Joseph G. Harrison

Kinetics of superoxide dismutase- and iron-catalyzed nitration of phenolics by peroxynitrite.

Superoxide dismutase and Fe3+EDTA catalyzed the nitration by peroxynitrite (ONOO-) of a wide range of phenolics including tyrosine in proteins. Nitration was not mediated by a free radical mechanism because hydroxyl radical scavengers did not reduce either superoxide dismutase or Fe3+EDTA-catalyzed nitration and nitrogen dioxide was not a significant product from either catalyst. Rather, metal ions appear to catalyze the heterolytic cleavage of peroxynitrite to form a nitronium-like species (NO2+). The calculated energy for separating peroxynitrous acid into hydroxide ion and nitronium ion is 13 kcal.mol-1 at pH 7.0. Fe3+EDTA catalyzed nitration with an activation energy of 12 kcal.mol-1 at a rate of 5700 M-1.s-1 at 37 degrees C and pH 7.5. The reaction rate of peroxynitrite with bovine Cu,Zn superoxide dismutase was 10(5) M-1.s-1 at low superoxide dismutase concentrations, but the rate of nitration became independent of superoxide dismutase concentration above 10 microM with only 9% of added peroxynitrite yielding nitrophenol. We propose that peroxynitrite anion is more stable in the cis conformation, whereas only a higher energy species in the trans conformation can fit in the active site of Cu,Zn superoxide dismutase. At high superoxide dismutase concentrations, phenolic nitration may be limited by the rate of isomerization from the cis to trans conformations of peroxynitrite as well as by competing pathways for peroxynitrite decomposition. In contrast, Fe3+EDTA appears to react directly with the cis anion, resulting in greater nitration yields.

Electron affinities in the self‐interaction‐corrected local spin density approximation

Electron affinities are calculated for first‐ and second‐row atoms in the self‐interaction‐corrected local spin density approximation (SIC‐LSDA). We compare results obtained by the orbital SIC method of Perdew and Zunger to those obtained by a new method which employs orbital SIC for exchange and Stoll’s spin‐density SIC for correlation. The latter method exhibits exceptional accuracy in correlation and total energy for neutral atoms and negative ions. The orbital SIC method yields more accurate electron affinities overall. This represents a significant improvement over earlier results which employed a spherical approximation for the orbital densities. Both methods follow the experimental trends closely and yield results within 0.2 eV of experiment. This accuracy is shown to be the result of a striking cancellation of errors between exchange and correlation.

Gas-phase thermodynamic models of nitrogen-induced nanocrystallinity in chemical vapor-deposited diamond

Gas-phase thermodynamic equilibrium calculations involving H2/CH4/N2 mixtures were performed to investigate the chemical interactions leading to nitrogen-induced nanocrystallinity in microwave plasma chemical vapor deposition of diamond films. The strong influence of the CN radical in causing nanocrystallinity is confirmed by the correlation of its modeled composition in the gas phase with the degree of nanocrystallinity as determined experimentally for diamond films grown with different N2 additions. For a given CH4 feedgas concentration, there exists a critical N2 feedgas concentration, above which the change in the CH3/CN ratio is minimal and further induced nanocrystallinity is diminished. This is verified experimentally where it is observed that the same critical N2 feedgas concentration exists, above which a further decrease in diamond crystallinity and surface roughness of the grown diamond films is minimal.

Hydrogenation of polycyclic aromatic hydrocarbons as a factor affecting the cosmic 6.2 micron emission band

While many of the characteristics of the cosmic unidentified infrared (UIR) emission bands observed for interstellar and circumstellar sources within the Milky Way and other galaxies, can be best attributed to vibrational modes of the variants of the molecular family known as polycyclic aromatic hydrocarbons (PAH), there are open questions that need to be resolved. Among them is the observed strength of the 6.2 micron (1600 cm(-1)) band relative to other strong bands, and the generally low strength for measurements in the laboratory of the 1600 cm(-1) skeletal vibration band of many specific neutral PAH molecules. Also, experiments involving laser excitation of some gas phase neutral PAH species while producing long lifetime state emission in the 3.3 micron (3000 cm(-1)) spectral region, do not result in significant 6.2 micron (1600 cm(-1)) emission. A potentially important variant of the neutral PAH species, namely hydrogenated-PAH (H(N)-PAH) which exhibit intriguing spectral correlation with interstellar and circumstellar infrared emission and the 2175 A extinction feature, may be a factor affecting the strength of 6.2 micron emission. These species are hybrids of aromatic and cycloalkane structures. Laboratory infrared absorption spectroscopy augmented by density function theory (DFT) computations of selected partially hydrogenated-PAH molecules, demonstrates enhanced 6.2 micron (1600 cm(-1)) region skeletal vibration mode strength for these molecules relative to the normal PAH form. This along with other factors such as ionization or the incorporation of nitrogen or oxygen atoms could be a reason for the strength of the cosmic 6.2 micron (1600 cm(-1)) feature.

