Structure of Nonplanar Octabromotetraphenyl Porphyrin and Kinetics of Rapid Metalation Reactions

Octabromotetraphenylporphyrin adopts a severe saddle-shaped distorted structure owing to the steric crowding of heavy bromine substituents. The rate enhancement of porphyrin metalation reaction is primarily due to the nonplanarity of the ring while the electronic effect diminishes the affinity of the porphyrin towards metal ions.

Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway

Mutation and/or dysfunction of signaling proteins in the mitogen activated protein kinase (MAPK) signal transduction pathway are frequently observed in various kinds of human cancer. Consistent with this fact, in the present study, we experimentally observe that the epidermal growth factor (EGF) induced activation profile of MAP kinase signaling is not straightforward dose-dependent in the PC3 prostate cancer cells. To find out what parameters and reactions in the pathway are involved in this departure from the normal dose-dependency, a model-based pathway analysis is performed. The pathway is mathematically modeled with 28 rate equations yielding those many ordinary differential equations (ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations (RDE) system in which the parameters are random variables. We show that our RDE model captures the uncertainty in the kinetic rate constants as seen in the behavior of the experimental data and more importantly, upon simulation, exhibits the abnormal EGF dose-dependency of the activation profile of MAP kinase signaling in PC3 prostate cancer cells. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. The last computation identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behavior in the PC3 prostate cancer cells. The reactions in which these most sensitive parameters participate emerge as candidate drug targets on the signaling pathway. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Heterogeneous permanganate oxidation of 1,5-dienes: a novel synthesis of 5-substituted butanolides

In the presence of a catalytic amount of water, 1,5-dienes undergo novel and unusual oxidation with potassium permanganate�copper sulfate in dichloromethane to give substituted butanolides in good yields under very mild conditions.

Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Competing peroxidase and oxidase reactions in scopoletin-dependent H2O2-initiated oxidation of NADH by horseradish peroxidase

Addition of NADH inhibited the peroxidative loss of scopoletin in presence of horseradish peroxidase and H2O2 and decreased the ratio of scopoletin (consumed):H2O2 (added). Concomitantly NADH was oxidized and oxygen was consumed with a stoichiometry of NADH: O-2 of 2:1. On step-wise addition of a small concentration of H2O2 a high rate of NADH oxidation was obtained for a progressively decreasing time period followed by termination of the reaction with NADH:H2O2 ratio decreasing from about 40 to 10. The rate of NADH oxidation increased linearly with increase in scopoletin concentration. Other phenolic compounds including p-coumarate also supported this reaction to a variable degree. A 418-nm absorbing compound;d accumulated during oxidation of NADH. The effectiveness of a small concentration of H2O2 in supporting NADH oxidation increased in presence of SOD and decreased in presence of cytochrome c, but the reaction terminated even in their presence. The results indicate that the peroxidase is not continuously generating H2O2 during scopolerin-mediated NADH oxidation and that both peroxidase and oxidase reactions occur simultaneously competing for an active form of the enzyme.

Methanol oxidation on carbon-supported platinum-tin electrodes in sulfuric acid

A study is made of the electrooxidation of methanol in sulfuric acid on carbon-supported electrodes containing platinum-tin bimetal catalysts that are prepared by an in situ potentiometric-characterization route. The catalysts are investigated by employing chemical analyses, X-ray diffraction (XRD), X-ray absorption-near-edge spectroscopy (XANES) and X-ray photoelectron spectroscopy (XPS) data in conjunction with electrochemical measurements. From the electrochemical data, it is inferred that while an electrode with (3:1) Pt-Sn/C catalyst involves a two-electron rate-limiting step akin to platinum-on-carbon electrodes, it is shifted to a one-electron mechanism on electrodes with (3:2)Pt-Sn/C, (3:3)Pt-Sn/C, and (3:4)Pt-Sn/C catalysts. The study suggests that the tin content in the platinum-tin bimetal catalyst produces: (i) a charge transfer from tin to platinum; (ii) an increase in the coverage of adsorbed methanolic residues with increase in the tin content, as indicated by the shift in rest potential of the electrodes towards the reversible value for oxidation of methanol (0.043 V versus SHE), and (iii) a decrease in the overall content of higher valent platinum sites in the catalyst.

