Common Rate-determining Step Research Articles

Mechanism of the generation of benzaldehyde and benzoic acid on Pd (1 1 1) surface during the destruction of toluene: Verification of experiments and models

Catalytic oxidation technology is still the mainstream technology of VOCs treatment at present, and it is of great significance to study the main active components of catalysts and clarify the evolution and transformation process of intermediate products in the catalytic process for clarifying the reaction mechanism and guiding the catalyst design. Pd was identified as the main active component in catalytic oxidation of toluene, and the important intermediate products in the degradation of toluene, i.e., benzaldehyde and benzoic acid, were obtained through experiment and In-situ DRIFT spectra. However, the specific evolution process of intermediates is difficult to observe experimentally. The conversion of toluene on Pd (111) surface was studied by DFT calculation. Benzaldehyde was the most stable intermediate and benzoic acid was the most stable energy state of the reaction products. Then the activation energies and reaction energies of all possible reaction paths from toluene to benzaldehyde or benzoic acid were calculated, and the only transition state was obtained. Two pathways for the formation of benzaldehyde and benzoic acid were identified, in which the oxidation reaction after dehydrogenation may be the common rate-determining step of the two pathways, with a maximum energy barrier of 0.80 eV.

Enhancing the electrocatalytic activity of Fe phthalocyanines for the oxygen reduction reaction by the presence of axial ligands: Pyridine-functionalized single-walled carbon nanotubes

We have examined the electrocatalytic activity of iron phthalocyanine (FePc) and perchlorinated iron phthalocyanine 16(Cl)FePc for the oxygen reduction reaction (ORR) in alkaline medium with the two molecules either adsorbed on the external surface of single-wall carbon nanotubes (SWCNT) or covalently anchored via an axial pyridine ligand on pyridine-functionalized single-wall carbon nanotubes (py-SWCNT). Regardless of the particular phthalocyanine type, the ORR activity is higher when the substrate is py-SWCNT rather than SWCNT. The Tafel slopes for ORR are very similar for the two Fe macrocyclic complexes attached to SWCNTs in the two different configurations, suggesting a common rate-determining step for the ORR for all four catalysts. It is also observed that, for both the SWCNT and py-SWCNT supports, the ORR activity is higher for 16(Cl)FePc than for FePc. This is attributed to the electron-withdrawing effect of the peripheral and non-peripheral chlorine atoms in the macrocyclic ligand. While FeN4 macrocycles are known to be located on the strong binding side of a volcano correlation including several MN4 species, the chlorine substituents decrease the binding energy of O2 on the central Fe cation, thereby moving up the macrocycle catalyst towards the apex of the volcano correlation. Both the carbon surface and macrocyclic ligand effects were optimized with 16(Cl)FePc attached to py-SWCNT, which is more active than both FePc on SWCNT and FePc on py-SWCNT. Here we show that both the axial ligand and the electron withdrawing groups (-Cl) have a combined collaborative effect in increasing the catalytic activity for ORR of Fe-phthalocyanines confined on the external walls of single-wall carbon nanotubes.

Quantification and Theoretical Analysis of the Electrophilicities of Michael Acceptors.

