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Sample records for atomic structure ii

  1. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    PubMed Central

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  2. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis.

    PubMed

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-09-21

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts.

  3. Atom exchange between aqueous Fe(II) and structural Fe in clay minerals.

    PubMed

    Neumann, Anke; Wu, Lingling; Li, Weiqiang; Beard, Brian L; Johnson, Clark M; Rosso, Kevin M; Frierdich, Andrew J; Scherer, Michelle M

    2015-03-03

    Due to their stability toward reductive dissolution, Fe-bearing clay minerals are viewed as a renewable source of Fe redox activity in diverse environments. Recent findings of interfacial electron transfer between aqueous Fe(II) and structural Fe in clay minerals and electron conduction in octahedral sheets of nontronite, however, raise the question whether Fe interaction with clay minerals is more dynamic than previously thought. Here, we use an enriched isotope tracer approach to simultaneously trace Fe atom movement from the aqueous phase to the solid ((57)Fe) and from the solid into the aqueous phase ((56)Fe). Over 6 months, we observed a significant decrease in aqueous (57)Fe isotope fraction, with a fast initial decrease which slowed after 3 days and stabilized after about 50 days. For the aqueous (56)Fe isotope fraction, we observed a similar but opposite trend, indicating that Fe atom movement had occurred in both directions: from the aqueous phase into the solid and from the solid into aqueous phase. We calculated that 5-20% of structural Fe in clay minerals NAu-1, NAu-2, and SWa-1 exchanged with aqueous Fe(II), which significantly exceeds the Fe atom layer exposed directly to solution. Calculations based on electron-hopping rates in nontronite suggest that the bulk conduction mechanism previously demonstrated for hematite1 and suggested as an explanation for the significant Fe atom exchange observed in goethite2 may be a plausible mechanism for Fe atom exchange in Fe-bearing clay minerals. Our finding of 5-20% Fe atom exchange in clay minerals indicates that we need to rethink how Fe mobility affects the macroscopic properties of Fe-bearing phyllosilicates and its role in Fe biogeochemical cycling, as well as its use in a variety of engineered applications, such as landfill liners and nuclear repositories.

  4. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    PubMed

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin.

  5. Electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clays. Role in U and Hg(II) transformations

    SciTech Connect

    Scherer, Michelle

    2016-08-31

    During this project, we investigated Fe electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clay minerals. We used selective chemical extractions, enriched Fe isotope tracer experiments, computational molecular modeling, and Mössbauer spectroscopy. Our findings indicate that structural Fe(III) in clay minerals is reduced by aqueous Fe(II) and that electron transfer occurs when Fe(II) is sorbed to either basal planes and edge OH-groups of clay mineral. Findings from highly enriched isotope experiments suggest that up to 30 % of the Fe atoms in the structure of some clay minerals exhanges with aqueous Fe(II). First principles calculations using a small polaron hopping approach suggest surprisingly fast electron mobility at room temperature in a nontronite clay mineral and are consistent with temperature dependent Mössbauer data Fast electron mobility suggests that electrons may be able to conduct through the mineral fast enough to enable exchange of Fe between the aqueous phase and clay mineral structure. over the time periods we observed. Our findings suggest that Fe in clay minerals is not as stable as previously thought.

  6. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    PubMed

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  7. Relativistic atomic beam spectroscopy II

    SciTech Connect

    1989-12-31

    The negative ion of H is one of the simplest 3-body atomic systems. The techniques we have developed for experimental study of atoms moving near speed of light have been productive. This proposal request continuing support for experimental studies of the H{sup -} system, principally at the 800 MeV linear accelerator (LAMPF) at Los Alamos. Four experiments are currently planned: photodetachment of H{sup -} near threshold in electric field, interaction of relativistic H{sup -} ions with matter, high excitations and double charge escape in H{sup -}, and multiphoton detachment of electrons from H{sup -}.

  8. Iron Atom Exchange between Hematite and Aqueous Fe(II).

    PubMed

    Frierdich, Andrew J; Helgeson, Maria; Liu, Chengshuai; Wang, Chongmin; Rosso, Kevin M; Scherer, Michelle M

    2015-07-21

    Aqueous Fe(II) has been shown to exchange with structural Fe(III) in goethite without any significant phase transformation. It remains unclear, however, whether aqueous Fe(II) undergoes similar exchange reactions with structural Fe(III) in hematite, a ubiquitous iron oxide mineral. Here, we use an enriched (57)Fe tracer to show that aqueous Fe(II) exchanges with structural Fe(III) in hematite at room temperature, and that the amount of exchange is influenced by particle size, pH, and Fe(II) concentration. Reaction of 80 nm-hematite (27 m(2) g(-1)) with aqueous Fe(II) at pH 7.0 for 30 days results in ∼5% of its structural Fe(III) atoms exchanging with Fe(II) in solution, which equates to about one surface iron layer. Smaller, 50 nm-hematite particles (54 m(2) g(-1)) undergo about 25% exchange (∼3× surface iron) with aqueous Fe(II), demonstrating that structural Fe(III) in hematite is accessible to the fluid in the presence of Fe(II). The extent of exchange in hematite increases with pH up to 7.5 and then begins to decrease as the pH progresses to 8.0, likely due to surface site saturation by sorbed Fe(II). Similarly, when we vary the initial amount of added Fe(II), we observe decreasing amounts of exchange when aqueous Fe(II) is increased beyond surface saturation. This work shows that Fe(II) can catalyze iron atom exchange between bulk hematite and aqueous Fe(II), despite hematite being the most thermodynamically stable iron oxide.

  9. Atomic-Scale Characterization of II-VI Compound Semiconductors

    NASA Astrophysics Data System (ADS)

    Smith, David J.

    2013-11-01

    Alloys of II-VI compound semiconductors with suitable band gap selection potentially provide broad coverage of wavelengths for photodetector applications. Achievement of high-quality epitaxial growth is, however, essential for successful development of integrated photonic and optoelectronic devices. Atomic-scale characterization of structural defects in II-VI heterostructures using electron microscopy plays an invaluable role in accomplishing this goal. This paper reviews some recent high-resolution studies of II-VI compound semiconductors with zincblende crystal structure, as grown epitaxially on commonly used substrates. Exploratory studies using aberration-corrected electron microscopes are also briefly considered.

  10. Atomic far-IR fine-structure line mapping of L1630, M17, and W3: Comparison of (O I) and (C II) distributions

    NASA Technical Reports Server (NTRS)

    Howe, J. E.; Jaffe, Dan T.; Zhou, Shudong

    1995-01-01

    We mapped the distribution of atomic far-IR line emission from (O I) and (C II) over parsec scales in the Galactic star-forming regions L1630, M17, and W3 using the MPE Far-Infrared Fabry-Perot Imaging spectrometer (FIFI) on board the NASA Kuiper Airborne Observatory. The lines mapped include (O I) 63 microns, (O I) 146 microns, and (C II) 158 microns. Comparison of the intensities and ratios of these lines with models of photodissociation regions (e.g., Tielens & Hollenbach 1985, ApJ, 344, 770) allows us to derive temperatures and densities of the primarily neutral atomic gas layers lying on the surfaces of UV-illuminated molecular gas. In general, the (C II) line arises ubiquitously throughout the molecular clouds while the (O I) lines are mainly confined to warm, dense gas (T is greater than 100 K, n is greater than 10(exp 4)/cu cm) near the sites of O and B stars. The distribution of (C II) in the star-forming clouds implies that the (C II) emission arises on the surfaces of molecular clumps throughout the clouds, rather than only at the boundary layer between molecular gas and H II regions.

  11. Atomic and Electronic Structure of Solids

    NASA Astrophysics Data System (ADS)

    Kaxiras, Efthimios

    2003-01-01

    Preface; Acknowledgements; Part I. Crystalline Solids: 1. Atomic structure of crystals; 2. The single-particle approximation; 3. Electrons in crystal potential; 4. Band structure of crystals; 5. Applications of band theory; 6. Lattice vibrations; 7. Magnetic behaviour of solids; 8. Superconductivity; Part II. Defects, Non-Crystalline Solids and Finite Structures: 9. Defects I: point defects; 10. Defects II: line defects; 11. Defects III: surfaces and interfaces; 12. Non-crystalline solids; 13. Finite structures; Part III. Appendices: A. Elements of classical electrodynamics; B. Elements of quantum mechanics; C. Elements of thermodynamics; D. Elements of statistical mechanics; E. Elements of elasticity theory; F. The Madelung energy; G. Mathematical tools; H. Nobel Prize citations; I. Units and symbols; References; Index.

  12. Millisecond dynamics of RNA polymerase II translocation at atomic resolution

    PubMed Central

    Silva, Daniel-Adriano; Weiss, Dahlia R.; Pardo Avila, Fátima; Da, Lin-Tai; Levitt, Michael; Wang, Dong; Huang, Xuhui

    2014-01-01

    Transcription is a central step in gene expression, in which the DNA template is processively read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA transcript. At each cycle, Pol II moves exactly one register along the DNA, a process known as translocation. Although X-ray crystal structures have greatly enhanced our understanding of the transcription process, the underlying molecular mechanisms of translocation remain unclear. Here we use sophisticated simulation techniques to observe Pol II translocation on a millisecond timescale and at atomistic resolution. We observe multiple cycles of forward and backward translocation and identify two previously unidentified intermediate states. We show that the bridge helix (BH) plays a key role accelerating the translocation of both the RNA:DNA hybrid and transition nucleotide by directly interacting with them. The conserved BH residues, Thr831 and Tyr836, mediate these interactions. To date, this study delivers the most detailed picture of the mechanism of Pol II translocation at atomic level. PMID:24753580

  13. Can atom-surface potential measurements test atomic structure models?

    PubMed

    Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D

    2011-06-30

    van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.

  14. Modelling the metal atom positions of the Photosystem II water oxidising complex: a density functional theory appraisal of the 1.9 Å resolution crystal structure.

