Positions Of Oxygen Atoms Research Articles

Elucidating the Domain Structure of the Cobalt Oxide Water Splitting Catalyst by X-ray Pair Distribution Function Analysis

Pair distribution function (PDF) analysis was applied for structural characterization of the cobalt oxide water-splitting catalyst films using high energy X-ray scattering. The catalyst was found to be composed of domains consistent with a cobalt dioxide lattice sheet structure, possibly containing a Co(4)O(4) cubane-type "defect". The analysis identifies the film to consist of domains composed of 13-14 cobalt atoms with distorted coordination geometries that can be modeled by alteration in terminal oxygen atom positions at the domain edge. Phosphate is seen as a disordered component in the films. This work establishes an approach that can be applied to study the structure of in situ cobalt oxide water-splitting film under functional catalytic conditions.

Epitaxial oxide bilayer on Pt (001) nanofacets

We observed an epitaxial, air-stable, partially registered (2 × 1) oxide bilayer on Pt (001) nanofacets [V. Komanicky, A. Menzel, K.-C. Chang, and H. You, J. Phys. Chem. 109, 23543 (2005)]. The bilayer is made of two half Pt layers; the top layer has four oxygen bonds and the second layer two. The positions and oxidation states of the Pt atoms are determined by analyzing crystal truncation rods and resonance scattering data. The positions of oxygen atoms are determined by density functional theory (DFT) calculations. Partial registry on the nanofacets and the absence of such registry on the extended Pt (001) surface prepared similarly are explained in DFT calculations by strain relief that can be accommodated only by nanoscale facets.

Effect of Al-doping on crystal structure and ionic conductivity of apatite-type La9.33+x/3Si6-xAlxO26 solid electrolytes

La9.33+x/3Si6−xAlxO26 (0 ≤ x ≤ 2.0) sinters with an apatite-type crystal structure were synthesized by solid-state reaction at 1600°C for 5 h, and the sintered discs were examined by AC impedance analysis and X-ray Diffraction (XRD). The total conductivity was significantly increased with an increase in the Al-content and showed a maximum value for x = 1.5 (8.8 × 10−3 S cm−1 at 700°C). The crystal structure model can refine the profiles obtained by XRD with the P63 space group and the channel oxygen atoms were displaced from the ideal site at (0, 0, ≈0.25) with an increase in the Al-content and showed a maximum displacement for x = 1.5. These results show that the position of the channel oxygen atoms is the key parameter that governed the conductivity.

The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

The recognition of carbohydrates by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate–protein interactions is a prerequisite for the rational design of synthetic ligands. Here we report the high- to ultra-high-resolution crystal structures of the carbohydrate recognition domain of galectin-3 (Gal3C) in the ligand-free state (1.08 Å at 100 K, 1.25 Å at 298 K) and in complex with lactose (0.86 Å) or glycerol (0.9 Å). These structures reveal striking similarities in the positions of water and carbohydrate oxygen atoms in all three states, indicating that the binding site of Gal3C is preorganized to coordinate oxygen atoms in an arrangement that is nearly optimal for the recognition of β-galactosides. Deuterium nuclear magnetic resonance (NMR) relaxation dispersion experiments and molecular dynamics simulations demonstrate that all water molecules in the lactose-binding site exchange with bulk water on a time scale of nanoseconds or shorter. Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution. All heavy atoms of glycerol are positioned like the corresponding atoms of lactose in the Gal3C complexes. However, binding of glycerol to Gal3C is insignificant in solution at room temperature, as monitored by NMR spectroscopy or isothermal titration calorimetry under conditions where lactose binding is readily detected. These observations make a case for protein cryo-crystallography as a valuable screening method in fragment-based drug discovery and further suggest that identification of water sites might inform inhibitor design.

Study of Oxidation Behavior of Zn Nanoparticles

Abstract. Zn nanoparticles prepared by the arc was used in the present study. The microsturcture, oxygen content and oxygen atom position in Zn nanoparticles were investigated. Furthermore, the variation of oxygen content with time in the Zn nanoparticles was also studied. The results showed that the effective size of oxidized Zn nanoparticles was about 100nm, and oxidation process was conducted on the surface. On the other hand, the oxygen content in oxidized Zn nanoparticles reduced by comparing with that laying in the air for the same time.

Study of Oxidation and Passivation Behavior of Fe Noparticles

Fe nanoparticles prepared by the arc was used in the present study. It was oxidized by laying in the air and passivated by argon ion bombardment. The microsturcture, oxygen content and oxygen atom position in oxidized Fe nanoparticles were investigated. Furthermore, the variation of oxygen content with time in the passivated Fe nanoparticles and Fe nonparticles was also studied. The results showed that the effective size of oxidized Fe nanoparticles was about 10nm-40nm, and oxidation process was conducted on the surface. On the other hand, the oxygen content in passivated Fe nanoparticles reduced by comparing with that laying in the air for the same time.