In order to quantify the electrophilic reactivities of common Michael acceptors, we measured the kinetics of the reactions of monoacceptor-substituted ethylenes (H2C═CH-Acc, 1) and styrenes (PhCH═CH-Acc, 2) with pyridinium ylides 3, sulfonium ylide 4, and sulfonyl-substituted chloromethyl anion 5. Substitution of the 57 measured second-order rate constants (log k) and the previously reported nucleophile-specific parameters N and sN for 3-5 into the correlation log k = sN(E + N) allowed us to calculate 15 new empirical electrophilicity parameters E for Michael acceptors 1 and 2. The use of the same parameters sN, N, and E for these different types of reactions shows that all reactions proceed via a common rate-determining step, the nucleophilic attack of 3-5 at the Michael acceptors with formation of acyclic intermediates, which subsequently cyclize to give tetrahydroindolizines (stepwise 1,3-dipolar cycloadditions with 3) and cyclopropanes (with 4 and 5), respectively. The electrophilicity parameters E thus determined can be used to calculate the rates of the reactions of Michael acceptors 1 and 2 with any nucleophile of known N and sN. DFT calculations were performed to confirm the suggested reaction mechanisms and to elucidate the origin of the electrophilic reactivities. While electrophilicities E correlate poorly with the LUMO energies and with Parr's electrophilicity index ω, good correlations were found between the experimentally observed electrophilic reactivities of 44 Michael acceptors and their calculated methyl anion affinities, particularly when solvation by dimethyl sulfoxide was taken into account by applying the SMD continuum solvation model. Because of the large structural variety of Michael acceptors considered for these correlations, which cover a reactivity range of 17 orders of magnitude, we consider the calculation of methyl anion affinities to be the method of choice for a rapid estimate of electrophilic reactivities.

Contributions of water transfer energy to protein‐ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

In our previous work, we proposed that desolvation and resolvation of the binding sites of proteins can serve as the slowest steps during ligand association and dissociation, respectively, and tested this hypothesis on two protein-ligand systems with known binding kinetics behavior. In the present work, we test this hypothesis on another kinetically-determined protein-ligand system-that of p38α and eight Type II BIRB 796 inhibitor analogs. The kon values among the inhibitor analogs are narrowly distributed (10⁴ ≤ kon ≤ 10⁵ M⁻¹ s⁻¹), suggesting a common rate-determining step, whereas the koff values are widely distributed (10⁻¹ ≤ koff ≤ 10⁻⁶ s⁻¹), suggesting a spectrum of rate-determining steps. We calculated the solvation properties of the DFG-out protein conformation using an explicit solvent molecular dynamics simulation and thermodynamic analysis method implemented in WaterMap to predict the enthalpic and entropic costs of water transfer to and from bulk solvent incurred upon association and dissociation of each inhibitor. The results suggest that the rate-determining step for association consists of the transfer of a common set of enthalpically favorable solvating water molecules from the binding site to bulk solvent. The rate-determining step for inhibitor dissociation consists of the transfer of water from bulk solvent to specific binding site positions that are unfavorably solvated in the apo protein, and evacuated during ligand association. Different sets of unfavorable solvation are evacuated by each ligand, and the observed dissociation barriers are qualitatively consistent with the calculated solvation free energies of those sets.

Reaction mechanism for cocaine esterase-catalyzed hydrolyses of (+)- and (-)-cocaine: unexpected common rate-determining step.

First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to examine the catalytic mechanism for cocaine esterase (CocE)-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. It has been shown that the acylation of (+)-cocaine consists of nucleophilic attack of the hydroxyl group of Ser117 on the carbonyl carbon of (+)-cocaine benzoyl ester and the dissociation of (+)-cocaine benzoyl ester. The first reaction step of deacylation of (+)-cocaine, which is identical to that of (-)-cocaine, is rate-determining, indicating that CocE-catalyzed hydrolyses of (+)- and (-)-cocaine have a common rate-determining step. The computational results predict that the catalytic rate constant of CocE against (+)-cocaine should be the same as that of CocE against (-)-cocaine, in contrast with the remarkable difference between human butyrylcholinesterase-catalyzed hydrolyses of (+)- and (-)-cocaine. The prediction has been confirmed by experimental kinetic analysis on CocE-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. The determined common rate-determining step indicates that rational design of a high-activity mutant of CocE should be focused on the first reaction step of the deacylation. Furthermore, the obtained mechanistic insights into the detailed differences in the acylation between the (+)- and (-)-cocaine hydrolyses provide indirect clues for rational design of amino acid mutations that could more favorably stabilize the rate-determining transition state in the deacylation and, thus, improve the catalytic activity of CocE. This study provides a valuable mechanistic base for rational design of an improved esterase for therapeutic treatment of cocaine abuse.

