Browsing by Subject "Oxidation-reduction reaction"

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Amperometric DNA sensing using wired enzyme based electrodes
(2003) Zhang, Yongchao; Heller, Adam (Professor of chemical engineering)
A water soluble copolymer of acrylamide and 4-vinylpyridine complexed with [Os(bpy)2Cl]+/2+ (bpy = 2,2’-bipyridine), was synthesized. An electrodeposition method of making redox polymer films on electrodes was developed. This method was also shown to be effective in incorporating enzymes and amine-terminated DNA sequences in the redox polymer film. A 38-base DNA sequence was detected at 20 pM concentration in 15-35 μL droplets by an electrochemical enzyme-amplified sandwich-type assay on a mass-manufacturable screen printed carbon electrode with a diameter of 3.5 mm. A DNA-capturing oligonucleotide was attached to the pre-deposited redox polymer film using the electrodeposition method. The electrode was exposed to the droplet containing the tested DNA sample, and was then treated with a droplet containing horseradish peroxidase-labeled detection sequence. Formation of the capture-target-detection sandwich brought the horseradish peroxidase-label of the detection sequence in electrical contact with the redox polymer, making the sandwich an electrocatalyst for the reduction of hydrogen peroxide to water at + 0.2 V (Ag/AgCl). The radial diffusion of electrons through the redox polymer film on the microelectrode allowed the electrodeposition of a thicker film of the redox polymer, an increase in the loading of the capture sequence, and increased the collection efficiency of the electron vacancies originating in the electroreduced H2O2. With a 10-μm diameter carbon fiber microelectrode, as few as 3000 copies of the 38-basse DNA sequence were detected at 0.5 fM concentration in a 10 μL sample. A biofuel cell operating at a power density of 50 μW cm–2 at 0.5 V under physiological conditions (air saturated, pH 7.4, 0.14 M NaCl, 37.5°C, 15 mM glucose) was developed. The cell had a glucose electro-oxidizing anode and an O2 electro-reducing cathode. The anode and the cathode were 7 μm diameter, 2 cm long carbon fibers, on which the catalytic enzyme-redox polymer adducts were cross-linked. When the miniature cell operated at 0.5 V, the power output dropped to about 60% of its initial value after 2 days of continuous operation at 37.5°C.
Evaluation of genome designs for oxidation resistance: guanine minimization and scavenger guanine
(2003) Friedman, Keith Albert; Heller, Adam (Professor of chemical engineering)
The genome's environment contains strong oxidizers, some of which selectively attack guanine, the most readily oxidized nucleotide. The ranking of guanine oxidation rates is central G in GGG (GGG) ≥ 5' G in GG (GG) > isolated or 3' G. Vulnerability to selective oxidants puts mutation pressure on guanine. This is apparent in the differences between observed levels of GGG and levels predicted by probability from total G. GGG is below probability predictions in the genomes of D. melanogaster, C. elegans, A. thaliana, S. cerevisiae and S. pombe. GGG is statistically under-represented in H. sapiens exons, but over-represented in H. sapiens introns and intergenic domains. It is not under-represented in E. cuniculi. It is over-represented P. falciparum chromosomes 2 and 3, but this organism's total G levels are extremely low. GG generally is not underrepresented in these genomes. Beyond enzymatic elimination of the oxidizing agents and their precursors, and excision and repair of oxidative lesions, we propose that genomes are built to mitigate damage to essential domains. Resistance to oxidation could be enhanced by making genomes more “noble” by reducing the fractions of total G, GG and particularly GGG. Alternately, if the duplex conducts electron vacancies (holes) over ∼100 bp, oxidation could be shifted from essential domains to sacrificially oxidizable GGG and GG in nonessential domains. The distribution of GGG and GG in exons, introns and intergenic domains of eight model genomes suggests ennoblement in six, protection by sacrificial anodes in one, and no guanine-based protection in one (E. cuniculi). GGG triads are excluded or are statistically underrepresented in exons and short splicing-controlling introns of D. melanogaster, C. elegans, A. thaliana, S. cerevisiae, S. pombe and P. falciparum chromosomes 2 and 3. The introns of H. sapiens, which are about twenty times longer than those of the other organisms, are rich in sacrificially oxidizable GGG triads that are 50-100 bp from the exons. Their frequency correlates with the presence of protection-requiring GGG triads in the exons.
Oxidative chemistry on gold : unraveling molecular transformations at surfaces
(2009-05) Gong, Jinlong, 1979-; Mullins, C. B.
Gold has been considered catalytically inert due to its resistance to oxidation and corrosion. However, decades ago, it was discovered that gold nano-particles (<5nm) on metal oxides demonstrate superior chemical activity towards many reactions. These seminal findings spurred considerable interest in investigations of the mechanistic details of oxidative reactions on gold-based catalysts. However, the active site and structure of supported Au nanoclusters as well as the active oxygen species remains elusive. Achieving high selectivity toward partial oxidation products also remains a challenge. In this dissertation, an oxygen-covered Au(111) crystal under ultra vacuum conditions was used as a model system to gain insights into oxidative reactions in gold-based catalysis. I have been able to demonstrate that (i) surface-bound oxygen atoms are metastable at low temperature; (ii) the oxygen atoms participate in surface reactions as a Brønsted base or a nucleophilic base; and (iii) the acid-base reactions that have been observed on silver and copper may also occur on gold. Low temperature CO oxidation and the associated mechanistic aspects are investigated. CO reacts with hydroxyls formed from water-oxygen interactions to produce CO₂ on Au(111) populated with atomic oxygen at low temperatures. Directing an ¹⁶O beam toward C¹⁸O₂ pre-adsorbed Au(111), the formation of carbonate is significantly enhanced. This reaction is suggested to follow a hot-precursor-mediated mechanism. The identification of reaction pathways in oxidation of N-containing molecules such as ammonia and propylamine is presented. Abstraction of hydrogen from ammonia or propylamine by O atoms is the initial step in the surface decomposition of NHx (or RNHx-1) on Au(111). Atomic oxygen or hydroxyl-assisted dehydrogenation steps have lower barriers than the recombination steps under relevant conditions. 100% selectivity of N₂ or propionitrile can be obtained if the oxygen coverage is below the stoichiometric value. The surface oxidative chemistry of alcohols on Au(111) is also investigated. Except for methanol that is fully oxidized, alcohols initially undergo O-H bond cleavage (producing alcoxides) followed by selective β-C-H bond activation to form aldehydes or ketones. This finding reveals that the interaction of Au with the metal oxide support might not be essential to facilitate the reactions if active oxygen species are readily present, particularly at low temperatures.