Estimation of thermodynamic and Beyer's parameter ( B/ A) in liquid crystalline 5. m, 5O. m, 5.O m, 5O.O m compounds with m=5 and 16

The thermodynamic parameters such as Sharma parameter ( S o ), Huggins parameter ( F), reduced volume ( V ˜ ), reduced compressibility ( V ˜ C 1 ), etc. are studied using the volume expansion coefficient ( α), which is estimated from density for N-( p- n-pentyl benzylidene)- p- n-pentyl aniline (5.5), N-( p-n-pentyloxy benzylidene)- p-n-pentyl aniline (5O.5), N-( p-n-pentyl benzylidene)- p- n-pentyloxy aniline (5.O5), N-( p- n-pentyloxy benzylidene)- p- n-pentyloxy aniline (5O.O5), N-( p- n-pentyl benzylidene)- p- n-hexadecyl aniline (5.16), N-( p- n-pentyloxy benzylidene)- p- n-hexadecyl aniline (5O.16), N-( p- n-pentyl benzylidene)- p- n-hexadecyloxy aniline (5.O16) and N-( p- n-pentyloxy benzylidene)- p- n-hexadecyloxy aniline (5O.O16) compounds in isotropic and liquid crystalline phases. The parameters like intermolecular free length ( L f ), molecular radius ( m r ) and Beyer's non-linearity parameter ( B/ A) are also computed from density data for the above compounds. The results are discussed in the light of these parameters variation with temperature in a particular phase in a liquid crystal molecule and with the position of oxygen atom. The thermodynamic parameter S o exhibits a constant characteristic value 1.11±0.01 in all the compounds like other reported liquid crystalline compounds, liquids and polymers. The variation of other thermodynamic parameters in LC phases of these compounds with temperature is discussed in the light of the body of the data available.

Synthesis and structure of tri-m-tolylantimony bis(1-adamantanecarboxylate)

Tri(m-tolyl)antimony bis(1-adamantanecarboxylate) (3-MeC6H4)3Sb[OC(O)C10H15]2 has been synthesized with a yield of 90.0% by the reaction of tri(m-tolyl)antimony with 1-adamantanecarboxylic acid in the presence of hydrogen peroxide in ether. According to X-ray diffraction analysis data, the antimony atom has a distorted trigonal-bipyramidal coordination with the axially positioned oxygen atoms of carboxyl groups. The axial OSbO angle is 173.1(2)°; the equatorial CSbC angles are 112.0(1)°, 112.0(1)°, and 136.0(3)°; the Sb-O distance is 2.109(3)A; the Sb-C distances are 2.103(5), 2.103(5), and 2.121(7) A; intramolecular Sb…O(=C) contacts are 3.069(5) A.

FERROELECTRIC SWITCHING PATH IN MONODOMAIN RHOMBOHEDRAL BiFeO3 CRYSTAL: A FIRST-PRINCIPLES STUDY

Based on density-functional calculations, we have studied possible ferroelectric switching path in monodomain single crystal of rhombohedral BiFeO3 , a prototypical multiferroic compound. By carefully studying the behaviors of FeO6 corner-sharing double-tetrahedrons, we find abrupt changes in total energy and oxygen atomic positions, and therefore polarizations, occur in the ferroelectric switching path of rhombohedral BiFeO3 . Detailed analyses suggest that such behavior might be caused by the frustrated magnetic ordering in the paraelectric phase of rhombohedral BiFeO3 , where three O atoms and the Bi atom are in the same plane perpendicular to the polarization direction. This is supported by the fact that the ferroelectric switching for paramagnetic BiFeO3 is smooth and has a much lower energy barrier than that of antiferromagnetic BiFeO3 .

Ab‐initio Structure Determination of the New Ion Conductor K2Al2O3F2 from Powder Diffraction Data

AbstractThe crystal structure of K2Al2O3F2, prepared at 800 °C by ceramic methods, was determined from conventional laboratory X‐ray powder diffraction data. The compound crystallizes in the monoclinic space group C2/m (No. 12) with a = 11.21675(8), b = 8.16351(6), c = 6.12301(5) Å β = 88.8108(6) ° and Z = 4. Unit cell and space group suggestions were found by using the TOPAS program. Starting positional parameters for potassium and aluminum atoms were obtained from 548 reflections by the methods implemented in the FOX program. Oxygen and fluorine atom positions were determined by structural considerations. The structure was refined using the fundamental parameter approach of TOPAS, which gave the final residuals (%) RBragg = 1.6 and Rwp = 4.6. The crystal structure consists of individual layers of oxygen connected AlO3F tetrahedral groups with the fluorine atoms separating the layers. Empirical energy calculations agree with the crystal structure refinements and suggest no or little oxygen–fluorine exchange. Between and perpendicular to the sheets, the potassium ion can move without steric hindrance. Conductivity measurements from room temperature to 300 °C show decent potassium ion conductivity.