Capsule Formation, Carboxylate Exchange, and DFT Exploration of Cadmium Cluster Metallocavitands: Highly Dynamic Supramolecules

A family of molecular heptacadmium carboxylate clusters templated inside [3 + 3] Schiff base macrocycles has been isolated and studied by variable temperature solution and solid-state NMR spectroscopy, single-crystal X-ray diffraction (SCXRD), and density functional theory (DFT) calculations. These metallocavitand cluster complexes adopt bowl-shaped structures, induced by metal coordination, giving rise to interesting host-guest and supramolecular phenomena. Specifically, dimerization of these metallocavitands yields capsules with vacant coordination and hydrogen-bonding sites accessible to encapsulated guests. Strong host-guest interactions explain the exceptionally high packing coefficient (0.80) observed for encapsulated N,N-dimethylformamide (DMF). The guest-accessible hydrogen-bonding sites arise from an unusual mu(3)-OH ligand bridging three cadmium ions. Thermodynamic and kinetic studies show that dimerization is an entropy-driven process with a highly associative mechanism. In DMF the exchange rate of peripheral cluster supporting carboxylate ligands is intrinsically linked to the rate of dimerization and these two seemingly different events have a common rate-determining step. Investigation of guest dynamics with solid-state (2)H NMR spectroscopy revealed 3-fold rotation of an encapsulated DMF molecule. These studies provide a solid understanding of the host-guest and dynamic properties of a new family of metallocavitands and may help in designing new supramolecular catalysts and materials.

Kinetic Modeling of Polychlorinated Dibenzo-p-dioxin and Dibenzofuran Formation Based on Carbon Degradation Reactions

Combustion experiments in a laboratory-scale fixed bed reactor were performed to determine the role of temperature and time in polychlorinated dibenzo-p-dioxin (PCDD) and polychlorinated dibenzofuran (PCDF) formation, allowing a global kinetic expression to be written for PCDD/F formation due to soot oxidation in fly ash deposits. Rate constants were calculated for the reactions of carbon degradation, PCDD/F formation, desorption, and degradation. For the first time, values for activation and thermodynamic parameters for the overall reactions have been calculated for PCDD/F formation, desorption, and destruction reactions. Good agreement was found between the calculated rate constants for carbon degradation and for PCDD/F formation, indicating that the two processes have a common rate-determining step. Moreover, PCDD/F formation was found to be still active after long reaction times (24 h). These results points out the importance of carbon deposits in the postcombustion stages that can account for emissions long after their formation (memory effects). The calculated formation rates were 7-15 times higher than those reported in the literature from fly ash-only experiments, indicating the importance of both soot and a continuous source of chlorine. A comparison between full-scale incinerator rates and model calculated rates indicates that our model based on carbon degradation kinetic can be a tool to estimate emissions.

Biodegradation kinetics of select polycyclic aromatic hydrocarbon (PAH) mixtures by Sphingomonas paucimobilis EPA505

Many contaminated sites commonly have complex mixtures of polycyclic aromatic hydrocarbons (PAHs) whose individual microbial biodegradation may be altered in mixtures. Biodegradation kinetics for fluorene, naphthalene, 1,5-dimethylnaphthalene and 1-methylfluorene were evaluated in sole substrate, binary and ternary systems using Sphingomonas paucimobilis EPA505. The first order rate constants for fluorene, naphthalene, 1,5-dimethylnaphthalene, and 1-methylfluorene were comparable; yet Monod parameters were significantly different for the tested PAHs. S. paucimobilis completely degraded all the components in binary and ternary mixtures; however, the initial degradation rates of individual components decreased in the presence of competitive PAHs. Results from the mixture experiments indicate competitive interactions, demonstrated mathematically. The generated model appropriately predicted the biodegradation kinetics in mixtures using parameter estimates from the sole substrate experiments, validating the hypothesis of a common rate-determining step. Biodegradation kinetics in mixtures were affected by the affinity coefficients of the co-occurring PAHs and mixture composition. Experiments with equal concentrations of substrates demonstrated the effect of concentration on competitive inhibition. Ternary experiments with naphthalene, 1,5-dimethylnaphthalene and 1-methylfluorene revealed delayed degradation, where depletion of naphthalene and 1,5-dimethylnapthalene occurred rapidly only after the complete removal of 1-methylfluorene. The substrate interactions observed in mixtures require a multisubstrate model to account for simultaneous degradation of substrates. PAH contaminated sites are far more complex than even ternary mixtures; however these studies clearly demonstrate the effect that interactions can have on individual chemical kinetics. Consequently, predicting natural or enhanced degradation of PAHs cannot be based on single compound kinetics as this assumption would likely overestimate the rate of disappearance.