Infrared absorption of cis‐ and trans‐alkali‐metal peroxynitrites (MOONO, M=Li, Na, and K) in solid argon

Potassium nitrate (KNO3) isolated in solid argon at 13 K was irradiated with emission from an ArF excimer laser at 193 nm. Recombination of the photofragments led to formation of both cis‐ and trans‐potassium peroxynitrites (KOONO). The cyclic conformer, cis‐KOONO, absorbs at 1444.5, 952.3, 831.6, and 749.1 cm−1, whereas trans‐KOONO absorbs at 1528.4, 987.4, and 602.2 cm−1. The assignments are based on observed 18O‐ and 15N‐isotopic shifts and comparison with similar compounds, cis–cis and trans–perp HOONO. Ab initio calculations using density functional theory at a Becke3LYP level predicted similar line positions and isotopic shifts for both conformers. Photoconversion among these three isomers was achieved at various wavelengths and periods of irradiation; cis‐KOONO was photolyzed readily at 308 nm, whereas trans‐KOONO increased slightly in intensity initially and was eventually transformed to KNO3 on prolonged irradiation. Similar results were obtained for LiNO3 and NaNO3; cis‐LiOONO and cis‐NaOONO absorb at (1423.4, 1422.0), 966.2, 874.2, 792.3 cm−1 and (1437.4, 1434.6), 961.4, 840.7, (770.9, 768.7) cm−1, respectively, whereas trans‐LiOONO and trans‐NaOONO absorb at (1581.6, 1580.4), (998.3, 995.6), 600.4 cm−1 and (1549.3, 1540.6), (996.3, 994.1), (609.4, 607.4) cm−1, respectively; the numbers in parentheses are due to line splitting.

Critical Mg doping on the blue-light emission in p-type GaN thin films grown by metal–organic chemical-vapor deposition

The photoluminescence and photocurrent from p-type GaN films were investigated at temperatures of 30 and 297 K for various Mg-doping concentrations. At a low Mg-doping level, there exists a photoluminescence center of the donor and acceptor pair transition at the 3.28 eV band. This center correlates with the defects for a shallow donor of the VGa and for an acceptor of MgGa. The acceptor level shows a binding energy of 0.2–0.25 eV, which was observed by measuring the photocurrent signal at a photon energy of 3.02–3.31 eV. At a high Mg-doping level, we found a photoluminescence center of a deep donor and acceptor pair transition of the 2.76 eV blue band. This center is attributed to the defect structures of MgGa –VN for the deep donor and MgGa for the acceptor. For low-doped samples, thermal annealing provides an additional photocurrent signal for unoccupied deep acceptor levels of 0.87–1.35 eV above the valence band, indicating p-type activation.The photoluminescence and photocurrent from p-type GaN films were investigated at temperatures of 30 and 297 K for various Mg-doping concentrations. At a low Mg-doping level, there exists a photoluminescence center of the donor and acceptor pair transition at the 3.28 eV band. This center correlates with the defects for a shallow donor of the VGa and for an acceptor of MgGa. The acceptor level shows a binding energy of 0.2–0.25 eV, which was observed by measuring the photocurrent signal at a photon energy of 3.02–3.31 eV. At a high Mg-doping level, we found a photoluminescence center of a deep donor and acceptor pair transition of the 2.76 eV blue band. This center is attributed to the defect structures of MgGa –VN for the deep donor and MgGa for the acceptor. For low-doped samples, thermal annealing provides an additional photocurrent signal for unoccupied deep acceptor levels of 0.87–1.35 eV above the valence band, indicating p-type activation.

Density functional calculations of positron annihilation lifetimes from positron bound states in atoms

Positron annihilation from positron bound states in atomic systems has been investigated by using density functional theory. The shifts of the positron lifetime have been analysed in terms of competing influences of correlation potentials. The results suggest that inclusion of electron - positron correlation is crucial in the assignment of positron orbitals to lifetime components in density functional investigations of bound states of the positron in negative and neutral atomic systems. The eigenvalues of positron bound states consistently correspond to the positron annihilation lifetimes in our calculations.

Growth chemistry for the fabrication of designer diamonds for high pressure research

We report our observations on the catalytic effect of nitrogen in the growth of diamond on top of a diamond anvil substrate by microwave plasma chemical vapor deposition technique. The diamond deposition experiments were carried out by varying the nitrogen content in the range 0–3500 ppm in a standard hydrogen/methane/oxygen plasma. We employ isotopically enriched C-13 methane gas as the source of carbon in the plasma to clearly distinguish the grown diamond layer from the underlying substrate using Raman spectroscopy. The measured diamond growth rate shows a sharp peak at a nitrogen content of 1000 ppm in our growth experiments carried out at 1212°C and atomic force microscopy reveals a dramatic change in surface morphology. Thermodynamic calculations of the plasma show that this growth enhancement could be the result of a competition between the CN and CH3 radicals in the plasma. Finally, we show an application of this ‘unique chemistry’ by synthesizing several designer diamonds with embedded sensors for high-pressure materials research experiments.

The effect of a crystal field on density functional calculations of positron lifetimes in alkali halides

A first-principles theoretical investigation of positron annihilation in alkali halide crystals is carried out using a simplified cluster-embedding scheme. The system is represented as a halide-centred cluster with basis functions only at the centre. The rest of the crystal is modelled in two ways: (i) point ions located at lattice positions; and (ii) frozen-orbital ions derived from an energy band calculation for the pure crystal. Calculations for both models are carried out within the self-interaction-corrected local spin-density approximation and by incorporating an electron - positron correlation functional. The effect of the model assumed on the calculated positron lifetimes is analysed by demonstrating the sensitivity of the results to the inclusion of the Madelung potential. A comparison of positron lifetimes of the ground state of the positron to lifetime components identified in experimental work on lithium and sodium halide systems is made.

Studies of Large Lithium Clusters and their Vacancies with Highly Optimized Localized Orbitals

A first-principles local-density based algorithm which employs optimized Gaussian-type orbitals is used to carry out calculations on a large variety of lithium clusters consisting of one to twenty-seven atoms. Bulk moduli, bond lengths and cohesive energies for the isolated clusters are presented and the results are extrapolated so as to predict the bulk (BCC) cohesive energy as well. Vacancy formation energies and vacancy induced lattice relaxation are also presented for three BCC fragments and compared to the bulk experimental results. For our largest cluster, we obtain a vacancy formation energy of 0.36 eV which is in good agreement with the experimental result of 0.34 eV.