear to be three routes leading to product; one, a permanganate-independent reaction catalyzed by general acids, a second which is also permanganate independent and involves hydration of the substrate, and a third which is permanganate dependent and involves attack by permanganate on the conjugate acid of the substrate.The utility of oxidation as a means of locating hydration sites in heterocyclic compounds is discussed and some comments are made on the mechanism of the enzymic oxidation of the ribityl analog of 1.