Electrochemical reduction of nitrate to ammonia at modified gold electrodes

The electrocatalytic activity of Au electrodes modified with thiourea (TU), urea (U), iodide ions (I −) and sulfide ions (S 2−) towards reduction of NO 3 − to NH 3 have been tested. Cyclic voltammetry (CV) of the TU/Au electrode in 0.5 M NaNO 3 (N 2-saturated, pH 12.5) revealed an increase of the reduction peak of NO 3 − at ca. +0.75 V versus reversible hydrogen electrode (RHE) more than at the bare (i.e., unmodified) Au electrode. On the other hand, the intensity of this peak is more depressed at I −/Au, S 2−/Au and U/Au electrodes. The Tafel slope is almost the same for the two reactions, i.e., the hydrogen evolution reaction (HER) and the nitrate reduction reaction suggesting a common rate-determining step (r.d.s.) for both reactions. Galvanostatic electrolysis of the basic nitrate solution resulted in three major reduction products i.e., NH 3, NO 2 − and H 2. The TU/Au electrode showed the highest current efficiency, Q, of the NH 3 production (about 85%), which is about 6.5 times higher than that of the NO 2 − production. While the I −/Au and S 2−/Au showed a sharp increase in the current efficiency for the hydrogen evolution reaction to about 43 and 47%, respectively, with a concurrent depression of the total current efficiency of the nitrate reduction.

Carbon isotope fractionation during permanganate oxidation of chlorinated ethylenes (cDCE, TCE, PCE).

Permanganate oxidation of chlorinated ethylenes is an attractive technique to effect remediation of these important groundwater contaminants. Stable carbon isotope fractionation associated with permanganate oxidation of trichloroethylene (TCE), tetrachloroethylene (PCE), and cis-1,2-dichloroethylene (cDCE) has been measured, to study the possibility of applying stable carbon isotope analysis as a technique to assess the efficacy of remediation implemented by permanganate oxidation. Average carbon isotope fractionation factors of alphaTCE = 0.9786, alphaPCE = 0.9830, and alphacDCE = 0.9789 were obtained, although the fractionation factor for PCE may be interpreted to change from a value of 0.9779-0.9871 during the course of the reaction. The fractionation factors for all three compounds are quite similar, in contrast to the variation of fractionation factors vs degree of chlorination observed for other degradative processes, such as microbial dechlorination. This may be due to a common rate-determining step for permanganate oxidation of all three compounds studied. The large fractionation factors and the relative lack of dependence of the fractionation factors upon other environmental factors (e.g. oxidation rate, presence of multiple contaminants, incomplete oxidation, presence of chloride in solution) indicate that monitoring delta13C values of chlorinated ethylenes during oxidation with permanganate may be a sensitive, and potentially quantitative, technique to investigate the extent of degradation.

