Introduction Of Oxygen Atom Research Articles

PL. Plenary lectures

Research during the 54 years since the discovery of non-heme iron oxygenase enzymes has revealed a remarkable diversity in the strategies used for O2 activation. Many of these are represented in dioxygenase enzymes that introduce oxygen atoms from O2 into aromatic compounds (1). These include direct oxygen activation by external electron transfer to the redox-active mononuclear iron in Rieske dioxygenases, Fe(II)-mediated internal electron transfer from the substrate to O2 in extradiol dioxygenases, and Fe(III)-mediated spin inversion during internal electron transfer from substrate to O2 in intradiol dioxygenases. Recently, the exploration of these mechanisms has moved forward through the combined use of transient kinetics, spectroscopic characterizations, high level computations, and X-ray crystallographic techniques that allow the visualization of discrete intermediates. For each enzyme class, catalysis is found to depend on an elegant balance between the Lewis acidity, redox, and ligand exchange properties of the metal, the traditional structural and catalytic properties of the second sphere residues of the active site, and the less-appreciated contributions from structural dynamics that encompass the entire enzyme. Together, these mediate not only specific catalysis, but just as importantly, regulated catalysis that mitigates against the activation of O2 without attendant substrate oxygenation.

Effects of oxygen impurity on the energy distribution of gap states in hydrogenated amorphous silicon studied by post-transit photocurrent spectroscopy

Oxygen is normally present in the highest concentration (${10}^{18}--{10}^{20}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$ range) among the impurities in hydrogenated amorphous silicon $(a\text{\ensuremath{-}}\mathrm{Si}:\mathrm{H})$ and affects the electrical properties and light-induced changes in this material. However, little is known about how the energy distribution of trap states, $g(E)$, in undoped $a\text{\ensuremath{-}}\mathrm{Si}:\mathrm{H}$ changes with the presence of oxygen. In this study, we prepare undoped $a\text{\ensuremath{-}}\mathrm{Si}:\mathrm{H}$ samples in an ultrahigh-vacuum plasma-enhanced chemical-vapor-deposition chamber and intentionally introduce oxygen atoms at a concentration of $3\ifmmode\times\else\texttimes\fi{}{10}^{19}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$ by adding $\mathrm{C}{\mathrm{O}}_{2}$ to the source gases. By comparing the results obtained for high-purity and oxygen-doped samples by post-transit photocurrent spectroscopy, we discuss the effects of oxygen on the energy distribution of electron and hole trap states before and after long exposure to light. It is found that the presence of oxygen atoms enhances the defect reactions during prolonged illumination, while the shapes of $g(E)$ in the as-deposited state are similar between the high-purity and oxygen-doped samples in the energy range studied (from ${E}_{c}\ensuremath{-}0.35\phantom{\rule{0.3em}{0ex}}\mathrm{eV}\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}{E}_{c}\ensuremath{-}0.65\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ for electron traps and from ${E}_{v}+0.38\phantom{\rule{0.3em}{0ex}}\mathrm{eV}\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}{E}_{c}+0.78\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ for hole traps). A light-induced decrease of the hole trap density in the energy range from ${E}_{v}+0.5\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}{E}_{v}+0.75\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ is observed and discussed.

Chlorophylls, ligands and assembly of light-harvesting complexes in chloroplasts.

Chlorophyll (Chl) b serves an essential function in accumulation of light-harvesting complexes (LHCs) in plants. In this article, this role of Chl b is explored by considering the properties of Chls and the ligands with which they interact in the complexes. The overall properties of the Chls, not only their spectral features, are altered as consequences of chemical modifications on the periphery of the molecules. Important modifications are introduction of oxygen atoms at specific locations and reduction or desaturation of sidechains. These modifications influence formation of coordination bonds by which the central Mg atom, the Lewis acid, of Chl molecules interacts with amino acid sidechains, as the Lewis base, in proteins. Chl a is a versatile Lewis acid and interacts principally with imidazole groups but also with sidechain amides and water. The 7-formyl group on Chl b withdraws electron density toward the periphery of the molecule and consequently the positive Mg is less shielded by the molecular electron cloud than in Chl a. Chl b thus tends to form electrostatic bonds with Lewis bases with a fixed dipole, such as water and, in particular, peptide backbone carbonyl groups. The coordination bonds are enhanced by H-bonds between the protein and the 7-formyl group. These additional strong interactions with Chl b are necessary to achieve assembly of stable LHCs.