Synthesis and fluorescence and electrochemical properties of D–π-A structural isomers of benzofuro[2,3-c]oxazolo[4,5-a]carbazole-type and benzofuro[2,3-c]oxazolo[5,4-a]carbazole-type fluorescent dyes

Heteropolycyclic donor--acceptor (D--A) structural isomers of benzofuro[2,3-c]oxazolo[4,5-a]carbazole-type (2a-f) and benzofuro[2,3-c]oxazolo[5,4-a]carbazole-type fluorescent dyes (3a-f), which differ in the position of oxygen and nitrogen atoms of the oxazole ring, have been synthesized, and their photophysical and electrochemical properties have been investigated. The fluorescent dyes 2a-f exhibit much stronger intramolecular charge transfer (ICT) absorption and fluorescence bands than 3a-f. Both of the D-pi-A structural isomers showed bathochromic shifts of the fluorescence band and a decrease in the fluorescence quantum yields with increasing solvent polarity (i.e., positive fluorescence solvatochromism), and the bathochromic shifts for 3a-f were larger than those for 2a-f. The fluorescent dyes 2a-c and 3a-c, which have cyano and carboxyl groups, and carboxylic acid ester as electron-withdrawing substituents, exhibited significant fluorescence solvatochromic properties, compared to 2e, 2f, 3e and 3f without an electron-withdrawing substituent. The fluorescence solvatochromism of the fluorescent dyes were analyzed with the Lippert-Mataga correlation. Moreover, to elucidate the differences of photophysical properties among the fluorescent dyes, we have performed time-resolved fluorescence spectroscopic measurements, and a change of the electronic or molecular structures between the ground and excited states was evaluated by a comparison of the experimental radiative rate constant (k(r)) with the Strickler-Berg rate constant (kSB(r)). The electrochemical properties of 2a-f and 3a-f were determined by cyclic voltammetry, which demonstrated that these fluorescent dyes have similar HOMO energy levels, but different LUMO energy levels. Semi-empirical molecular orbital calculations (AM1 and INDO/S) have been carried out to elucidate the effects of the substituents and chromophore skeleton on photophysical properties of the two D-pi-A structural isomers. These studies indicated that the ICT characteristics in the excited state are different among the fluorescent dyes, which is a principal reason for the differences of the fluorescence solvatochromism and the substituent dependent fluorescence properties among the two D-pi-A structural isomers.

Photocatalytic Activity for Water Decomposition to Hydrogen over Nitrogen‐doped TiO2 Nanoparticle

AbstractNitrogen‐doped TiO2 nanoparticle photocatalysts were obtained by an annealing method with gaseous ammonia and nitrogen. The influence of dopant N on the crystal structure was characterized by XRD, XPS, BET, TEM and UV‐Vis spectra. The results of XRD indicate that, the crystal phase transforms from anatase to rutile structure gradually with increase of annealing temperature from 300 to 700 °C. XPS studies indicate that the nitrogen atom enters the TiO2 lattice and occupies the position of oxygen atom. Agglomeration of particles is found in TEM images after annealing. BET results show that the specific surface areas of N‐doped samples from 44.61 to 38.27 m2/g are smaller than that of Degussa TiO2. UV‐Vis spectra indicate that the absorption threshold shifts gradually with increase of annealing temperature, which shows absorption in the visible region. The influence of annealing condition on the photocatalytic property has been researched over water decomposition to hydrogen, indicating that nitrogen raises the photocatalytic activity for hydrogen evolution, and the modified TiO2 annealed for 2 h at 400 °C under gas of NH3/N2 (V/V=1/2) mixture shows better efficiency of hydrogen evolution. Furthermore, the N‐doped TiO2 nanoparticle catalysts have obvious visible light activity, evidenced by hydrogen evolution under visible light (λ>400 nm) irradiation. However, the catalytic activity under visible light irradiation is absent for Degussa as reference and the N‐doped TiO2 annealed at 700 °C.

Atomic Resolution Crystal Structures and Quantum Chemistry Meet to Reveal Subtleties of Hydroxynitrile Lyase Catalysis

Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

Bis(1-adamantanecarboxylato)triphenylantimony: Synthesis and structure

Bis(1-adamantanecarboxylato)triphenylantimony Ph3Sb[OC(O)C10H15]2 was synthesized in 92% yield by reacting triphenylantimony with 1-adamantanecarboxylic acid in the presence of hydrogen peroxide in diethyl ether. X-ray crystallography shows that the antimony atom has a distorted trigonal-pyramidal coordination with axially positioned oxygen atoms of carboxy groups. The axial angle OSbO and equatorial angles CSbC are 179.93(6)° and 99.90(5)°, 99.90(5)°, and 160.20(9)°, respectively; intramolecular contacts Sb···O(=C) are 2.613(1) A. Structure data on structurally characterized triarylantimony dicarboxylates are systematized.