Methanol oxidation on carbon-supported Pt---Sn electrodes in silicotungstic acid

Electro-oxidation of methanol was studied on carbon-supported Pt---Sn/C electrodes in silcotungstic acid (SiWA) at various concentrations. The porous-carbon electrodes employing Pt---Sn/C catalyst have been characterized using chemical analyses, X-ray powder diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) in conjunction with electrochemistry. The presence of Pt---Sn and Pt3Sn alloys along with Pt and SnO2 phases in the catalyst were identified by XRD. XPS analysis showed a lower amount of PtO species in the Pt---Sn/C catalyst with respect to the corresponding Pt/C sample. From the steady-state galvanostatic polarization data on Pt---Sn/C electrodes in SiWA, it is inferred that a one-electron process is the rate determining step. The performance of the electrodes in 0.084 M SiWA was better than in 2.5 M H2SO4 under similar conditions up to load currents of about 100 mA cm−2 indicating the promoting behaviour of the electrolyte. At currents larger than 100 mA cm−2, the performance of the electrodes in 0.084 SiWA was poorer than that in 2.5 M H2SO4 mainly due to the dominance of mass polarization in the former owing to the large size of keggin units associated with the structure of SiWA. This aspect was supported by cyclic voltammetry and ac impedance studies on Pt---Sn/C electrodes. Simulation of the electrochemical impedance response for the oxidation of methanol in SiWA was carried out using the equivalent electrical circuit model.

Methanol oxidation on carbon-supported platinum-tin electrodes in sulfuric acid

A study is made of the electrooxidation of methanol in sulfuric acid on carbon-supported electrodes containing platinum-tin bimetal catalysts that are prepared by an in situ potentiometric-characterization route. The catalysts are investigated by employing chemical analyses, X-ray diffraction (XRD), X-ray absorption-near-edge spectroscopy (XANES) and X-ray photoelectron spectroscopy (XPS) data in conjunction with electrochemical measurements. From the electrochemical data, it is inferred that while an electrode with (3:1) Pt-Sn/C catalyst involves a two-electron rate-limiting step akin to platinum-on-carbon electrodes, it is shifted to a one-electron mechanism on electrodes with (3:2)Pt-Sn/C, (3:3)Pt-Sn/C, and (3:4)Pt-Sn/C catalysts. The study suggests that the tin content in the platinum-tin bimetal catalyst produces: (i) a charge transfer from tin to platinum; (ii) an increase in the coverage of adsorbed methanolic residues with increase in the tin content, as indicated by the shift in rest potential of the electrodes towards the reversible value for oxidation of methanol (0.043 V versus SHE), and (iii) a decrease in the overall content of higher valent platinum sites in the catalyst.

Methanol oxidation on carbon-supported Pt---Sn electrodes in silicotungstic acid

Electro-oxidation of methanol was studied on carbon-supported Pt-Sn/C electrodes in silcotungstic acid (SiWA) at various concentrations. The porous-carbon electrodes employing Pt-Sn/C catalyst have been characterized using chemical analyses, X-ray powder diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) in conjunction with electrochemistry. The presence of Pt-Sn and Pt3Sn alloys along with Pt and SnO2 phases in the catalyst were identified by XRD. XPS analysis showed a lower amount of PtO species in the Pt-Sn/C catalyst with respect to the corresponding Pt/C sample. From the steady-state galvanostatic polarization data on Pt-Sn/C electrodes in SiWA, it is inferred that a one-electron process is the rate determining step. The performance of the electrodes in 0.084 M SiWA was better than in 2.5 M H2SO4 under similar conditions up to load currents of about 100 mA cm-2 indicating the promoting behaviour of the electrolyte. At currents larger than 100 mA cm-2, the performance of the electrodes in 0.084 SiWA was poorer than that in 2.5M H2SO4 mainly due to the dominance of mass polarization in the former owing to the large size of Keggin units associated with the structure of SiWA. This aspect was supported by cyclic voltammetry and ac impedance studies on Pt-Sn/C electrodes. Simulation of the electrochemical impedance response for the oxidation of methanol in SiWA was carried out using the equivalent electrical circuit model.