Effect of Self-Biased Nitrous Oxide Plasma on Plasma-Enhanced Chemical-Vapor-Deposited Silicon Oxide

A new plasma treatment method was proposed to improve silicon oxide films. The improvement of the films was attributed to the introduction of oxygen atoms, which were extracted from self-biased nitrous oxide plasma. The introduced oxygen atoms decreased the number of defect sites in the silicon oxide film by forming new silicon-oxygen bonds. After the proposed nitrous oxide plasma treatment, the nonstoichiometric silicon oxide film showed good quality similarly to the silicon dioxide film. However, when the self-bias was very high, extra nitrogen atoms were generated from the nitrous oxide plasma and were incorporated into the silicon oxide film. This generated many defect sites degrading the quality of the silicon oxide film.

Enzymatic hydroxylation of aromatic compounds.

Selective hydroxylation of aromatic compounds is among the most challenging chemical reactions in synthetic chemistry and has gained steadily increasing attention during recent years, particularly because of the use of hydroxylated aromatics as precursors for pharmaceuticals. Biocatalytic oxygen transfer by isolated enzymes or whole microbial cells is an elegant and efficient way to achieve selective hydroxylation. This review gives an overview of the different enzymes and mechanisms used to introduce oxygen atoms into aromatic molecules using either dioxygen (O(2)) or hydrogen peroxide (H(2)O(2)) as oxygen donors or indirect pathways via free radical intermediates. In this context, the article deals with Rieske-type and alpha-keto acid-dependent dioxygenases, as well as different non-heme monooxygenases (di-iron, pterin, and flavin enzymes), tyrosinase, laccase, and hydroxyl radical generating systems. The main emphasis is on the heme-containing enzymes, cytochrome P450 monooxygenases and peroxidases, including novel extracellular heme-thiolate haloperoxidases (peroxygenases), which are functional hybrids of both types of heme-biocatalysts.

Electronic properties of barium chalcogenides from first-principles calculations: Tailoring wide-band-gap II-VI semiconductors

Electronic properties of barium chalcogenides were systematically studied using density functional theory computations, based on both generalized gradient approximation and local density approximation functionals. Different linear relationships are observed between theoretical band gap and $1∕{a}^{2}$ (where $a$ is lattice constant) for barium chalcogenides containing oxygen and not containing oxygen, respectively. An abnormal behavior of electronic properties are found for compounds containing oxygen. The effects are attributed to the special properties of $\mathrm{Ba}--\mathrm{O}$ bonds, which is different from other chemical bonds between barium and chalcogen atoms. Pauling electronegativity indicates that only $\mathrm{Ba}--\mathrm{O}$ bonds are highly ionic bonds, and theoretical charge densities also show that electrons would be restricted to oxygen atoms when oxygen is in compound. The results reveal that it is possible to adjust the band gap significantly in barium chalcogenide by introducing oxygen atoms into its lattice for the gap tailoring of wide-band-gap II-VI semiconductors.

Oxidative degradation of cis- and trans-1,4-polybutadienes by horseradish peroxidase/1-hydroxybenzotriazole

Emulsions of cis- and trans-1,4-polybutadienes and cast films of trans-1,4-polybutadiene were treated by an enzyme-mediator system, horseradish peroxidase/1-hydroxybenzotriazole (HRP/1-HBT), at 37 °C for 48 h. Gel permeation chromatography showed that the HRP/1-HBT system was capable of degrading both emulsified 1,4-polybutadienes significantly, but not cast films of trans-1,4-polybutadiene. The weight-average molecular weights of the emulsions after the enzymatic treatment reduced to 34% and 38% of the values for the starting polymers, for cis- and trans-1,4-polybutadienes, respectively. In their infrared spectra, strong absorption bands appeared at 1100 cm −1 and 1111 cm −1 which are assigned to C–O groups for cis- and trans-1,4-polybutadienes, respectively. These results suggest that oxidation of 1,4-polybutadienes progresses during the treatment by HRP/1-HBT system to introduce oxygen atoms into the polymer chains.