    PubMed

    Petrie, Simon; Gatt, Phillip; Stranger, Rob; Pace, Ron J

    2012-08-28

    Density functional theory (DFT) calculations are reported for a set of model compounds intended to represent the structure of the Photosystem II (PSII) water oxidising complex (WOC) as determined by the recent 1.9 Å resolution single crystal X-ray diffraction (XRD) study of Umena et al. In contrast with several other theoretical studies addressing this structure, we find that it is not necessary to invoke photoreduction of the crystalline sample below the S(1)'resting state' in order to rationalise the observed WOC geometry. Our results are consistent with crystallised PSII in the S(1) state, with S(1) corresponding to either (Mn(III))(4) or (Mn(III))(2)(Mn(IV))(2) as required by the two competing paradigms for the WOC oxidation state pattern. Of these two paradigms, the 'low-oxidation-state' paradigm provides a better match for the crystal structure, with the comparatively long Mn(2)-Mn(3) distance in particular proving difficult to reconcile with the 'high-oxidation-state' model. Best agreement with the set of metal-metal distances is obtained with a S(1) model featuring μ-O, μ-OH bridging between Mn(3) and Mn(4) and deprotonation of one water ligand on Mn(4). Theoretical modelling of the 1.9 Å structure is an important step in assessing the validity of this recent crystal structure, with implications for our understanding of the mechanism of water oxidation by PSII.

  15. Electronic structure interpolation via atomic orbitals.

    PubMed

    Chen, Mohan; Guo, G-C; He, Lixin

    2011-08-17

    We present an efficient scheme for accurate electronic structure interpolation based on systematically improvable optimized atomic orbitals. The atomic orbitals are generated by minimizing the spillage value between the atomic basis calculations and the converged plane wave basis calculations on some coarse k-point grid. They are then used to calculate the band structure of the full Brillouin zone using the linear combination of atomic orbitals algorithms. We find that usually 16-25 orbitals per atom can give an accuracy of about 10 meV compared to the full ab initio calculations, and the accuracy can be systematically improved by using more atomic orbitals. The scheme is easy to implement and robust, and works equally well for metallic systems and systems with complicated band structures. Furthermore, the atomic orbitals have much better transferability than Shirley's basis and Wannier functions, which is very useful for perturbation calculations.

  16. Atomic structure of the sweet-tasting protein thaumatin I at pH 8.0 reveals the large disulfide-rich region in domain II to be sensitive to a pH change

    SciTech Connect

    Masuda, Tetsuya; Ohta, Keisuke; Mikami, Bunzo; Kitabatake, Naofumi; Tani, Fumito

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Structure of a recombinant thaumatin at pH 8.0 determined at a resolution of 1.0 A. Black-Right-Pointing-Pointer Substantial fluctuations of a loop in domain II was found in the structure at pH 8.0. Black-Right-Pointing-Pointer B-factors for Lys137, Lys163, and Lys187 were significantly affected by pH change. Black-Right-Pointing-Pointer An increase in mobility might play an important role in the heat-induced aggregation. -- Abstract: Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at 50 nM. Although the sweetness remains when thaumatin is heated at 80 Degree-Sign C for 4 h under acid conditions, it rapidly declines when heating at a pH above 6.5. To clarify the structural difference at high pH, the atomic structure of a recombinant thaumatin I at pH 8.0 was determined at a resolution of 1.0 A. Comparison to the crystal structure of thaumatin at pH 7.3 and 7.0 revealed the root-mean square deviation value of a C{alpha} atom to be substantially greater in the large disulfide-rich region of domain II, especially residues 154-164, suggesting that a loop region in domain II to be affected by solvent conditions. Furthermore, B-factors of Lys137, Lys163, and Lys187 were significantly affected by pH change, suggesting that a striking increase in the mobility of these lysine residues, which could facilitate a reaction with a free sulfhydryl residue produced via the {beta}-elimination of disulfide bonds by heating at a pH above 7.0. The increase in mobility of lysine residues as well as a loop region in domain II might play an important role in the heat-induced aggregation of thaumatin above pH 7.0.

  17. Electrochemical Potential Derived from Atomic Cluster Structures.

    PubMed

    Du, Jinglian; Xiao, Debao; Wen, Bin; Melnik, Roderick; Kawazoe, Yoshiyuki

    2016-02-04

    Based on the atomic cluster structures and free electron approximation model, it is revealed that the electrochemical potential (ECP) for the system of interest is proportional to the reciprocal of atomic cluster radius squared, i.e., φ = k·(1/r(2)). Applied to elemental crystals, the correlation between atomic cluster radii and the ECP that we have predicted agrees well with the previously reported results. In addition, some other physicochemical properties associated with the ECP have also been found relevant to the atomic cluster radii of materials. Thus, the atomic cluster radii can be perceived as an effective characteristic parameter to measure the ECP and related properties of materials. Our results provide a better understanding of ECP directly from the atomic structures perspective.

  18. Some Experiments in Atomic Structure

    ERIC Educational Resources Information Center

    Logan, Kent R.

    1974-01-01

    The role of spectral color slides in laboratory situations is discussed, then experiments for secondary school students concerning color and wave length, evidence of quantization, and the ionization energy of the hydrogen atom are outlined. Teaching guidelines for creating a set of spectrograms and photographic specifications are provided. (DT)

  19. Agricultural Structures, Volume II.

    ERIC Educational Resources Information Center

    Linhardt, Richard E.; Burhoe, Steve

    This guide to a curriculum unit in agricultural structures is designed to expand the curriculum materials available in vocational agriculture in Missouri. It and Agricultural Structures I (see note) provide reference materials to systematize the curriculum. The six units cover working with concrete (19 lessons, 2 laboratory exercises), drawing and…

  20. About the atomic structures of icosahedral quasicrystals

    NASA Astrophysics Data System (ADS)

    Quiquandon, Marianne; Gratias, Denis

    2014-01-01

    This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

  1. Introduction to Atomic Structure: Demonstrations and Labs.

    ERIC Educational Resources Information Center

    Ciparick, Joseph D.

    1988-01-01

    Demonstrates a variety of electrical phenomena to help explain atomic structure. Topics include: establishing electrical properties, electrochemistry, and electrostatic charges. Recommends demonstration equipment needed and an explanation of each. (MVL)

  2. Direct atomic structure determination by the inspection of structural phase.

    PubMed

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  3. Direct atomic structure determination by the inspection of structural phase

    PubMed Central

    Nakashima, Philip N. H.; Moodie, Alexander F.; Etheridge, Joanne

    2013-01-01

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities. PMID:23940343

  4. Gas Atomization of Amorphous Aluminum Powder: Part II. Experimental Investigation

    NASA Astrophysics Data System (ADS)

    Zheng, Baolong; Lin, Yaojun; Zhou, Yizhang; Lavernia, Enrique J.

    2009-12-01

    The optimal processing parameters that are required to atomize amorphous Al were established on the basis of numerical simulations in part I of this study. In this part II, the characterization of cooling rate experienced by gas-atomized, Al-based amorphous powders was studied via experiments. An experimental investigation was implemented to validate the numerical predictions reported in part I of this study. The cooling rate experienced by the powders, for example, was experimentally determined on the basis of dendrite arm spacing correlations, and the results were compared with the numerical predictions. The experimental studies were completed using commercial Al 2024 as a baseline material and Al90Gd7Ni2Fe1 metallic glass (MG). The results showed that the cooling rate of droplets increases with decreasing particle size, with an increasing proportion of helium in the atomization gas and with increasing melt superheat. The experimental results reported in this article suggest good agreement between experiments and numerical simulations.

  5. Atomic Data and Spectral Model for Fe II

    NASA Astrophysics Data System (ADS)

    Bautista, Manuel A.; Fivet, Vanessa; Ballance, Connor; Quinet, Pascal; Ferland, Gary; Mendoza, Claudio; Kallman, Timothy R.

    2015-08-01

    We present extensive calculations of radiative transition rates and electron impact collision strengths for Fe ii. The data sets involve 52 levels from the 3d7, 3d64s, and 3{d}54{s}2 configurations. Computations of A-values are carried out with a combination of state-of-the-art multiconfiguration approaches, namely the relativistic Hartree-Fock, Thomas-Fermi-Dirac potential, and Dirac-Fock methods, while the R-matrix plus intermediate coupling frame transformation, Breit-Pauli R-matrix, and Dirac R-matrix packages are used to obtain collision strengths. We examine the advantages and shortcomings of each of these methods, and estimate rate uncertainties from the resulting data dispersion. We proceed to construct excitation balance spectral models, and compare the predictions from each data set with observed spectra from various astronomical objects. We are thus able to establish benchmarks in the spectral modeling of [Fe ii] emission in the IR and optical regions as well as in the UV Fe ii absorption spectra. Finally, we provide diagnostic line ratios and line emissivities for emission spectroscopy as well as column densities for absorption spectroscopy. All atomic data and models are available online and through the AtomPy atomic data curation environment.

  6. Atomic vapor spectroscopy in integrated photonic structures

    SciTech Connect

    Ritter, Ralf; Kübler, Harald; Pfau, Tilman; Löw, Robert; Gruhler, Nico; Pernice, Wolfram

    2015-07-27

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of complex waveguide structures.

  7. Quartet structure in atomic nuclei

    NASA Astrophysics Data System (ADS)

    Fu, G. J.; Zhao, Y. M.; Arima, A.

    2015-05-01

    A quartet is a tightly bound cluster of two protons and two neutrons, similar to the α particle but occasionally with nonzero spin and/or isospin. If the interaction between two quartets is weak in given states, such states are concluded to be well represented by a quartet structure. In this paper, we study the quartet structure of eight valence nucleons in two cases. The first is a single j shell, demonstrating that the so-called stretch scheme [M. Danos and V. Gillet, Phys. Rev. Lett. 17, 703 (1966), 10.1103/PhysRevLett.17.703] is very good for low-spin states with a quadruple-quadruple interaction, and is reasonably good under realistic interactions. The second case is the ground state of 92Pd in the p1 /2p3 /2f5 /2g9 /2 shell with the JUN45 effective interaction. We show that the quartet correlation is essential in the ground state of 92Pd.

  8. Atomic Structure Calculations from the Los Alamos Atomic Physics Codes

    DOE Data Explorer

    Cowan, R. D.

    The well known Hartree-Fock method of R.D. Cowan, developed at Los Alamos National Laboratory, is used for the atomic structure calculations. Electron impact excitation cross sections are calculated using either the distorted wave approximation (DWA) or the first order many body theory (FOMBT). Electron impact ionization cross sections can be calculated using the scaled hydrogenic method developed by Sampson and co-workers, the binary encounter method or the distorted wave method. Photoionization cross sections and, where appropriate, autoionizations are also calculated. Original manuals for the atomic structure code, the collisional excitation code, and the ionization code, are available from this website. Using the specialized interface, you will be able to define the ionization stage of an element and pick the initial and final configurations. You will be led through a series of web pages ending with a display of results in the form of cross sections, collision strengths or rates coefficients. Results are available in tabular and graphic form.

