A numerical approach to modeling the catalytic voltammetry of surface-confined redox enzymes

A finite difference method for simulating voltammograms of electrochemically driven enzyme catalysis is presented. The method enables any enzyme mechanism to be simulated. The finite difference equations can be represented as a matrix equation containing a nonlinear sparse matrix. This equation has been solved using the software package Mathematica. Our focus is on the use of cyclic voltammetry since this is the most commonly employed electrochemical method used to elucidate mechanisms. The use of cyclic voltammetry to obtain data from systems obeying Michaelis-Menten kinetics is discussed, and we then verify our observations on the Michaelis-Menten system using the finite difference simulation. Finally, we demonstrate how the method can be used to obtain mechanistic information on a real redox enzyme system, the complex bacterial molybdoenzyme xanthine dehydrogenase.

Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 angstrom) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

Calibration of the channel that determines the omega-hydroxylation regiospecificity of cytochrome P4504A1 - Catalytic oxidation of 12-halododecanoic acids

The fatty acid omega-hydroxylation regiospecificity of CYP4 enzymes may result from presentation of the terminal carbon to the oxidizing species via a narrow channel that restricts access to the other carbon atoms. To test this hypothesis, the oxidation of 12-iodo-, 12-bromo-, and 12-chlorododecanoic acids by recombinant CYP4A1 has been examined. Although all three 12-halododecanoic acids bind to CYP4A1 with similar dissociation constants, the 12-chloro and 12-bromo fatty acids are oxidized to 12-hydroxydodecanoic acid and 12-oxododecanoic acid, whereas the 12-iodo analogue is very poorly oxidized. Incubations in (H2O)-O-18 show that the 12-hydroxydodecanoic acid oxygen derives from water, whereas that in the aldehyde derives from O-2. The alcohol thus arises from oxidation of the halide to an oxohalonium species that is hydrolyzed by water, whereas the aldehyde arises by a conventional carbon hydroxylation-elimination mechanism. No irreversible inactivation of CYP4A1 is observed during 12-halododecanoic acid oxidation. Control experiments show that CYP2E1, which has an omega-1 regiospecificity, primarily oxidizes 12-halododecanoic acids to the omega-aldehyde rather than alcohol product. Incubation of CYP4A1 with 12,12-[H-2](2)-12-chlorododecanoic acid causes a 2-3-fold increase in halogen versus carbon oxidation. The fact that the order of substrate oxidation (Br > Cl >> I) approximates the inverse of the intrinsic oxidizability of the halogen atoms is consistent with presentation of the halide terminus via a channel that accommodates the chloride and bromide but not iodide atoms, which implies an effective channel diameter greater than 3.90 angstrom but smaller than 4.30 angstrom.

Synthesis and characterization of turbostratic carbons prepared by catalytic chemical vapour decomposition of acetylene

The turbostratic mesoporous carbon blacks were prepared by catalytic chemical vapour decomposition (CCVD) of acetylene using Ni/MgO catalysts prepared by co-precipitation. The relationship between deposition conditions and the nanostructures of resultant carbon black materials was investigated. It was found that the turbostratic and textural structures of carbon blacks are dependent on the deposition temperature and nickel catalyst loading. Higher deposition temperature increases the carbon crystallite unit volume V-nano and reduces the surface area of carbon samples. Moreover, a smaller V-nano is produced by a higher Ni loading at the same deposition temperature. In addition of the pore structure and the active metal surface area of the catalyst, the graphitic degree or electronic conductivity of the carbon support is also a key issue to the activity of the supported catalyst. V-nano is a very useful parameter to describe the effect of the crystalline structure of carbon blacks on the reactivity of carbon blacks in oxygen-carbon reaction and the catalytic activity of carbon-supported catalyst in ammonia decomposition semi-quantitatively. (C) 2006 Elsevier B.V. All rights reserved.

Catalytic effects of subsurface carbon in the chemisorption of hydrogen on a Mg(0001) surface: an ab-initio study

Ab initio density functional theory (DFT) calculations are performed to explore possible catalytic effects on the dissociative chemisorption of hydrogen on a Mg(0001) surface when carbon is incorporated into Mg materials. The computational results imply that a C atom located initially on a Mg(0001) surface can migrate into the subsurface and occupy an fcc interstitial site, with charge transfer to the C atom from neighboring Mg atoms. The effect of subsurface C on the dissociation of H-2 on the Mg(0001) surface is found to be relatively marginal: a perfect sublayer of interstitial C is calculated to lower the barrier by 0.16 eV compared with that on a pure Mg(0001) surface. Further calculations reveal, however, that sublayer C may have a significant effect in enhancing the diffusion of atomic hydrogen into the sublayers through fcc channels. This contributes new physical understanding toward rationalizing the experimentally observed improvement in absorption kinetics of H2 when graphite or single walled carbon nanotubes (SWCNT) are introduced into the Mg powder during ball milling.