Residual order within thermally grown amorphousSiO2on crystalline silicon

The origin of x-ray diffraction peaks observed on the crystal truncation rods (CTR's) in reciprocal space for thermally grown ${\mathrm{SiO}}_{2}$ films has been investigated by large-scale atomistic simulation of silicon oxidation. Three models of ${\mathrm{SiO}}_{2}$ on Si(001), Si(111), and Si(113) were formed by introducing oxygen atoms in crystalline Si from the surfaces in an atom-by-atom manner. The ${\mathrm{SiO}}_{2}$ structures are classified as being amorphous in conventional characterizations, but retain the residual order originating from the {111} atomic planes in their parent crystals. The calculated diffraction patterns exhibit intensity peaks with Laue-function-like fringe profiles along the CTR's, at positions depending on the substrate orientations, agreeing quite well with experimental results.

Large-Scale Atomistic Modeling of Thermally Grown SiO2 on Si(111) Substrate

Large-scale SiO2/Si(111) models were constructed by introducing oxygen atoms in c-Si models in an atom-by-atom manner. Molecular dynamics calculation at a constant temperature was repeatedly carried out for the growing oxide model. By comparing the oxidation simulation of Si(111) substrate with that of Si(001) substrate performed previously, the influence of substrate orientation on the oxide structure was discussed. Owing to the significant feature of bonding arrangement within a Si bilayer in the Si(111) substrate, the inherent stress induced at the SiO2/Si interface by oxygen insertions is originally higher for the Si(111) oxidation than for the Si(001) oxidation, resulting in frequent changes in the bonding network. The resulting structure of bulk SiO2 on Si(111) has less strain and a lower density than that on Si(001), but involves a larger number of dangling bonds. The X-ray diffraction pattern calculated for the SiO2/Si(111) model exhibits a diffraction peak with a Laue-function-like profile on each of the crystal-truncation-rods from the 111 and 111 points, agreeing well with experimental results. These diffraction peaks indicate that the thermally grown SiO2 retains the residual order emanating from the {111} atomic planes in the original c-Si. Because of differences in the angles between the surface and the {111} atomic planes, the residual order within the SiO2 differs depending on the substrate orientation.

Effects of Thermal History on Residual Order of Thermally Grown Silicon Dioxide

By simulation of silicon oxidation and measurement of X-ray crystal-truncation-rod (CTR) scattering, the structures of silicon dioxide films grown at different temperatures and the structural changes due to thermal annealing have been investigated. Large-scale SiO2/Si(001) models were formed by introducing oxygen atoms, atom-by-atom, in crystalline Si from the surfaces. Molecular dynamics (MD) calculation at a constant temperature was repeatedly carried out for the growing oxide model. The intensity and position of the extra diffraction peak observed for the oxide, correlating with the residual order emanating from the parent Si crystal, depend on the growth temperature and change after thermal annealing. The peak intensity becomes smaller with increasing growth temperature. Thermal annealing monotonically decreases the peak intensity and shifts the position along the CTR, toward the lower angle side. There is a good agreement between the results of simulation and experiment. It is shown that (1) the oxide grown at a higher temperature has a lower degree of residual order, (2) thermal annealing decreases the residual order, ultimately leads to complete amorphization and never restores the ordering, and (3) the peak shift along the CTR corresponds to the volumetric expansion of the SiO2 in the surface-normal direction.