THE USE OF THE ARRHENIUS EQUATION IN THE STUDY OF DETERIORATION AND OF COOKING OF FOODS – SOME SCIENTIFIC AND PEDAGOGIC ASPECTS

Conservation and cooking of foods can be used by students and instructors to demonstrate a fundamental relation of chemical kinetics, the Arrhenius equation. By plotting the logarithms of available conservation and cooking times versus the corresponding inverse temperatures, apparent activation energies for both the deterioration and the cooking of foods of various compositions can be obtained. Such simple applications lead to meaningful results. Examples of deviation from the Arrhenius equation are given by plotting data (shelf-life of certain frozen food at various temperatures) given on the food package. A better fit is obtained by applying a second order polynomial regression to the data. Cooking time (lnt) vs. the inverse of temperature for five categories of foods is also examined and for each category there appears to be a common rate-determining step. Detailed results are presented for the meat category. The pedagogic aspects of the use of Arrhenius equation in the study of deterioration and of cooking of foods are also presented. [Chem. Educ. Res. Pract. Eur.: 2002, 3, 87-97]

Probing the mechanism of the anomalous intramolecular C–H insertion reaction of rhodium carbenoids by analysis of kinetic isotope effects

The mechanism of the anomalous intramolecular insertion reaction of a rhodium carbenoid into an ethereal C–H bond has been explored using deuterium labelled substrates. Comparison of primary kinetic isotope effects and analysis of ratios of diastereoisomeric deuterated products suggests the reactions leading to the anomalous and conventional C–H insertion products are mechanistically distinct and do not share a common rate-determining step.

The effect of the presence of fine YSZ particles on the performance of porous nickel electrodes

The electrochemical performance of a porous nickel electrode with its surface modified by deposition with fine yttria-stabilised zirconia (YSZ) powder is compared with that of the ‘bare’ electrode. Image analysis of the electrode microstructure yields values for the triple phase boundary (TPB) length in the range of 45–61 m cm −2. The nickel coverage is in the range of 55–72%. The hydrogen oxidation reaction studied on the two types of electrodes indicates that the electrode reaction is dominated by one process, suggesting a common rate-determining step. The total electrode conductivity increases with increasing TPB length. However, at similar TPB length the electrode conductivity of the modified porous nickel electrode is considerably higher than that of the bare nickel electrode. This result indicates that the presence of fine YSZ particles on the nickel electrode surface creates additional active sites onto which the electrode reaction can proceed. The data of this study are interpreted to reflect an active role for YSZ in the Ni/YSZ SOFC cermet anode.

Oligomerization and cis-trans isomerization equilibria in dichloropalladium(II) metallacrown ethers and a dichloropalladium(II) complex of 1,12-bis(diphenylphosphino)dodecane

Quantitative 31P{1H} NMR spectroscopic studies of monomer–oligomer and cis-trans equilibria in chloroform-d solutions of PdCl2{Ph2P(CH2CH2O)nCH2CH2PPh2-P,P′}n (n = 3, 4, 5) metallacrown ethers and of PdCl2{Ph2P(CH2)12PPh2-P,P′} are reported. The NMR data for all of the complexes can be adequately modeled using a single cis-trans isomerization equilibrium and two step-polymerization (dimerization, oligomerization) equilibria. As expected, both the dimerization and oligomerization equilibrium constants for the metallacrown ethers increase as n increases. However, the dimerization equilibrium constants of the metallacrown ethers are much smaller than are the oligomerization equilibrium constants. In contrast, the dimerization and oligomerization equilibrium constants for PdCl2{Ph2P(CH2)12PPh2-P,P′} are nearly identical and are significantly larger than are those of the metallacrown ethers. Kinetic studies of monomer–oligomer and cis-trans equilibria in solutions of cis-PdCl2{Ph2P(CH2CH2O)3CH2CH2PPh2-P,P′} indicate that the trans monomer and trans oligomers are formed at approximately the same rates and that the reactions follow reversible first-order kinetics. The very different dimerization constants for the metallacrown ethers and PdCl2{Ph2P(CH2)12PPh2-P,P′}and the similar rates of formation for the trans monomer and trans oligomers suggest that the isomerization and dimerization reactions have a common rate-determining step that involves cleavage of a palladium–phosphorus bond.

Equilibrium Dynamics in the Thallium(III)-Cyanide System in Aqueous Solution.