  9. Atomic structure of Beta-tantalum nanocrystallites.

    PubMed

    Tillmann, Karsten; Thust, Andreas; Gerber, Andreas; Weides, Martin P; Urban, Knut

    2005-12-01

    The structural properties of beta-phase tantalum nanocrystallites prepared by room temperature magnetron sputter deposition on amorphous carbon substrates are investigated at atomic resolution. For these purposes spherical aberration-corrected high-resolution transmission electron microscopy is applied in tandem with the numerical retrieval of the exit-plane wavefunction as obtained from a through-focus series of experimental micrographs. We demonstrate that recent improvements in the resolving power of electron microscopes enable the imaging of the atomic structure of beta-tantalum with column spacings of solely 0.127 nm with directly interpretable contrast features. For the first time ever, we substantiate the existence of grain boundaries of 30 degrees tilt type in beta-Ta whose formation may be well explained by atomic agglomeration processes taking place during sputter deposition.

  10. Imaging DNA Structure by Atomic Force Microscopy.

    PubMed

    Pyne, Alice L B; Hoogenboom, Bart W

    2016-01-01

    Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine superstructure and secondary structure of surface-bound DNA. The method is also readily applicable to probe DNA-DNA interactions and DNA-protein complexes.

  11. High-pressure synthesis and structural characterization of the type II clathrate compound Na(30.5)Si(136) encapsulating two sodium atoms in the same silicon polyhedral cages.

    PubMed

    Yamanaka, Shoji; Komatsu, Masaya; Tanaka, Masashi; Sawa, Hiroshi; Inumaru, Kei

    2014-05-28

    Single crystals of sodium containing silicon clathrate compounds Na8Si46 (type I) and NaxSi136 (type II) were prepared from the mixtures of NaSi and Si under high-pressure and high-temperature conditions of 5 GPa at 600-1000 °C. The type II crystals were obtained at relatively low-temperature conditions of 700-800 °C, which were found to have a Na excess composition Na30.5Si136 in comparison with the compounds NaxSi136 (x ≤ 24) obtained by a thermal decomposition of NaSi under vacuum. The single crystal study revealed that the Na excess type II compound crystallizes in space group Fd3̅m with a lattice parameter of a = 14.796(1) Å, slightly larger than that of the ambient phase (Na24Si136), and the large silicon hexakaidecahedral cages (@Si28) are occupied by two sodium atoms disordered in the two 32e sites around the center of the @Si28 cages. At temperatures <90 K, the crystal symmetry of the compound changes from the face-centered to the primitive cell with space group P213, and the Na atoms in the @Si28 cages are aligned as Na2 pairs. The temperature dependence of the magnetic susceptibility of Na30.5Si136 suggests that the two Na ions (2 Na(+)) in the cage are changed to a Na2 molecule. The Na atoms of Na30.5Si136 can be deintercalated from the cages topochemically by evacuation at elevated temperatures. The single crystal study of the deintercalated phases NaxSi136 (x = 25.5 and 5.5) revealed that only excess Na atoms have disordered arrangements.

  12. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

    Yu, Yi; Cui, Fan; Sun, Jianwei; Yang, Peidong

    2016-05-11

    Understanding of the atomic structure and stability of nanowires (NWs) is critical for their applications in nanotechnology, especially when the diameter of NWs reduces to ultrathin scale (1-2 nm). Here, using aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM), we report a detailed atomic structure study of the ultrathin Au NWs, which are synthesized using a silane-mediated approach. The NWs contain large amounts of generalized stacking fault defects. These defects evolve upon sustained electron exposure, and simultaneously the NWs undergo necking and breaking. Quantitative strain analysis reveals the key role of strain in the breakdown process. Besides, ligand-like morphology is observed at the surface of the NWs, indicating the possibility of using AC-HRTEM for surface ligand imaging. Moreover, the coalescence dynamic of ultrathin Au NWs is demonstrated by in situ observations. This work provides a comprehensive understanding of the structure of ultrathin metal NWs at atomic-scale and could have important implications for their applications.

  13. Single molecule imaging of RNA polymerase II using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Rhodin, Thor; Fu, Jianhua; Umemura, Kazuo; Gad, Mohammed; Jarvis, Suzi; Ishikawa, Mitsuru

    2003-03-01

    An atomic force microscopy (AFM) study of the shape, orientation and surface topology of RNA polymerase II supported on silanized freshly cleaved mica was made. The overall aim is to define the molecular topology of RNA polymerase II in appropriate fluids to help clarify the relationship of conformational features to biofunctionality. A Nanoscope III atomic force microscope was used in the tapping mode with oxide-sharpened (8-10 nm) Si 3N 4 probes in aqueous zinc chloride buffer. The main structural features observed by AFM were compared to those derived from electron-density plots based on X-ray crystallographic studies. The conformational features included a bilobal silhouette with an inverted umbrella-shaped crater connected to a reaction site. These studies provide a starting point for constructing a 3D-AFM profiling analysis of proteins such as RNA polymerase complexes.

  14. Hyperfine structure measurement of 87Rb atoms injected into superfluid helium as highly energetic ion beam

    NASA Astrophysics Data System (ADS)

    Imamura, Kei; Furukawa, Takeshi; Yang, Xiaofei; Fujita, Tomomi; Wakui, Takashi; Mitsuya, Yousuke; Hayasaka, Miki; Ichikawa, Yuichi; Hatakeyama, Atsushi; Kobayashi, Tohru; Odashima, Hitoshi; Ueno, Hideki; Matsuo, Yukari; Orochi Collaboration

    2014-09-01

    We have developed a new nuclear laser spectroscopy technique that is called OROCHI (Optical RI-atoms Observation in Condensed Helium as Ioncatcher). In OROCHI, highly energetic ion beam is injected into superfluid helium (He II) and is trapped as atoms. Hyperfine structure (HFS) and Zeeman splitting of trapped atoms is measured using laser-microwave (MW)/radiofrequency (RF) double resonance method. We deduce nuclear moments and spin values from the measured splittings, respectively So far, we measured Zeeman splitting of 84-87Rb atoms To evaluate the validity of the OROCHI method, it is necessary to investigate the following two points not only for Zeeman but also for HFS splitings. (i) What is the accuracy in frequency in our measurement? (ii) How high beam intensity is necessary to observe resonance spectra? For this purpose we conducted online experiment using 87Rb beam and measured the HFS splitting of injected 87Rb atoms in He II.

  15. Atomic Structure and Valence: Level II, Unit 10, Lesson 1; Chemical Bonding: Lesson 2; The Table of Elements: Lesson 3; Electrolysis: Lesson 4. Advanced General Education Program. A High School Self-Study Program.

    ERIC Educational Resources Information Center

    Manpower Administration (DOL), Washington, DC. Job Corps.

    This self-study program for high-school level contains lessons on: Atomic Structure and Valence, Chemical Bonding, The Table of Elements, and Electrolysis. Each of the lessons concludes with a Mastery Test to be completed by the student. (DB)

  16. Atomic Structure and Dynamics in Debye Plasmas

    SciTech Connect

    Liu, L.; Qi, Y. Y.; Wang, J. G.; Janev, R. K.

    2009-05-02

    Atomic structure and dynamics in Debye plasmas are investigated by a series of methods including the classical, semi-classical and quantum-mechanical ones. It's found that both the binding energies and number of bound states are reduced, and the wave functions become broaden due to the plasma screening interactions. Taking into account the Coulomb screening on the energy levels, wave functions and interactions, we have studied the photo processes, electron-impact processes and heavy particle collisions in a large plasma screening conditions. Our works demonstrated that the screening effect is important in the Debye plasmas, which should be considered in the simulation and diagnostics of plasmas.

  17. Crystal structure and encapsulation dynamics of ice II-structured neon hydrate.

    PubMed

    Yu, Xiaohui; Zhu, Jinlong; Du, Shiyu; Xu, Hongwu; Vogel, Sven C; Han, Jiantao; Germann, Timothy C; Zhang, Jianzhong; Jin, Changqing; Francisco, Joseph S; Zhao, Yusheng

    2014-07-22

    Neon hydrate was synthesized and studied by in situ neutron diffraction at 480 MPa and temperatures ranging from 260 to 70 K. For the first time to our knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II-structured hydrates. The guest Ne atoms occupy the centers of D2O channels and have substantial freedom of movement owing to the lack of direct bonding between guest molecules and host lattices. Molecular dynamics simulation confirms that the resolved structure where Ne dissolved in ice II is thermodynamically stable at 480 MPa and 260 K. The density distributions indicate that the vibration of Ne atoms is mainly in planes perpendicular to D2O channels, whereas their distributions along the channels are further constrained by interactions between adjacent Ne atoms.

  18. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    SciTech Connect

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  19. Crystal structures of copper(II) nitrate, copper(II) chloride, and copper(II) perchlorate complexes with 2-formylpyridine semicarbazone

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Antosyak, B. Ya.; Bairac, N. N.; Simonov, Yu. A.; Bocelli, G.; Pahontu, E.; Gulea, A. P.

    2009-05-15

    Compounds dinitrato(2-formylpyridinesemicarbazone)copper (I), dichloro(2-formylpyridinesemicarbazone) copper hemihydrate (II), and bis(2-formylpyridinesemicarbazone)copper(2+) perchlorate hydrate (III) are synthesized and their crystal structures are determined. In compounds I-III, the neutral 2-formylpyridine semicarbazone molecule (L) is tridentately attached to the copper atom via the N,N,O set of donor atoms. In compounds I and II, the Cu: L ratio is equal to 1: 1, whereas, in III, it is 1: 2. In complex I, the coordination sphere of the copper atom includes two nitrate ions with different structural functions in addition to the L ligand. The structure is built as a one-dimensional polymer in which the NO{sub 3} bidentate group fulfills a bridging function. The coordination polyhedron of the copper(2+) atom can be considered a distorted tetragonal bipyramid (4 + 1 + 1). Compound II has an ionic structure in which the main element is the [CuLCl{sub 2} . Cu(H{sub 2}O)LCl]{sup +} dimer. In the dimer, the copper atoms are linked via one of the {mu}{sub 2}-bridging chlorine atoms. The coordination polyhedra of the central atoms of the Cu(H{sub 2})LCl and CuLCl{sub 2} complex fragments are tetragonal bipyramid and tetragonal pyramid, respectively. In compound III, the copper atom is octahedrally surrounded by two L ligands in the mer configuration.

  20. Evolution of atomic structure during nanoparticle formation

    PubMed Central

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; Christensen, Mogens; Bøjesen, Espen D.; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J. L.; Iversen, Bo B.