Oxygen-Exchange Reactions Accompanying Oxidation of Vanadyl Sulfate by Diperoxovanadate

The absorption spectrum in the visible range and the, ESR spectrum of vanadyl sulfate were lost on addition of diperoxovanadate. The V-51-NMR spectra revealed that diperoxovanadate was reduced to vanadate and its oligomers. With excess vanadyl, tetrameric vanadate was found to be the major product, During this reaction oxygen was released into the medium. The oxygen-release reaction was inhibited by a variety of organic ligands-imidazole, benzoate, formate, mannitol, ethanol, Tris, DMPO, malate, and asparagine. An oxygen-consuming reaction emerged at high concentrations of some of these compounds, e.g. benzoate and ethanol. Using DMPO as the spin-trap, an oxygen-radical species with a 1:2:2:1 type of ESR spectrum was detected in the reaction mixtures resulting from vanadyl oxidation by diperoxovanadate which was unaffected by addition of catalase or ethanol. The results showed that secondary oxygen-exchange reactions occur which depend on and utilize the intermediates in the primary reaction during diperoxovanadate-dependent oxidation of vanadyl sulfate.

Kinetics of self-assembled InN quantum dots grown on Si (111) by plasma-assisted MBE

One of the scientific challenges of growing InN quantum dots (QDs), using Molecular beam epitaxy (MBE), is to understand the fundamental processes that control the morphology and distribution of QDs. A systematic manipulation of the morphology, optical emission, and structural properties of InN/Si (111) QDs is demonstrated by changing the growth kinetics parameters such as flux rate and growth time. Due to the large lattice mismatch, between InN and Si (similar to 8%), the dots formed from the Strannski-Krastanow (S-K) growth mode are dislocated. Despite the variations in strain (residual) and the shape, both the dot size and pair separation distribution show the scaling behavior. We observed that the distribution of dot sizes, for samples grown under varying conditions, follow the scaling function.

Kinetics and mechanism for dye degradation with ionic Pd-substituted ceria

The degradation of the dye, Orange G, was carried out in the presence of H2O2 and Pd-substituted/impregnated CeO2. The effects of pH, initial dye concentration, initial H2O2 concentration, temperature, catalyst loading, and Pd content in the catalyst on the degradation of the dye were investigated. Eight to twelve percent degradation of the dye was obtained in 1 h when the reaction was carried out in the presence of CeO2 or H2O2 or Pd-substituted/impregnated CeO2 while 17% and 97% degradation was obtained when H2O2 was used with Pd-impregnated CeO2 and Pd-substituted CeO2, respectively. This difference clearly indicated that the ionic substitution of Pd played a key role in the degradation of the dye. A mechanism for the reaction was proposed based upon the catalyst structure and the electron transfer processes that take place in the metal ion substituted system in a reducible oxide. The reaction was found to follow first order kinetics and the influence of all the parameters on the degradation kinetics was compared using the rate constants. (c) 2011 Elsevier B.V. All rights reserved.

Cyclization of enediyne radical cations through chemical, photochemical, and electrochemical oxidation: The role of state symmetry

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Ethanol-dependent oxygen consumption and acetaldehyde formation during vanadyl oxidation by H2O2

Sequential addition of vanadyl sulfate to a phosphate-buffered solution of H2O2 released oxygen only after the second batch of vanadyl. Ethanol added to such reaction mixtures progressively decreased oxygen release and increased oxygen consumption during oxidation of vanadyl by H2O2. Inclusion of ethanol after any of the three batches of vanadyl resulted in varying amounts of oxygen consumption, a property also shared by other alcohols (methanol, propanol and octanol). On increasing the concentration of ethanol, vanadyl sulfate or H2O2, both oxygen consumption and acetaldehyde formation increased progressively. Formation of acetaldehyde decreased with increase in the ratio of vanadyl:H2O2 above 2:1 and was undetectable with ethanol at 0.1 mM. The reaction mixture which was acidic in the absence of phosphate buffer (pH 7.0), released oxygen immediately after the first addition of vanadyl and also in presence of ethanol soon after initial rapid consumption of oxygen, with no accompanying acetaldehyde formation. The results underscore the importance of some vanadium complexes formed during vanadyl oxidation in the accompanying oxygen-transfer reactions.