Ligand exchange reactions of thallium(III) cyano complexes, Tl(CN)(n)()(3)(-)(n)(), have been systematically studied in aqueous solution containing 4 M ionic medium {[ClO(4)(-)](tot) = 4 M, [Na(+)](tot) = 1 M, [Li(+)](tot) + [H(+)](tot) = 3 M}, at 25 degrees C, using (205)Tl and (13)C NMR one-dimensional inversion transfer techniques. Rate constants for all dominating exchange pathways were determined and compared to the previously studied thallium(III) halide complexes. Also in the case of cyanide ligands the ligand exchange is dominated by the rare type of reactions occurring via a direct encounter of two complexes (self-exchange reactions), e.g. Tl(CN)(3) + Tl(CN)(2)(+) right harpoon over left harpoon Tl(CN)(2)(+) + Tl(CN)(3) (k(32), k(23)) or Tl(CN)(2)(+) + Tl(CN)(4)(-) right harpoon over left harpoon 2Tl(CN)(3) (k(24), k(33)). The determined cyanide exchange rate constants between complexes Tl(CN)(m)()(3)(-)(m)() and Tl(CN)(n)()(3)(-)(n)(), for the rate-determining step have all similar values, about 100-1000 s(-)(1), that are 5 orders of magnitude smaller than for the corresponding halide exchange processes. This indicates the presence of a common rate-determining step for the self-exchange reactions of the cyanide ligand, proposed to be the breaking of the thermodynamically very stable Tl-CN bond. This is in contrast to the Tl(III)-halide systems, where the breaking of the Tl-OH(2) bond was proposed to determine the reaction rate. The second type of cyanide exchange, namely anation, has been found only in two cases: Tl(CN)(2)(+) + CN(-) right harpoon over left harpoon Tl(CN)(3) (k'(23), k'(32)); and Tl(CN)(3) + CN(-) right harpoon over left harpoon Tl(CN)(4)(-) (k'(34), k'(43)). These reactions are very fast, k'(mn)() approximately 10(9) M(-)(1) s(-)(1), and are proposed to proceed through an associative interchange mechanism, where the rate-determining step is a water dissociation mediated by the incoming ligand, i.e. similarly as for the corresponding halide complexes. The third type of cyanide exchange reactions was possible to study due to the presence of an NMR-active nucleus ((13)C) in the ligand. Only the following ligand substitution reaction was observed: Tl(CN)(2)(+) + HCN right harpoon over left harpoon Tl(CN)(2)(+) + HCN The reason for the dominant role of the self-exchange reactions is the very low concentration of free CN(-) and the inertness of the HCN species in the ligand exchange reactions. The obtained dynamic information is discussed and compared to the corresponding data for the thallium(III) halide complexes.