    2014-01-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  1. Evolution of atomic structure during nanoparticle formation

    DOE PAGES

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

    2014-04-14

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structuremore » is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.« less

  2. Structural and electronic properties for atomic clusters

    NASA Astrophysics Data System (ADS)

    Sun, Yan

    We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

  3. I. Atomic Effects in Tritium Beta-Decay II. Muon to Electron Conversion in Atoms.

    NASA Astrophysics Data System (ADS)

    Wampler, Kevin Dean

    I. The final-state, atomic effects in the low energy end of the tritium beta decay spectrum are studied in detail. I treat the instantaneous, two-electron repulsion in the final state, effectively to all orders in perturbation theory, by solving the eigenvalue problem with a discretized and truncated form of the Hamiltonian. I find that these effects fail to explain the distortion in the spectrum observed by Simpson (Phys. Rev. Lett. 54, 649 (1985)). Simpson attributed this distortion to the admixture of a heavy mass antineutrino in the outgoing electron antineutrino state. In fact, the final-state Coulomb effects enhance the distortion. This calculation clears up some of the ambiguities of other theoretical analyses based on considerations of screening functions and perturbation theory. II. I present a phenomenological study of separate lepton number violating muon to electron conversion in atoms. Previous work on this process has concentrated on elastic transitions where the nucleus remains in the ground state. I present an analysis of the branching ratios of inelastic to elastic transitions. This analysis uses realistic muon wavefunctions and electron plane waves. A multipole analysis is used for the nuclear matrix elements. The particular case of ^{32}S is studied in detail. It is found that, if anomalous muon capture occurs, the coherent (ground-state to ground-state) transition dominates the rate, if this transition is allowed by the coupling constants. However, incoherent (excited state) transitions could be significant in some cases, particularly if coupling to the nuclear pseudo-scalar current occurs, and would permit one to obtain stringent limits on the corresponding couplings that mediate muon number violation.

  4. Cobalt(II), nickel(II) and copper(II) complexes of a hexadentate pyridine amide ligand. Effect of donor atom (ether vs. thioether) on coordination geometry, spin-state of cobalt and M(III)-M(II) redox potential.

    PubMed

    Pandey, Sharmila; Das, Partha Pratim; Singh, Akhilesh Kumar; Mukherjee, Rabindranath

    2011-10-28

    Using an acyclic hexadentate pyridine amide ligand, containing a -OCH(2)CH(2)O- spacer between two pyridine-2-carboxamide units (1,4-bis[o-(pyrydine-2-carboxamidophenyl)]-1,4-dioxabutane (H(2)L(9)), in its deprotonated form), four new complexes, [Co(II)(L(9))] (1) and its one-electron oxidized counterpart [Co(III)(L(9))][NO(3)]·2H(2)O (2), [Ni(II)(L(9))] (3) and [Cu(II)(L(9))] (4), have been synthesized. Structural analyses revealed that the Co(II) centre in 1 and the Ni(II) centre in 3 are six-coordinate, utilizing all the available donor sites and the Cu(II) centre in 4 is effectively five-coordinated (one of the ether O atoms does not participate in coordination). The structural parameters associated with the change in the metal coordination environment have been compared with corresponding complexes of thioether-containing hexadentate ligands. The μ(eff) values at 298 K of 1-4 correspond to S = 3/2, S = 0, S = 1 and S = 1/2, respectively. Absorption spectra for all the complexes have been investigated. EPR spectral properties of the copper(II) complex 4 have been investigated, simulated and analyzed. Cyclic voltammetric experiments in CH(2)Cl(2) reveal quasireversible Co(III)-Co(II), Ni(III)-Ni(II) and Cu(II)-Cu(I) redox processes. In going from ether O to thioether S coordination, the effect of the metal coordination environment on the redox potential values of Co(III)-Co(II) (here the effect of spin-state as well), Ni(III)-Ni(II) and Cu(II)-Cu(I) processes have been systematically analyzed.

  5. Synthesis, structural characterization, thermal and electrochemical studies of Mn(II), Co(II), Ni(II) and Cu(II) complexes containing thiazolylazo ligands

    NASA Astrophysics Data System (ADS)

    Chavan, S. S.; Sawant, V. A.

    2010-02-01

    Some thiazolylazo derivatives and their metal complexes of the type [M(L)(H 2O)Cl]; M = Mn(II), Co(II), Ni(II), Cu(II) and L = 6-(2'-thiazolylazo)-2-mercapto-quinazolin-4-one (HL 1), 6-(4'-phenyl-2'-thiazolylazo)-2-mercapto-quinazolin-4-one (HL 2), 6-(2'-thiazolylazo)-2-mercapto-3-( m-tolyl)-quinazolin-4-one (HL 3) and 6-(4'-phenyl-2'-thiazolylazo)-2-mercapto-3-( m-tolyl)-quinazolin-4-one (HL 4) have been prepared. All the complexes were characterized on the basis of elemental analysis, molar conductance, magnetic moment, IR, UV-vis, ESR, TG-DTA and powder X-ray diffraction studies. IR spectra of these complexes reveal that the complex formation occurred through thiazole nitrogen, azo nitrogen, imino nitrogen and sulfur atom of the ligands. On the basis of electronic spectral data and magnetic susceptibility measurement octahedral geometry has been proposed for the Mn(II), Co(II) and Ni(II) complexes and distorted octahedral geometry for the Cu(II) complexes. Electrochemical behavior of Ni(II) complexes exhibit quasireversible oxidation corresponding to Ni(III)/Ni(II) couple along with ligand reduction. X-ray diffraction study is used to elucidate the crystal structure of the complexes.

  6. Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

    ERIC Educational Resources Information Center

    Cipolla, Laura; Ferrari, Lia A.

    2016-01-01

    A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

  7. Type-II Weyl points in three-dimensional cold-atom optical lattices

    NASA Astrophysics Data System (ADS)

    Xu, Yong; Duan, L.-M.

    2016-11-01

    Topological Lifshitz phase transition characterizes an abrupt change of the topology of the Fermi surface through a continuous deformation of parameters. Recently, Lifshitz transition has been predicted to separate two types of Weyl points: type-I and type-II (or called structured Weyl points), which has attracted considerable attention in various fields. Although recent experimental investigation has seen a rapid progress on type-II Weyl points, it still remains a significant challenge to observe their characteristic Lifshitz transition. Here, we propose a scheme to realize both type-I and type-II Weyl points in three-dimensional ultracold atomic gases by introducing an experimentally feasible configuration based on current spin-orbit coupling technology. In the resultant Hamiltonian, we find three degenerate points: two Weyl points carrying a Chern number -1 and a fourfold degenerate point carrying a Chern number 2. Remarkably, by continuous tuning of a convenient experimental knob, all these degenerate points can transition from type-I to type-II, thereby providing an ideal platform to study different types of Weyl points and directly probe their Lifshitz phase transition.

  8. Muonic Atoms and the Nuclear Structure

    NASA Astrophysics Data System (ADS)

    Antognini, A.

    High-precision laser spectroscopy of atomic energy levels enables the measurement of nuclear properties. Sensitivity to these properties is particularly enhanced in muonic atoms which are bound systems of a muon and a nucleus. Exemplary is the measurement of the proton charge radius from muonic hydrogen performed by the CREMA collaboration which resulted in an order of magnitude more precise charge radius as extracted from other methods but at a variance of 7 standard deviations. Here, we summarize the role of muonic atoms for the extraction of nuclear charge radii, we present the status of the so called "proton charge radius puzzle", and we sketch how muonic atoms can be used to infer also the magnetic nuclear radii, demonstrating again an interesting interplay between atomic and particle/nuclear physics.

  9. RNA polymerase II transcription: structure and mechanism.

    PubMed

    Liu, Xin; Bushnell, David A; Kornberg, Roger D

    2013-01-01

    A minimal RNA polymerase II (pol II) transcription system comprises the polymerase and five general transcription factors (GTFs) TFIIB, -D, -E, -F, and -H. The addition of Mediator enables a response to regulatory factors. The GTFs are required for promoter recognition and the initiation of transcription. Following initiation, pol II alone is capable of RNA transcript elongation and of proofreading. Structural studies reviewed here reveal roles of GTFs in the initiation process and shed light on the transcription elongation mechanism. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.

  10. Synthesis and crystal structure of thiosemicarbazide complexes of nickel(II) and copper(II)

    NASA Astrophysics Data System (ADS)

    Sadikov, G. G.; Antsyshkina, A. S.; Koksharova, T. V.; Sergienko, V. S.; Kurando, S. V.; Gritsenko, I. S.

    2012-07-01

    Thiosemicarbazide complexes of nickel(II) [Ni( TSC)2](H Sal)2 ( I) and copper(II) [Cu( TSC)2](H Sal)2 ( Ia) ( TSC is thiosemicarbazide and H Sal is a salycilate anion), as well as complexes [Ni( TSC)2](SO4) · 2H2O ( II) and [Ni( TSC)3]Cl2 · H2O ( III), are synthesized and characterized by IR spectroscopy and X-ray diffraction. Monoclinic crystals I and Ia are isostructural; space group P21/ n, Z = 2. Crystals II are monoclinic, space group P21/ m, Z = 2. Crystals III are orthorhombic, space group Pbca, Z = 8. In I and Ia, two planar salycilate anions sandwich a planar centrosymmetric [Ni( TSC)2]2+ cation to form a supermolecule. The cation and anions are additionally bound by hydrogen bonds. Other hydrogen bonds connect supermolecules into planar layers. In structure II, centrosymmetric [Ni( TSC)2]2+ cations are connected by π-stacking interactions into supramolecular ensembles of a specific type. The ensembles, water molecules, and (SO4)2- anions are bound in the crystal via hydrogen bonds. In the [Ni( TSC)3]2+ cation of structure III, ligands coordinate the Ni atom by the bidentate chelate pattern with the formation of five-membered metallocycles. These metallocycles have an envelope conformation unlike those in I and II, which are planar. In III (unlike in analogous complexes), a meridional isomer of the coordination octahedron of the Ni atom is formed. Together with Cl1- and Cl2- anions, cations form supermolecules, which are packed into planar layers with a square-cellular structure. The layers are linked by hydrogen bonds formed by crystallization water molecules that are located between the layers.

  11. A Variational Monte Carlo Approach to Atomic Structure

    ERIC Educational Resources Information Center

    Davis, Stephen L.

    2007-01-01

    The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

  12. Role Playing: The Atomic Bomb and the End of World War II

    ERIC Educational Resources Information Center

    Eggleston, Noel C.

    1978-01-01

    Describes how a role playing exercise can be used to teach students in a college level history course about the use of the atomic bomb in World War II. Information is presented on general use of role playing in history courses, objectives, questions to consider about use of the atomic bomb, and course evaluation. For journal availability, see so…

  13. The Last Act: The Atomic Bomb and the End of World War II.

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC. National Air And Space Museum.