Inhibition studies of purple acid phosphatases: Implications for the catalytic mechanism

Purple acid phosphatases (PAPs) belong to the family of binuclear metallohydrolases and catalyse the hydrolysis of a large group of phosphoester substrates at acidic pH. Despite structural conservation in their active sites PAPs appear to display mechanistic versatility. Here, aspects of the catalytic mechanism of two PAPs are investigated using the inhibitors vanadate and fluoride as probes. While the magnitude of their vanadate inhibition constants are similar the two enzymes differ with respect to the mode of inhibition; vanadate interacts in a non-competitive fashion with pig PAP (K-i = 40 mu mol L-1) while it inhibits red kidney bean PAP competitively (K-i = 30 mu mol L-1). Similarly, fluoride also acts as a competitive inhibitor for red kidney bean PAP, independent of pH, while the inhibition of pig PAP by fluoride is uncompetitive at low pH and non-competitive at higher pH, independent of metal ion composition. Furthermore, while fluoride acts as a slow-binding inhibitor in pig PAP it binds rapidly to the catalytic site of the red kidney bean enzyme. Since vanadate and fluoride are proposed to act as transition state and nucleophile mimics, respectively, the observed differences in inhibition kinetics indicate subtle but distinct variations in the reaction mechanism of these enzymes.

Effect of the preparation technique on the catalytic properties of mesoporous V-HMS for the oxidation of toluene

Various mesoporous catalysts with vanadium loadings between 0.5 and 6 V wt.% and surface areas around 1300 m(2)/g were synthesized using the isomorphous substitution (IS) and molecular designed dispersion (MDD) techniques. Their catalytic properties were tested using toluene as a model VOC in a fixed bed reactor at temperatures between 300 and 550 degrees C. It was found that during the oxidation of toluene, over V-HMS synthesized via IS, conversion of toluene mainly results in carbon oxides, benzene, benzaldehyde and water. Total conversion is greatly improved when the vanadium content is increased from around 1.5 to 3.0 wt.%, but an increase in the textural porosity (V-TEX/V-MESO) from 0.3 to 0.6 had no discernable effect on the conversion. This can be explained by the fact that a V-TEX/V-MESO as low as 0.3 is sufficient to facilitate the access of toluene into the framework confined mesopores without any molecular transport limitations. However, when using V-HMS synthesized by MDD, conversion of toluene is greatly improved when the V-TEX/ V-MESO ratio is increased from 0.1 to 0.6. This is because the diffusion limitations are minimized by this increase. V-HMS synthesized via MDD does not exhibit selectivity to benzaldehyde, favoring total oxidation to CO and CO2. This different oxidation mechanism can be explained in terms of location, accessibility and number of active species on the surface of the HMS support. (c) 2005 Elsevier Inc. All rights reserved.

Hydrogen generation from liquid phase catalytic reforming of sugar solutions using metal-supported catalysts

Most of the hydrogen production processes are designed for large-scale industrial uses and are not suitable for a compact hydrogen device to be used in systems like solid polymer fuel cells. Integrating the reaction step, the gas purification and the heat supply can lead to small-scale hydrogen production systems. The aim of this research is to study the influence of several reaction parameters on hydrogen production using liquid phase reforming of sugar solution over Pt, Pd, and Ni supported on nanostructured supports. It was found that the desired catalytic pathway for H-2 production involves cleavage of C-C, C-H and O-H bonds that adsorb on the catalyst surface. Thus a good catalyst for production of H2 by liquid-phase reforming must facilitate C-C bond cleavage and promote removal of adsorbed CO species by the water-gas shift reaction, but the catalyst must not facilitate C-O bond cleavage and hydrogenation of CO or CO2. Apart from studying various catalysts, a commercial Pt/gamma-alumina catalyst was used to study the effect of temperature at three different temperatures of 458, 473 and 493 K. Some of the spent catalysts were characterised using TGA, SEM and XRD to study coke deposition. The amorphous and organised form of coke was found on the surface of the catalyst. (C) 2006 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.