Ab initio study electronic structures of LiYF 4 crystal containing interstitial oxygen atoms

The positions of the interstitial oxygen atoms in LiYF 4 crystal are simulated by computer technologies. It is found that the total energy of cluster is low when interstitial oxygen atoms exist around the Li + ion. Basing on the computer results, the electronic structures of perfect LiYF 4 and the LiYF 4 containing interstitial oxygen atoms with the lattice structure optimized are studied within the framework of the density functional theory. By analyzing the calculated results it can be concluded that an interstitial oxygen atom could combine with formal lattice fluorine ions forming molecular ions, which cause the 260 nm absorption band.

Effect of oxygen on structure and electronic properties of silicon nanoclusters Si n (n = 5, 6, 10, 18)

Methods of the theory of electron-density functional and pseudopotentials are used for studying the effect of oxygen on the geometry and electronic structure of small silicon clusters Sin, (n = 5, 6, 10, 18). It is shown that the energy gap varies and, as a rule, decreases for such systems depending on the position and number of oxygen atoms.

Inhomogeneity-Induced Enhancement of the Pairing Interaction in Cuprate Superconductors

Scanning tunneling spectroscopy has recently discovered a positive correlation between the magnitude of the superconducting gap and positions of dopant oxygen atoms in Bi-based cuprates. We propose a microscopic mechanism that could be responsible for this effect. In particular, we demonstrate that the dopant-induced spatial variation of the atomic levels always enhances the superexchange interaction.

Intrinsic Nanoscale Disorder and the Physical Properties of HTSC

Recent STM studies revealed nanoscale electronic disorder on the crystal surface in many cuprates. In BSCCO, strong correlations between oxygen defect distributions on its surface and both the gap map and the coherence peak amplitude showed that the off-center distortions in the positions of oxygen atoms are responsible for most of the electronic disorder. How do these nanoscale inhomogeneities affect the bulk macroscopic physical properties (such as transport properties) of these compounds? What is the effect of a local oxygen disorder on these properties? Persistent circulating supercurrents, which are known to bypass regions of a reduced order parameter (macroscopic crystal defects), have been used to investigate superconducting properties. Our investigations identified universal (sample independent) features in these properties (such as Josephson effects, filamentary and percolative flow of the transport current, etc.) which can be attributed to the presence of a nanoscale inhomogeneity. Local oxygen redistribution, induced either by careful low temperature annealing or by room temperature aging, was found to modify substantially both the superconducting and the normal state properties.

Effects of nitrogen doping on microstructure and photocatalytic activity of nanocrystalline TiO2 powders

Nitrogen-doped TiO2 nanocrystalline powders were prepared by hydrolysis of tetrachloride titanium (TiCl4) in a mixed solution of ethanol and ammonium nitrate (NH4NO3) at ambient temperature and atmosphere followed by calcination at 400 °C for 2 h in air. FTIR spectra demonstrate that amine group in original gel is eliminated by calcination, and the TiO2 powder is liable to absorb water onto its surface and into its capillary pore. XRD and SEM results show that the average size of nanocrystalline TiO2 particles is no more than 60 nm and with increasing the calcination temperature, the size of particles increases. XPS studies indicate the nitrogen atom enters into the TiO2 lattice and occupies the position of oxygen atom. The nitrogen doping not only depresses the grain growth of TiO2 particles, but also reduces the phase transformation temperature of anatase to rutile. The photocatalytic activity of the nitrogen-doped TiO2 powders has been evaluated by experiments of photocatalytic degradation aqueous methylene blue.

INTRINSIC NANOSCALE DISORDER IN HTSC: EFFECT ON THE PHYSICAL PROPERTIES

Recent STM studies revealed nanoscale electronic disorder on the crystal surface in many cuprates. In BSCCO strong correlations between oxygen defect distributions on its surface and both the gap map and the coherence peak amplitude showed that the off-center distortions in the positions of oxygen atoms are responsible for most of the electronic disorder. Additional information on nanoscale inhomogeneities and its relationship to the lattice strain and oxygen redistribution can be obtained from the electrical transport that uses Percolating Persistent Supercurrents which are known to bypass regions of a reduced order parameter (macroscopic crystal defects). Our investigations identified universal (sample independent) features in the superconducting properties which can be attributed to the presence of a nanoscale inhomogeneity, such as nanogranular Josephson effects, strain-induced filamentary and percolative flow of the transport current, etc. Local oxygen redistribution, induced either by careful low temperature annealing or by room temperature aging, modifies both the superconducting and the normal state properties.