    This text was to have been the script for the National Air and Space Museum's exhibition of the Enola Gay, focusing on the end of World War II and the decision of the United States to use of the atomic bomb. The Enola Gay was a B-29 aircraft that carried the atomic bomb dropped on Hiroshima, Japan, on August 6, 1945. The atomic bomb brought a…

  14. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

    Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

  15. A new chelating resin for preconcentration and determination of Mn(II), Ni(II), Cu(II), Zn(II), Cd(II), and Pb(II) by flame atomic absorption spectrometry.

    PubMed

    Maheswari, Mohan A; Subramanian, Mandakolathur S

    2003-01-01

    A new polychelatogen, AXAD-16-1,2-diphenylethanolamine, was developed by chemically modifying Amberlite XAD-16 with 1,2-diphenylethanolamine to produce an effective metal-chelating functionality for the preconcentration of Mn(II), Ni(II), Cu(II), Zn(II), Cd(II), and Pb(II) and their determination by flame atomic absorption spectrometry. Various physiochemical parameters that influence the quantitative preconcentration and recovery of metal were optimized by both static and dynamic techniques. The resin showed superior extraction efficiency with high-metal loading capacity values of 0.73, 0.80, 0.77, 0.87, 0.74, and 0.81 mmol/g for Mn(II), Ni(II), Cu(II), Zn(II), Cd(II), and Pb(II), respectively. The system also showed rapid metal-ion extraction and stripping, with complete saturation in the sorbent phase within 15 min for all the metal ions. The optimum condition for effective metal-ion extraction was found to be a neutral pH, which is a great advantage in the preconcentration of trace metal ions from natural water samples without any chemical pretreatment of the sample. The resin also demonstrated exclusive ion selectivity toward targeted metal ions by showing greater resistivity to various complexing species and more common metal ions during analyte concentration, which ultimately led to high preconcentration factors of 700 for Cu(II); 600 for Mn(II), Ni(II), and Zn(II); and 500 for Cd(II) and Pb(II), arising from a larger sample breakthrough volume. The lower limits of metal-ion detection were 7 ng/mL for Mn(II) and Ni(II); 5 ng/mL for Cu(II), Zn(II), and Cd(II), and 10 ng/mL for Pb(II). The developed resin was successful in preconcentrating metal ions from synthetic and real water samples, multivitamin-multimineral tablets, and curry leaves (Murraya koenigii) with relative standard deviations of < or = 3.0% for all analytical measurements, which demonstrated its practical utility.

  16. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    USGS Publications Warehouse

    Dowty, Eric; Clark, J.R.

    1972-01-01

    New crystal-structure refinements of Pca21 boracite, Mg3ClB7O13, and R??{lunate}c ericaite, Fe2.4Mg0.6ClB7O13, show that some boron and oxygen atoms are involved in the 'ferro' transitions as well as the metal and halogen atoms. The atomic displacements associated with the polarity changes are as large as 0.6A??. ?? 1972.

  17. Kinetic-energy density functional: Atoms and shell structure

    SciTech Connect

    Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |

    1996-09-01

    We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. {copyright} {ital 1996 The American Physical Society.}

  18. Algebraic direct methods for few-atoms structure models.

    PubMed

    Hauptman, Herbert A; Guo, D Y; Xu, Hongliang; Blessing, Robert H

    2002-07-01

    As a basis for direct-methods phasing at very low resolution for macromolecular crystal structures, normalized structure-factor algebra is presented for few-atoms structure models with N = 1, 2, 3, em leader equal atoms or polyatomic globs per unit cell. Main results include: [see text]. Triplet discriminant Delta(hk) and triplet weight W(hk) parameters, a approximately 4.0 and b approximately 3.0, respectively, were determined empirically in numerical error analyses. Tests with phases calculated for few-atoms 'super-glob' models of the protein apo-D-glyceraldehyde-3-phosphate dehydrogenase (approximately 10000 non-H atoms) showed that low-resolution phases from the new few-atoms tangent formula were much better than conventional tangent formula phases for N = 2 and 3; phases from the two formulae were essentially the same for N > or = 4.

  19. Atomic Structure of Au329(SR)84 Faradaurate Plasmonic Nanomolecules

    DOE PAGES

    Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; ...

    2015-04-03

    To design novel nanomaterials, it is important to precisely control the composition, determine the atomic structure, and manipulate the structure to tune the materials property. Here we present a comprehensive characterization of the material whose composition is Au329(SR)84 precisely, therefore referred to as a nanomolecule. The size homogeneity was shown by electron microscopy, solution X-ray scattering, and mass spectrometry. We proposed its atomic structure to contain the Au260 core using experiments and modeling of a total-scattering-based atomic-pair distribution functional analysis. HAADF-STEM images shows fcc-like 2.0 ± 0.1 nm diameter nanomolecules.

  20. HERSCHEL GALACTIC PLANE SURVEY OF [N ii] FINE STRUCTURE EMISSION

    SciTech Connect

    Goldsmith, Paul F.; Yıldız, Umut A.; Langer, William D.; Pineda, Jorge L.

    2015-12-01

    We present the first large-scale high angular resolution survey of ionized nitrogen in the Galactic Plane through emission of its two fine structure transitions ([N ii]) at 122 and 205 μm. The observations were largely obtained with the PACS instrument onboard the Herschel Space Observatory. The lines of sight were in the Galactic plane, following those of the Herschel OTKP project GOT C+. Both lines are reliably detected at the 10{sup −8}–10{sup −7} Wm{sup −2} sr{sup −1} level over the range –60° ≤ l ≤ 60°. The rms of the intensity among the 25 PACS spaxels of a given pointing is typically less than one third of the mean intensity, showing that the emission is extended. [N ii] is produced in gas in which hydrogen is ionized, and collisional excitation is by electrons. The ratio of the two fine structure transitions provides a direct measurement of the electron density, yielding n(e) largely in the range 10–50 cm{sup −3} with an average value of 29 cm{sup −3} and N{sup +} column densities 10{sup 16}–10{sup 17} cm{sup −2}. [N ii] emission is highly correlated with that of [C ii], and we calculate that between 1/3 and 1/2 of the [C ii] emission is associated with the ionized gas. The relatively high electron densities indicate that the source of the [N ii] emission is not the warm ionized medium (WIM), which has electron densities more than 100 times smaller. Possible origins of the observed [N ii] include the ionized surfaces of dense atomic and molecular clouds, the extended low-density envelopes of H ii regions, and low-filling factor high-density fluctuations of the WIM.

  1. Structures of 38-atom gold-platinum nanoalloy clusters

    SciTech Connect

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

  2. Presentation of Atomic Structure in Turkish General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Costu, Bayram

    2009-01-01

    Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general chemistry textbooks published in Turkey based on the eight criteria developed in previous research. Criteria used referred to the atomic models of…

  3. Quasiperiodic structures via atom-optical nanofabrication

    NASA Astrophysics Data System (ADS)

    Jurdik, E.; Myszkiewicz, G.; Hohlfeld, J.; Tsukamoto, A.; Toonen, A. J.; van Etteger, A. F.; Gerritsen, J.; Hermsen, J.; Goldbach-Aschemann, S.; Meerts, W. L.; van Kempen, H.; Rasing, Th.

    2004-05-01

    We deposit a laser-collimated chromium beam onto a substrate through a quasiperiodic laser standing-wave (SW) tuned above the atomic resonance at the 52Cr transition 7S3→7Po4 at 425.55 nm. This SW is created by interference of five laser beams crossing in one point at mutual angles of 72°. The resulting chromium pattern on the substrate surface mimics the geometry of the SW and it is thus itself quasiperiodic. On a surface area of 0.2×0.2 mm2 the spatial Fourier spectrum of the measured patterns is decagonal. Besides being of fundamental interest, this quasiperiodic nanofabrication via atom optics can find its applications in photonics.

  4. A Jigsaw Classroom - Illustrated by the Teaching of Atomic Structure.

    ERIC Educational Resources Information Center

    Eilks, Ingo; Leerhoff, Gabriele

    2001-01-01

    Discusses an approach to teaching the structure of atoms using a teaching technique referred to as a jigsaw classroom. Reports that the jigsaw classroom involves arranging students in various types of groups for cooperative learning. (Author/MM)

  5. Update on nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Hernandez, Oscar Javier; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia; Barnea, Nir

    2016-12-01

    We present calculations of the nuclear structure corrections to the Lamb shift in light muonic atoms, using state-of-the-art nuclear potentials. We outline updated results on finite nucleon size contributions.

  6. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Jeanneau, E.; Bairac, N. N.; Bocelli, G.; Poirier, D.; Roy, J.; Gulea, A. P.

    2008-09-15

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate (I), bromo-(2-formylpyridinethiosemicarbazono)copper (II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate (III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I-III at a concentration of 10{sup -5} mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  7. Atomic structure of graphene on SiO2.

    PubMed

    Ishigami, Masa; Chen, J H; Cullen, W G; Fuhrer, M S; Williams, E D

    2007-06-01

    We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.

  8. GRASP2K: Relativistic Atomic Structure Package

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; Gaigalas, G.; Bieroń, J.; Fischer, C. Froese; Grant, I. P.

    2016-11-01

    GRASP2K is a revised and greatly expanded version of GRASP (ascl:1609.008) and is adapted for 64-bit computer architecture. It includes new angular libraries, can transform from jj- to LSJ-coupling, and coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. GRASP2K identifies each atomic state by the total energy and a label for the configuration state function with the largest expansion coefficient in LSJLSJ intermediate coupling.

  9. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    NASA Astrophysics Data System (ADS)

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene; Martinazzo, Rocco

    2015-09-01

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (˜0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  10. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    SciTech Connect

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene

    2015-09-28

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  11. Quantum dynamics of hydrogen atoms on graphene. II. Sticking.

    PubMed

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

    2015-09-28

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  12. Relating Dynamic Properties to Atomic Structure in Metallic Glasses

    SciTech Connect

    Sheng, H.W.; Ma, E.; Kramer, Matthew J.