Equilibrium Dynamics in the Thallium(III)−Cyanide System in Aqueous Solution

Ligand exchange reactions of thallium(III) cyano complexes, Tl(CN)(n)()(3)(-)(n)(), have been systematically studied in aqueous solution containing 4 M ionic medium {[ClO(4)(-)](tot) = 4 M, [Na(+)](tot) = 1 M, [Li(+)](tot) + [H(+)](tot) = 3 M}, at 25 degrees C, using (205)Tl and (13)C NMR one-dimensional inversion transfer techniques. Rate constants for all dominating exchange pathways were determined and compared to the previously studied thallium(III) halide complexes. Also in the case of cyanide ligands the ligand exchange is dominated by the rare type of reactions occurring via a direct encounter of two complexes (self-exchange reactions), e.g. Tl(CN)(3) + Tl(CN)(2)(+) right harpoon over left harpoon Tl(CN)(2)(+) + Tl(CN)(3) (k(32), k(23)) or Tl(CN)(2)(+) + Tl(CN)(4)(-) right harpoon over left harpoon 2Tl(CN)(3) (k(24), k(33)). The determined cyanide exchange rate constants between complexes Tl(CN)(m)()(3)(-)(m)() and Tl(CN)(n)()(3)(-)(n)(), for the rate-determining step have all similar values, about 100-1000 s(-)(1), that are 5 orders of magnitude smaller than for the corresponding halide exchange processes. This indicates the presence of a common rate-determining step for the self-exchange reactions of the cyanide ligand, proposed to be the breaking of the thermodynamically very stable Tl-CN bond. This is in contrast to the Tl(III)-halide systems, where the breaking of the Tl-OH(2) bond was proposed to determine the reaction rate. The second type of cyanide exchange, namely anation, has been found only in two cases: Tl(CN)(2)(+) + CN(-) right harpoon over left harpoon Tl(CN)(3) (k'(23), k'(32)); and Tl(CN)(3) + CN(-) right harpoon over left harpoon Tl(CN)(4)(-) (k'(34), k'(43)). These reactions are very fast, k'(mn)() approximately 10(9) M(-)(1) s(-)(1), and are proposed to proceed through an associative interchange mechanism, where the rate-determining step is a water dissociation mediated by the incoming ligand, i.e. similarly as for the corresponding halide complexes. The third type of cyanide exchange reactions was possible to study due to the presence of an NMR-active nucleus ((13)C) in the ligand. Only the following ligand substitution reaction was observed: Tl(CN)(2)(+) + HCN right harpoon over left harpoon Tl(CN)(2)(+) + HCN The reason for the dominant role of the self-exchange reactions is the very low concentration of free CN(-) and the inertness of the HCN species in the ligand exchange reactions. The obtained dynamic information is discussed and compared to the corresponding data for the thallium(III) halide complexes.

Tetraethylorthosilicate reaction rates on SiO2 at 1000 K: Zero-order dependence on hydroxyl coverage and implications for reactions with three-membered siloxane rings

We have determined key kinetic parameters for the reaction of tetraethylorthosilicate (TEOS) on SiO2. This was accomplished under conditions (20–500 mTorr at 1000 K) that pertain directly to TEOS-based chemical vapor deposition processes. TEOS reactions were carried out using deuterated silanols (SiOD) on the initial SiO2 surface. This allowed Fourier transform infrared spectroscopy measurements to distinguish the consumption of SiOD by TEOS from the concurrent formation of SiOH which results from TEOS decomposition at 1000 K. While SiOD consumption did exhibit a first-order dependence on SiOD coverage, TEOS decomposition exhibited a zero-order dependence on the total coverage of hydroxyl groups. This suggests that reactions with hydroxyl groups alone cannot account for all of the TEOS decomposition reactions at 1000 K. Since the low coverage of two-membered siloxane [(Si–O)2] rings was consumed during the initial TEOS exposure, siloxane (Si–O–Si) bridges in three-membered siloxane [(Si–O)3] rings may be the additional species responsible for the constant rate of TEOS decomposition. However, it is not conclusive that this type of site-specific mechanism controls the chemistry. The data may also be explained with a site-independent mechanism in which intramolecular decomposition of TEOS on the surface provides a common rate-determining step for subsequent consumption of hydroxyls and siloxane bridges on SiO2. Regardless of the specific mechanism, our results predict that deposition rates will be insensitive to the relative coverages of siloxane bridges and hydroxyls on SiO2. Therefore, a precise knowledge of the coverages of these species on SiO2 is not essential for modeling thermal TEOS decomposition rates.

Thermal decomposition of acetate: III. Catalysis by mineral surfaces

The kinetics of thermal decarboxylation of aqueous solutions of acetic acid and sodium acetate were evaluated at 335 and 355°C in contact with various surfaces as potential catalysts. Quartz, fused quartz, calcite, natural pyrite, titanium oxide, and Au apparently do not catalyze aqueous decarboxylation reactions, in contrast to Pyrex, Ca-montmorillonite, Fe-bearing montmorillonite, hematite, synthetic pyrite, and magnetite. The dependence of the rate of acetic acid decarboxylation on the surface area of pyrite per unit solution volume was also studied. The results show that the decarboxylation of acetic acid and acetate is catalyzed heterogeneously, with the cleavage of the C-C bond occurring while the acetate molecule is adsorbed onto a surface. Entropies and enthalpies of activation obtained from these experiments are compatible with the isokinetic relationship established previously for acetic acid and acetate under similar experimental conditions, indicating the existence of a common rate-determining step. Experimental evidence indicates that oxidation of acetic acid can occur with hematite and defected magnetite. These oxidative decomposition reactions differ from the decarboxylation reaction in that CO 2 and polycondensates are produced instead of CO 2 and CH 4.