Diversity of Alkane Hydroxylase Systems in the Environment

The first step in the aerobic degradation of alkanes by bacteria, yeasts, and fungi is catalyzed by oxygenases. These enzymes, which introduce oxygen atoms derived from molecular oxygen into the alkane substrate, play an important role in oil bioremediation and in the cometabolic degradation of compounds such as trichloroethylene and fuel oxygenates. In addition, they are useful biocatalysts and important models for a difficult chemical reaction: the regio- and stereospecific activation of C-H bonds. Several unrelated enzyme classes catalyze the oxidation of alkanes. Alkane-degrading yeast strains contain multiple alkane hydroxylases belonging to the P450 superfamily, while many bacteria contain enzymes related to the Pseudomonas putida GPo1 membrane-bound alkane hydroxylase system. Short-chain alkanes are probably oxidized by alkane hydroxylases related to the soluble and particulate methane monooxygenases. Only the membrane-bound enzymes have been studied with respect to their prevalence in environments such as soils or aquifers.

New synthetic vitamin D analogs with antiproliferative activities.

The introduction of oxygen atoms into different positions of the vitamin D side chain is described. By combining the arising 23-oxa and 25-oxa elements with other structural modifications (19-nor, iso-19-nor, 20-methyl, 20-ene, 20,21-cyclo) calcitriol analogs with remarkable levels of dissociation between beneficial acitivities on cell growth regulation and undesired hypercalcemia were identified. Structure-activity relations are elaborated in a very systematic outline of the Schering drug finding program in this particular class of vitamin D compounds.

An EELS investigation of oxygen localization in the AlN structure

Abstract The aim of the present work is to investigate by electron energy loss spectroscopy the structural differences between oxygen-doped aluminium nitride deposits (AlON) which are characterized by strong changes in their surface morphology. The deposits have been obtained by chemical vapour deposition using AlCl3, and NH3 as precursors. Progressive addition of N2O in the gas mixture makes possible the introduction of oxygen atoms in the 2H-AlN lattice. Quantitative analysis suggests that well-crystallized materials showing a feather-like surface morphology correspond to the insertion of oxygen atoms in the empty sites of the AlN structure, while for less-crystallized materials, associated with spherolitic surface morphology and a higher oxygen content, the oxygen atoms are substituted for nitrogen atoms. These two kinds of localization for the oxygen atoms can be deduced from the radial distribution function, which was determined by analysing the extended energy loss fine structure, observed on the aluminium, nitrogen and oxygen K-edges.

Electrical conduction in rapidly annealed sputter-deposited SiO2 films (in O2Ar atmosphere) on Si

The poor quality of argon-sputtered SiO 2 is attributed to oxygen vacancies in the bulk of the oxide. Introducing oxygen atoms into the oxide during sputtering improves its quality. Further improvement can be obtained after rapid thermal annealing at high temperature. The barrier height (φ), breakdown electric field (E b ), and stability of oxygen-argon sputtered SiO 2 after annealing is attributed to the formation of bonds between loose oxygen and silicon atoms at high temperature and therefore causing further reduction of vacancies.

Neutron diffraction study of a (C,Cu)(Sr,Ca) 2(Y,Ca,Sr) Cu 2O 7 superconductor

The crystal structure of a cuprate containing CO 3 groups, (C 0.58Cu 0.42)(Sr 0.88Ca 0.12) 2(Y 0.50Ca 0.26Sr 0.24)Cu 2O 7, and its high-pressure oxygen-annealed samples were refined by means of the Rietveld method for neutron-powder-diffraction data. The as-prepared sample (non-superconducting) has neither oxygen defect nor carbonate defect in the structure. Noticeable absence of oxygen atoms and carbonate groups are detected for the annealed (superconducting) sample. It is suggested that hole doping is achieved during high-pressure oxygen annealing by the release of some CO 3 groups and by the introduction of oxygen atoms into the vacant ‘apical’ oxygen site, when the CO 3 group is not present.