    2012-07-18

    Atomic packing in metallic glasses is not completely random but displays various degrees of structural ordering. While it is believed that local structures profoundly affect the properties of glasses, a fundamental understanding of the structure–property relationship has been lacking. In this article, we provide a microscopic picture to uncover the intricate interplay between structural defects and dynamic properties of metallic glasses, from the perspective of computational modeling. Computational methodologies for such realistic modeling are introduced. Exploiting the concept of quasi-equivalent cluster packing, we quantify the structural ordering of a prototype metallic glass during its formation process, with a new focus on geometric measures of subatomic “voids.” Atomic sites connected with the voids are found to be crucial in terms of understanding the dynamic, including vibrational and atomic transport, properties. Normal mode analysis is performed to reveal the structural origin of the anomalous boson peak (BP) in the vibration spectrum of the glass, and its correlation with atomic packing cavities. Through transition-state search on the energy landscape of the system, such structural disorder is found to be a facilitating factor for atomic diffusion, with diffusion energy barriers and diffusion pathways significantly varying with the degree of structural relaxation/ordering. The implications of structural defects for the mechanical properties of metallic glasses are also discussed.

  13. Structures and energetics for O2 formation in photosystem II.

    PubMed

    Siegbahn, Per E M

    2009-12-21

    Water oxidation, forming O(2) from water and sunlight, is a fundamental process for life on earth. In nature, the enzyme photosystem II (PSII) catalyzes this reaction. The oxygen evolving complex (OEC), the complex within PSII that catalyzes the actual formation of the O-O bond, contains four manganese atoms and one calcium atom connected by oxo bonds. Seven amino acid side chains in the structure, mostly carboxylates, are ligated to the metal atoms. In the study of many enzyme mechanisms, theoretical modeling using density functional theory has served as an indispensable tool. This Account summarizes theoretical research to elucidate the mechanism for water oxidation in photosynthesis, including the most recent findings. The development of successively larger models, ranging from 50 atoms in the active site up to the present model size of 170 atoms, has revealed the mechanism of O(2) formation with increasing detail. The X-ray crystal structures of PSII have provided a framework for optimizing the theoretical models. By constraint of the backbone atoms to be at the same positions as those in the X-ray structures, the theoretical structures are in good agreement with both the measured electron density and extended X-ray absorption fine structure (EXAFS) interpretations. By following the structural and energetic changes in those structures through the different steps in the catalytic process, we have modeled the oxidation of the catalytic complex, the binding of the two substrate water molecules, and the subsequent deprotonations of those substrate molecules. In these models, the OEC forms a basin into which the water molecules naturally fit. These findings demonstrate that the binding of the second water molecule causes a reconstruction, results that are consistent with earlier EXAFS measurements. Most importantly, this Account describes a low-barrier mechanism for formation of the O-O bond, involving an oxygen radical that reacts with a mu-oxo ligand of the OEC

  14. Toward the Atomic Structure of PrPSc.

    PubMed

    Rodriguez, Jose A; Jiang, Lin; Eisenberg, David S

    2017-01-17

    In this review, we detail our current knowledge of PrP(Sc) structure on the basis of structural and computational studies. We discuss the progress toward an atomic resolution description of PrP(Sc) and results from the broader field of amyloid studies that may further inform our knowledge of this structure. Moreover, we summarize work that investigates the role of PrP(Sc) structure in its toxicity, transmissibility, and species specificity. We look forward to an atomic model of PrP(Sc), which is expected to bring diagnostics and/or therapeutics to the field of prion disease.

  15. Understanding Atomic Structure: Is There a More Direct and Compelling Connection between Atomic Line Spectra and the Quantization of an Atom's Energy?

    ERIC Educational Resources Information Center

    Rittenhouse, Robert C.

    2015-01-01

    The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…

  16. Actinide electronic structure and atomic forces

    NASA Astrophysics Data System (ADS)

    Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

    2000-07-01

    We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

  17. Probing atomic structure and Majorana wavefunctions in mono-atomic Fe chains on superconducting Pb surface

    NASA Astrophysics Data System (ADS)

    Pawlak, Rémy; Kisiel, Marcin; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst

    2016-11-01

    Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localisation of MBSs is a key feature and is crucial for their future implementation as qubits. Here we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunnelling microscopy and atomic force microscopy. We demonstrate that the Fe chains are mono-atomic, structured in a linear manner and exhibit zero-bias conductance peaks at their ends, which we interpret as signature for a MBS. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localised at the chain ends (≲25 nm), with two localisation lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum-computing devices.

  18. Crystal structures of salicylideneguanylhydrazinium chloride and its copper(II) and cobalt(III) chloride complexes

    SciTech Connect

    Chumakov, Yu. M. Tsapkov, V. I.; Bocelli, G.; Antosyak, B. Ya.; Shova, S. G.; Gulea, A. P.

    2006-01-15

    The crystal structures of salicylideneguanylhydrazinium chloride hydrate hemiethanol solvate (I), salicylideneguanylhydrazinium trichloroaquacuprate(II) (II), and bis(salicylideneguanylhydrazino)cobalt(III) chloride trihydrate (III) are determined using X-ray diffraction. The structures of compounds I, II, and III are solved by direct methods and refined using the least-squares procedure in the anisotropic approximation for the non-hydrogen atoms to the final factors R = 0.0597, 0.0212, and 0.0283, respectively. In the structure of compound I, the monoprotonated molecules and chlorine ions linked by hydrogen bonds form layers aligned parallel to the (010) plane. In the structure of compound II, the salicylaldehyde guanylhydrazone cations and polymer chains consisting of trichloroaquacuprate(II) anions are joined by an extended three-dimensional network of hydrogen bonds. In the structure of compound III, the [Co(LH){sub 2}]{sup +} cations, chloride ions, and molecules of crystallization water are linked together by a similar network.

  19. A 4096 atom model of amorphous silicon: Structure and dynamics

    NASA Astrophysics Data System (ADS)

    Feldman, Joseph L.; Bickham, Scott R.; Davidson, Brian N.; Wooten, Frederick

    1997-03-01

    We present structural and lattice dynamical information for a 4096 atom model of amorphous silicon. The structural model was obtained, similarly to previously published smaller models, using periodic boundary conditions, the Wooten-Winer-Weaire bond-switching algorithm, and the Broughton-Li relaxation with respect to the Stillinger-Weber potential. The structure is dynamically stable and there is no evidence in the radial distribution function of medium range order. For examining this large model, we use a 1000 processor Connection Machine to compute all the eigenvalues and eigenvectors exactly. The phonon density of states and inverse participation ratio are compared with results for related 216, 432 and 1000-atom models.

  20. Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

    2016-10-01

    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

  1. Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

    DOE PAGES

    Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

    2016-10-25

    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

  2. Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

    SciTech Connect

    Zhang, S.; Nordlund, Kai; Djurabekova, Flyura; Zhang, Yanwen; Velisa, Gihan; Wang, T. S.

    2016-10-25

    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

  3. Smart structures for rotorcraft control (SSRC) II

    NASA Astrophysics Data System (ADS)

    Jacot, A. Dean; Dadone, Leo

    1998-06-01

    The Smart Structures for Rotor Control (SSRC) is a consortium under the Defense Advanced Research Projects Agency (DARPA) Smart Structures program. Phase I of the program was administered by the Air Force Office of Scientific Research, with Boeing Seattle as the consortium administrator, and MIT, PSU and Boeing Helicopters as the other principal consortium members. Phase II, renamed Smart Materials and Structures Demonstration Consortium (SMSDC), is a combination of the proposed Phase II efforts of SSRC and the Boeing MESA Smart Materials Actuated Rotor Technology (SMART) program. This paper summarizes the SSRC efforts, introduces the SMSDC program, and provides a framework for the relationships between specific SSRC technical papers in this conference. The SSRC objectives were to research smart structure methods to achieve reduced rotorcraft vibration, reduce acoustic noise, and increased performance. The SSRC program includes dynamic piezoelectric actuation of flaps on the rotor blades, distributed dynamic piezo actuation of the rotor twist, and quasi-steady rotor twist control using shape memory alloys. The objective of Phase II is then to fly a rotorcraft to demonstrate such a system.

  4. Saturation of Energy Levels in Analytical Atomic Fluorescence Spectrometry. II. Experimental.

    DTIC Science & Technology

    1981-01-30

    RESEARCH Contract N14-76-C-0838 Task Ao. NR 051-622 TECHNICAL REPORT NO. 34 SATURATION OF ENERGY LEVELS IN ANALYTICAL ATOMIC FLUORESCENCE SPECTROMETRY II...an assumption which is valid only if the daral o’l of 111, cxcilIatio n pulse is mucl ) longer than the fluorescence life- time of the tjaii!,ition

  5. Statistical thermodynamics and atomic structure of metallic glasses

    NASA Astrophysics Data System (ADS)

    Lass, Eric Andrew

    The purpose of this research is to develop an improved atomic scale understanding of the thermodynamic and kinetic behavior of a metallic glass. A realistic link between the macroscopic and atomic behavior of a metallic glass has not yet been achieved. The most widespread model describing the amorphous state, borrowed from the description of liquids, is the free volume model. It is primarily phenomenological, and does not explain the observed properties of a metallic glass in many aspects. This is because the idea of free volume in a metallic glass is fundamentally flawed in several respects. For example, unlike in the liquid phase, atomic mobility is limited in a glass, and requires thermal activation. Recently, structural models have been developed based on the idea of efficient atomic packing. While geometric these models successfully describe atomic structure, the underlying governing principles, thermodynamics, are mitigated or often neglected. The model described in this work takes advantage of the short-range atomic order inherent in metallic glasses. Developed around the central atoms model (CAM), it uses a statistical thermodynamic approach, and can more accurately describe the amorphous state on the atomic level. Each atom is considered to be surrounded by a "cage" of nearest-neighbors (NNs). In an ideal metallic glass, these cages are described by geometrically preferred configurations. The enthalpy of each possible NN cage is calculated from the energy of a cluster of two, three, or four atoms. The structure and thermodynamics of the metallic glass are dependent on the probability distributions of NN cages. Defects, termed bond deficiencies (BDs), are introduced into the model, and are analogous to vacancies in a crystalline material, except they occupy less volume, and cost less energy to create. These defects are considered to be thermodynamically stable, and provide the primary vehicle of atomic transport. CAM is applied to ideal and defect

  6. Wavelengths, energy levels and hyperfine structure of Mn II and Sc II.

    NASA Astrophysics Data System (ADS)

    Nave, Gillian; Pickering, Juliet C.; Townley-Smith, Keeley I. M.; Hala, .