Kinetic Studies of Ammonia Monooxygenase Inhibition in Nitrosomonas europaea by Hydrocarbons and Halogenated Hydrocarbons in an Optimized Whole-Cell Assay

The inhibitory effects of 15 hydrocarbons and halogenated hydrocarbons on NH(3) oxidation by ammonia monooxygenase (AMO) in intact cells of the nitrifying bacterium Nitrosomonas europaea were determined. Determination of AMO activity, measured as NO(2) production, required coupling of hydroxylamine oxidoreductase (HAO) activity with NH(3)-dependent NH(2)OH production by AMO. Hydrazine, an alternate substrate for HAO, was added to the reaction mixtures as a source of reductant for AMO. Most inhibitors exhibited competitive or noncompetitive inhibition patterns. The competitive character generally decreased (K(i) (E)/K(i) (ES) increased) as the molecular size of the inhibitors increased. For example, CH(4) and C(2)H(4) were competitive inhibitors of NH(3) oxidation, whereas the remaining alkanes (up to C(4)) and monohalogenated (Cl, Br, I) alkanes were noncompetitive. Oxidation of C(2)H(5)Br (noncompetitive) increased as the NH(4) concentration increased up to 40 mM, whereas oxidations of inhibitors with competitive character (K(i) (E) << K(i) (ES)) were diminished at 40 mM NH(4). Multichlorinated compounds produced nonlinear Lineweaver-Burk plots. Iodinated alkanes (CH(3)I, C(2)H(5)I) and C(2)Cl(4) were potent inhibitors of NH(3) oxidation. Maximum rates of NH(3), C(2)H(4), and C(2)H(6) oxidations were approximately equivalent, suggesting a common rate-determining step. These data support an active-site model for AMO consisting of an NH(3)-binding site and a second site that binds noncompetitive inhibitors, with oxidation occurring at either site.

Reaction of nontoxic, potentially chemopreventive purinethiols with a direct-acting, electrophilic carcinogen, benzo[a]pyrene-7,8-diol 9,10-epoxide.

Several nontoxic purinethiols have been shown to block the ability of the carcinogen 7-r,8-t-dihydroxy-9-t,10-t-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) to bind covalently to DNA in Chinese hamster ovary cells. Two of these compounds also block BPDE-induced tumorigenesis in a two-stage mouse skin carcinogenesis model. The suggested mode of action of the purinethiols is through scavenging the electrophilic carcinogen by way of covalent reaction with the purinethiol. In the present work, we demonstrate that a series of five purinethiols (2,6-dithiopurine, thiopurinol, 6-thioxanthine, 2-mercaptopurine, and 9-methyl-6-mercaptopurine) react covalently in vitro with BPDE. The adducts formed have been characterized by UV-visible spectroscopy, solvent partitioning, and NMR spectroscopy; they result from addition of the thiol moiety at the 10-carbon of BPDE. Studies of the effects of Tris buffer and temperature on product ratios at completion of reaction indicate that the two major reaction pathways, hydrolysis of the epoxide and adduct formation, do not share a common rate-determining step. This suggests that the reaction mechanism for adduct formation is through SN2 attack of the thiol moiety at the 10 position of BPDE. The activation energies for the reaction of 5-purinethiols with various combinations of substituents at the 2 and 6 positions are all very similar, implying closely similar transition states. For compounds with a low pKa (2,6-dithiopurine, 2-mercaptopurine, and 6-thioxanthine) the most important reactant at physiological pH is the thiolate anion. However, for compounds with pKa's above 8, the physiologically important reactions appear to be more complicated.