Preparation, crystal structure and superconductivity of (C, Cu)(Sr, Ca) 2(Y, Ca, Sr)Cu 2O 7

A series of solid solutioins containing CO 3 groups, (c ycu 1−y)(Sr 1−z/2Ca z/2) 2(Y 1−xCa x−zSr z)Cu 2 O dd with 0.30≤ x≤0.70, was prepared at 1313 K under the atmosphere of O 2-CO 2. The values of y (0.48–0.67) and z (0.14–0.28) depend on the total Ca content, x. The length of the a-axis increase from 3.8374(2) Å ( x=0.30) to 3.8591(9) Å ( x=0.70) with increasing x, while the c-axis length decreases from 11.1198(6) to 10.9410(6) Å. All the as-prepared solid solutions are semiconductors, but superconducting transition is observed for the samples with 0.35≤ × ≤0.70 after annealing at 1273 K and an oxygen pressure of 4.0 MPa. The transition temperature ( T c increases with increasing x, and the highest T c =60 K is measured for the samples with 0.60≤ x≤0.70. All the annealed samples show appreciable expansion of the c-axis length and contraction of the a-axis length relative to the as-prepared ones. The crystal structures of the as-prepared and annealed samples with x = .50 were refined from neutron powder diffraction data by means of the Rietveld method. On the basis of the refined crystal structure data and wet chemical analysis, it is suggested that hole doping is caused, during high-pressure oxygen annealing, by the release of some CO 3 groups and by the introduction of oxygen atoms into the vacant “apical” oxygen site, where the CO 3 group is not present.

2- and 8-Functionalized 1,4,7,10-tetraoxaspiro [5.5] undecanes. Part 4. Conformational study by 1H and 13C NMR spectroscopy

1 H and 13C NMR spectra of new 1,4,7,10-tetraoxygenated spiroacetals 1, 2, 3 and 4, were analysed by using 1D and 2D methods. This allowed us to give a definite structural characterization of the E,E, Z,E and E,Z isomers obtained by a cyclodehydrative reaction carried out on a dihydroxyketone precursor, under thermodynamic control. The introduction of oxygen atoms in the 4 and 10 positions did not modify the structural features previously observed for 1,7-dioxygenated spiroacetals obtained from natural and synthetic sources.

The origin of mechanical stress in vacuum-deposited MgF 2 and ZnS films

In this paper an attempt is made to find an explanation for the observed intrinsic stresses of clean and contaminated vapour-deposited MgF 2 and ZnS films. The tensile stress of a stoichiometric and pure MgF 2 film 1000 Å thick can be calculated assuming a grain boundary model. Small quantities of impurities acting in the grain boundary region change the stress behaviour according to their space requirements. In MgF 2 films low concentrations of CaF 2 and ZnF 2 decrease the tensile stress appreciably. The compressive stress of ZnS films 1000 Å thick can be explained by an impurity grain boundary model. Calculation and measurement with both types of films are in a reasonable agreement. In the case of films deposited at low rates it is assumed that the introduction of oxygen atoms into the ZnS lattice, ogether with a resulting lower packing density, is responsible for the observed tensile stress. The tensile stresses of isolated crystalline aggregates may be produced by strain caused by the many point defects observed and by the partial disorder of the lattice. The stress behaviour of thicker films containing high concentrations of impurities seems to be determined by strains caused by distance variations in the lattice of the film of columnar crystals as well as by grain boundary effects. For stress calculations in this complex case the required mathematical formulations are still not available.

Functionalization of non-activated carbon atoms

Abstract

The thermal decomposition of polyperfluorotriazines

Abstract A comparative study has been made of the thermal degradation of polyperfluoroxyalkylenetriazine (polymer A) and polyperfluoroalkylenetriazine (polymer B). Introduction of oxygen atoms into the perfluorotriazine chains was found to increase thermal stability. A kinetic study of the gaseous degradation products formed during the decomposition of polyperfluoroxyalkylenetriazine showed this process to occur in two stages. The first stage decomposition arises from structural defects of the polymer chain. A scheme is suggested which accounts for the main degradation products