    2015-08-01

    For many decades, the Atomic Spectroscopy Groups at the National Institute of Standards and Technology (NIST) and Imperial College London (ICL) have measured atomic data of astronomical interest. Our spectrometers include Fourier transform (FT) spectrometers at NIST and ICL covering the region 1350 Å to 5.5 μm and a 10.7-m grating spectrometer at NIST covering wavelengths from 300 - 5000 Å. Sources for these spectra include high-current continuous and pulsed hollow cathode (HCL) lamps, Penning discharges, and sliding spark discharges. Recent work has focused on the measurement and analysis of wavelengths, energy levels, and hyperfine structure (HFS) constants for iron-group elements. The analysis of FT spectra of Cr I, Mn I, and Mn II is being led by ICL and is described in a companion poster [1]. Current work being led by NIST includes the analysis of HFS in Mn II, analysis of Mn II in the vacuum ultraviolet, and a comprehensive analysis of Sc II.Comprehensive HFS constants for Mn II are needed for the interpretation of stellar spectra and incorrect abundances may be obtained when HFS is omitted. Holt et al. [2] have measured HFS constants for 59 levels of Mn II using laser spectroscopy. We used FT spectra of Mn/Ni and Mn/Cu HCLs covering wavelength ranges from 1350 Å to 5.4 μm to confirm 26 of the A constants of Holt et al. and obtain values for roughly 40 additional levels. We aim to obtain HFS constants for the majority of lines showing significant HFS that are observed in chemically-peculiar stars.Spectra of Sc HCLs have been recorded from 1800 - 6700 Å using a vacuum ultraviolet FT spectrometer at NIST. Additional measurements to cover wavelengths above 6700 Å and below 1800 Å are in progress. The spectra are being analyzed by NIST and Alighar Muslim University, India in order to derive improved wavelengths, energy levels, and hyperfine structure parameters.This work was partially supported by NASA, the STFC and PPARC (UK), the Royal Society of the UK

  7. Crystal structure solution from experimentally determined atomic pair distribution functions

    SciTech Connect

    Juhas, P.; Granlund, L.; Gujarathi, S.R.; Duxbury, P.M.; Billinge, S.J.L.

    2010-05-25

    An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

  8. ISOTROPIC INELASTIC COLLISIONS IN A MULTITERM ATOM WITH HYPERFINE STRUCTURE

    SciTech Connect

    Belluzzi, Luca; Landi Degl’Innocenti, Egidio; Bueno, Javier Trujillo

    2015-10-10

    A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron–atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D{sub 1} and D{sub 2} lines is presented.

  9. Isotropic Inelastic Collisions in a Multiterm Atom with Hyperfine Structure

    NASA Astrophysics Data System (ADS)

    Belluzzi, Luca; Landi Degl'Innocenti, Egidio; Trujillo Bueno, Javier

    2015-10-01

    A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron-atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D1 and D2 lines is presented.

  10. STRUCTURAL STUDIES ON A MITOCHONDRIAL GLYOXLASE II*

    PubMed Central

    Marasinghe, Gishanthi P. K.; Sander, Ian M.; Bennett, Brian; Periyannan, Gopalraj; Yang, Ke-Wu; Makaroff, Christopher A.; Crowder, Michael W.

    2005-01-01

    Glyoxalase 2 is a β-lactamase fold containing enzyme that appears to be involved with cellular chemical detoxification. Although the cytoplasmic isozyme has been characterized from several organisms, essentially nothing is known about the mitochondrial proteins. As a first step in understanding the structure and function of mitochondrial glyoxalase 2 enzymes, a mitochondrial isozyme (GLX2-5) from Arabidopsis thaliana was cloned, over-expressed, purified, and characterized using metal analyses, EPR and 1H NMR spectroscopies, and X-ray crystallography. The recombinant enzyme was shown to bind 1.04 ± 0.15 equivalents of iron, 1.31 ± 0.05 equivalents of Zn(II), and exhibit kcat and Km values of 129 ± 10 s−1 and 391 ± 48 μM, respectively, when using S-D-lactoylglutathione as the substrate. EPR spectra revealed that recombinant GLX2-5 contains multiple metal centers including a predominant Fe(III)Zn(II) center and an antiferromagnetically-coupled Fe(III)Fe(II) center. Unlike cytosolic glyoxalase 2 from A. thaliana, GLX2-5 does not appear to specifically bind manganese. 1H NMR spectra revealed the presence of at least 8 paramagnetically-shifted resonances that arise from protons in close proximity to a Fe(III)Fe(II) center. Five of these resonances arise from solvent exchangeable protons, and four of these have been assigned to NH protons on metal bound histidines. A 1.74 Å resolution crystal structure of the enzyme revealed that GLX2-5 is a dimeric protein with a metal center that is similar to that of human GLX2. These data demonstrate that mitochondrial glyoxalase 2 can accommodate a number of different metal centers and that the predominant metal center is Fe(III)Zn(II). PMID:16227621

  11. Solid-phase extraction of Mn(II), Co(II), Ni(II), Cu(II), Cd(II) and Pb(II) ions from environmental samples by flame atomic absorption spectrometry (FAAS).

    PubMed

    Duran, Celal; Gundogdu, Ali; Bulut, Volkan Numan; Soylak, Mustafa; Elci, Latif; Sentürk, Hasan Basri; Tüfekci, Mehmet

    2007-07-19

    A new method using a column packed with Amberlite XAD-2010 resin as a solid-phase extractant has been developed for the multi-element preconcentration of Mn(II), Co(II), Ni(II), Cu(II), Cd(II), and Pb(II) ions based on their complex formation with the sodium diethyldithiocarbamate (Na-DDTC) prior to flame atomic absorption spectrometric (FAAS) determinations. Metal complexes sorbed on the resin were eluted by 1 mol L(-1) HNO3 in acetone. Effects of the analytical conditions over the preconcentration yields of the metal ions, such as pH, quantity of Na-DDTC, eluent type, sample volume and flow rate, foreign ions etc. have been investigated. The limits of detection (LOD) of the analytes were found in the range 0.08-0.26 microg L(-1). The method was validated by analyzing three certified reference materials. The method has been applied for the determination of trace elements in some environmental samples.

  12. Theoretical atomic physics code development I: CATS: Cowan Atomic Structure Code

    SciTech Connect

    Abdallah, J. Jr.; Clark, R.E.H.; Cowan, R.D.

    1988-12-01

    An adaptation of R.D. Cowan's Atomic Structure program, CATS, has been developed as part of the Theoretical Atomic Physics (TAPS) code development effort at Los Alamos. CATS has been designed to be easy to run and to produce data files that can interface with other programs easily. The CATS produced data files currently include wave functions, energy levels, oscillator strengths, plane-wave-Born electron-ion collision strengths, photoionization cross sections, and a variety of other quantities. This paper describes the use of CATS. 10 refs.

  13. Compound semiconductor alloys: From atomic-scale structure to bandgap bowing

    NASA Astrophysics Data System (ADS)

    Schnohr, C. S.

    2015-09-01

    Compound semiconductor alloys such as InxGa1-xAs, GaAsxP1-x, or CuInxGa1-xSe2 are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI2 chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family.

  14. Vortex-ring-fractal Structure of Atom and Molecule

    SciTech Connect

    Osmera, Pavel

    2010-06-17

    This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

  15. Atomic and electronic structure of Ni-Nb metallic glasses

    SciTech Connect

    Yuan, C. C.; Yang, Y.-F. Xi, X. K.

    2013-12-07

    Solid state {sup 93}Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. {sup 93}Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni{sub 60}Nb{sub 35}Sn{sub 5} has been found to be ∼100 ppm lower than that of Ni{sub 60}Nb{sub 35}Zr{sub 5} MG, which is correlated with their intrinsic fracture toughness. The evolution of {sup 93}Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.

  16. Atomic and electronic structure of twin growth defects in magnetite

    PubMed Central

    Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K.

    2016-01-01

    We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains. PMID:26876049

  17. Atomic and electronic structure of twin growth defects in magnetite

    NASA Astrophysics Data System (ADS)

    Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K.

    2016-02-01

    We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains.

  18. Atomic and electronic structure of twin growth defects in magnetite.

    PubMed

    Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K

    2016-02-15

    We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains.

  19. Crystal structure of the coordination polymer [Fe(III) 2{Pt(II)(CN)4}3].

    PubMed

    Seredyuk, Maksym; Muñoz, M Carmen; Real, José A; Iskenderov, Turganbay S

    2015-01-01

    The title complex, poly[dodeca-μ-cyanido-diiron(III)triplat-inum(II)], [Fe(III) 2{Pt(II)(CN)4}3], has a three-dimensional polymeric structure. It is built-up from square-planar [Pt(II)(CN)4](2-) anions (point group symmetry 2/m) bridging cationic [Fe(III)Pt(II)(CN)4](+) ∞ layers extending in the bc plane. The Fe(II) atoms of the layers are located on inversion centres and exhibit an octa-hedral coordination sphere defined by six N atoms of cyanide ligands, while the Pt(II) atoms are located on twofold rotation axes and are surrounded by four C atoms of the cyanide ligands in a square-planar coordination. The geometrical preferences of the two cations for octa-hedral and square-planar coordination, respectively, lead to a corrugated organisation of the layers. The distance between neighbouring [Fe(III)Pt(II)(CN)4](+) ∞ layers corresponds to the length a/2 = 8.0070 (3) Å, and the separation between two neighbouring Pt(II) atoms of the bridging [Pt(II)(CN)4](2-) groups corresponds to the length of the c axis [7.5720 (2) Å]. The structure is porous with accessible voids of 390 Å(3) per unit cell.

  20. Crystal structure of the coordination polymer [FeIII 2{PtII(CN)4}3

    PubMed Central

    Seredyuk, Maksym; Muñoz, M. Carmen; Real, José A.; Iskenderov, Turganbay S.

    2015-01-01

    The title complex, poly[dodeca-μ-cyanido-diiron(III)triplat­inum(II)], [FeIII 2{PtII(CN)4}3], has a three-dimensional polymeric structure. It is built-up from square-planar [PtII(CN)4]2− anions (point group symmetry 2/m) bridging cationic [FeIIIPtII(CN)4]+ ∞ layers extending in the bc plane. The FeII atoms of the layers are located on inversion centres and exhibit an octa­hedral coordination sphere defined by six N atoms of cyanide ligands, while the PtII atoms are located on twofold rotation axes and are surrounded by four C atoms of the cyanide ligands in a square-planar coordination. The geometrical preferences of the two cations for octa­hedral and square-planar coordination, respectively, lead to a corrugated organisation of the layers. The distance between neighbouring [FeIIIPtII(CN)4]+ ∞ layers corresponds to the length a/2 = 8.0070 (3) Å, and the separation between two neighbouring PtII atoms of the bridging [PtII(CN)4]2− groups corresponds to the length of the c axis [7.5720 (2) Å]. The structure is porous with accessible voids of 390 Å3 per unit cell. PMID:25705468

  1. Workshop on foundations of the relativistic theory of atomic structure

    SciTech Connect

    1981-03-01

    The conference is an attempt to gather state-of-the-art information to understand the theory of relativistic atomic structure beyond the framework of the original Dirac theory. Abstracts of twenty articles from the conference were prepared separately for the data base. (GHT)

  2. Nanoscale Structuring of Surfaces by Using Atomic Layer Deposition.

    PubMed

    Sobel, Nicolas; Hess, Christian

    2015-12-07

    Controlled structuring of surfaces is interesting for a wide variety of areas, including microelectronic device fabrication, optical devices, bio(sensing), (electro-, photo)catalysis, batteries, solar cells, fuel cells, and sorption. A unique feature of atomic layer deposition (ALD) is the possibility to form conformal uniform coatings on arbitrarily shaped materials with controlled atomic-scale thickness. In this Minireview, we discuss the potential of ALD for the nanoscale structuring of surfaces, highlighting its versatile application to structuring both planar substrates and powder materials. Recent progress in the application of ALD to porous substrates has even made the nanoscale structuring of high-surface-area materials now feasible, thereby enabling novel applications, such as those in the fields of catalysis and alternative energy.

  3. Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

    SciTech Connect

    Masuda, Tetsuya; Ohta, Keisuke; Tani, Fumito; Mikami, Bunzo; Kitabatake, Naofumi

    2011-07-08

    Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

  4. Determination of mercury(II) ion by electrochemical cold vapor generation atomic absorption spectrometry.

    PubMed

    Arbab-Zavar, M Hosein; Rounaghi, G Hosein; Chamsaz, Mahmoud; Masrournia, Mahboube

    2003-05-01

    A technique for determination of mercury is described; it is based on electrolytic reduction of Hg(II) ion on a graphite cathode, the trapping of mercury vapor and its volatilization into a quartz tube aligned in the optical path of an atomic absorption spectrometer. The electrochemical cell consisted of a graphite cathode and an anode operating with constant direct current for the production of mercury atoms. A pre-activated graphite rod was used as the cathode material. The optimum conditions for electrochemical generation of mercury cold vapor (the electrolysis time and current, the flow rate, the type of electrode and electrolyte) were investigated. The characteristic electrochemical data with chemical cold vapor using NaBH4-acid were compared. The presence of cadmium(II), arsenic(III), antimony(III), selenium(IV), bismuth(III), silver(I), lead(II), lithium(I), sodium(I) and potassium(I) showed interference effects which were eliminated by suitable separation techniques. The calibration curve is linear over the range of 5-90 ng ml(-1) mercury(II). The detection limit is 2 ng ml(-1) of Hg(II) and the RSD is 2.5% (n = 10) for 40 ng ml(-1). The accuracy and recovery of the method were investigated by analyzing spiked tap water and river water.

  5. Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

    USGS Publications Warehouse

    Rawn, C.J.; Rondinone, A.J.; Chakoumakos, B.C.; Circone, S.; Stern, L.A.; Kirby, S.H.; Ishii, Y.

    2003-01-01

    Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters.

  6. The shells of atomic structure in metallic glasses

    NASA Astrophysics Data System (ADS)

    Pan, S. P.; Feng, S. D.; Qiao, J. W.; Dong, B. S.; Qin, J. Y.

    2016-02-01

    We proposed a scheme to describe the spatial correlation between two atoms in metallic glasses. Pair distribution function in a model iron was fully decomposed into several shells and can be presented as the spread of nearest neighbor correlation via distance. Moreover, angle distribution function can also be decomposed into groups. We demonstrate that there is close correlation between pair distribution function and angle distribution function for metallic glasses. We think that our results are very helpful understanding the atomic structure of metallic glasses.

  7. Atomic Structure and Properties of Extended Defects in Silicon

    SciTech Connect

    Buczko, R.; Chisholm, M.F.; Kaplan, T.; Maiti, A.; Mostoller, M.; Pantelides, S.T.; Pennycook, S.J.

    1998-10-15

    The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

  8. Detailed Atomic Structure of Neutral and Near-Neutral Systems

    SciTech Connect

    Oliver, Paul; Hibbert, Alan

    2011-05-11

    This paper highlights the issues which need to be addressed in undertaking accurate calculations of multi-electron atoms and ions, particularly at or near the neutral end of an isoelectronic sequence. We illustrate the processes through two calculations--of transitions in Cl I and Sn II--and discuss the convergence of our results as well as updating previous work. In particular, in the case of Cl I, we propose new identifications of the levels involved in certain transitions which are important in determining the abundance of chlorine in the inter-stellar medium (ISM), while in singly ionised tin, our calculations suggest a re-evaluation of the the abundance of tin in the ISM. We also confirm recent identification of Sn II lines seen in tokamak plasmas.

  9. Low-temperature atomic layer deposition of copper(II) oxide thin films

    SciTech Connect

    Iivonen, Tomi Hämäläinen, Jani; Mattinen, Miika; Popov, Georgi; Leskelä, Markku; Marchand, Benoît; Mizohata, Kenichiro; Kim, Jiyeon; Fischer, Roland A.

    2016-01-15

    Copper(II) oxide thin films were grown by atomic layer deposition (ALD) using bis-(dimethylamino-2-propoxide)copper [Cu(dmap){sub 2}] and ozone in a temperature window of 80–140 °C. A thorough characterization of the films was performed using x-ray diffraction, x-ray reflectivity, UV‐Vis spectrophotometry, atomic force microscopy, field emission scanning electron microscopy, x-ray photoelectron spectroscopy, and time-of-flight elastic recoil detection analysis techniques. The process was found to produce polycrystalline copper(II) oxide films with a growth rate of 0.2–0.3 Å per cycle. Impurity content in the films was relatively small for a low temperature ALD process.

  10. Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory

    NASA Astrophysics Data System (ADS)

    Creaven, B. S.; Devereux, M.; Georgieva, I.; Karcz, D.; McCann, M.; Trendafilova, N.; Walsh, M.

    2011-12-01

    Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, 1H NMR, 13C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2) 2(H 2O) 2] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn 2(CCA2) 4(H 2O) 2] structure. Experimental and calculated 1H, 13C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.

  11. Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory.

    PubMed

    Creaven, B S; Devereux, M; Georgieva, I; Karcz, D; McCann, M; Trendafilova, N; Walsh, M

    2011-12-15

    Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2)(2)(H(2)O)(2)] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn(2)(CCA2)(4)(H(2)O)(2)] structure. Experimental and calculated (1)H, (13)C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.

  12. Atomic Data for Zn II: Improving Spectral Diagnostics of Chemical Evolution in High-redshift Galaxies

    NASA Astrophysics Data System (ADS)

    Kisielius, Romas; Kulkarni, Varsha P.; Ferland, Gary J.; Bogdanovich, Pavel; Som, Debopam; Lykins, Matt L.

    2015-05-01

    Damped Lyα (DLA) and sub-DLA absorbers in quasar spectra provide the most sensitive tools for measuring the element abundances of distant galaxies. The estimation of abundances from absorption lines depends sensitively on the accuracy of the atomic data used. We have started a project to produce new atomic spectroscopic parameters for optical and UV spectral lines using state-of-the-art computer codes employing a very broad configuration interaction (CI) basis. Here we report our results for Zn ii, an ion used widely in studies of the interstellar medium (ISM) as well as DLAs and sub-DLAs. We report new calculations of many energy levels of Zn ii and the line strengths of the resulting radiative transitions. Our calculations use the CI approach within a numerical Hartree-Fock framework. We use both nonrelativistic and quasi-relativistic one-electron radial orbitals. We have incorporated the results of these atomic calculations into the plasma simulation code Cloudy and applied them to a lab plasma and examples of a DLA and a sub-DLA. Our values of the Zn ii λ λ 2026, 2062 oscillator strengths are higher than previous values by 0.10 dex. The Cloudy calculations for representative absorbers with the revised Zn atomic data imply ionization corrections lower than calculated earlier by 0.05 dex. The new results imply that Zn metallicities should be lower by 0.1 dex for DLAs and by 0.13-0.15 dex for sub-DLAs than in past studies. Our results can be applied to other studies of Zn ii in the Galactic and extragalactic ISM.

  13. Energetics of atomic scale structure changes in graphene.

    PubMed

    Skowron, Stephen T; Lebedeva, Irina V; Popov, Andrey M; Bichoutskaia, Elena

    2015-05-21

    The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.

  14. Crystal and molecular structures of trichloro-cobalt(II) complexes of epiquinine, epiquinidine, and epidihydrocinchonine.

    PubMed

    Tesarowicz, Iwona; Oleksyn, Barbara J; Nitek, Wojciech

    2007-02-01

    Cinchona alkaloids are very well known antimalarials but the mechanism of their biological action still remains to be elucidated. The structural studies of active erythro and inactive threo alkaloid complexes are an important step to this aim. In this paper results of crystal structure analysis of three cobalt complexes of threo alkaloids are presented: (epiquininium)trichlorocobalt(II) (EpiQnCoCl3), (epiquinidinium)trichlorocobalt(II) (EpiQdCoCl3) and (epidihydrocinchoninium)trichlorocobalt(II) (EpiCnCoCl3). The complexes are zwitterions in which trichlorocobalt substituents are coordinated to quinoline nitrogen atoms and quinuclidine nitrogen atoms are protonated. EpiQnCoCl3 adopts uncommon conformation with quinoline moiety oriented in the opposite direction in comparison to the analogous uncomplexed alkaloid. The packing in the crystal structures is determined mainly by the hydrogen bonds, in which the chlorine atoms of substituents and solvent molecules contribute. Atoms participating in hydrogen bonds in EpiQnCoCl3 and EpiQdCoCl3 form large rings, while in EpiCnCoCl3 only chains are present. Solvent molecules are very important for the packing mode. In contrast to most erythro alkaloids, the hydroxyl oxygen atom in the title complexes forms weak or not well defined hydrogen bonds. The contribution of very weak intramolecular interactions N1--H1...O12 cannot be excluded. Such "trace" interactions can be considered a relic of the unprotonated status of an epi alkaloid.

  15. Concerning the structure of photobilirubin II.

    PubMed

    Stoll, M S; Vicker, N; Gray, C H; Bonnett, R

    1982-01-01

    Evidence is presented which supports the postulate that the photobilirubins IIA and IIB are diastereoisomers in which the C-3 vinyl group has cyclized intramolecularly. The evidence comes principally from proton n.m.r. spectroscopy at 400 MHz and from chemical considerations. The cyclic structures require the E-configuration at the C-4 double bond in the precursor; this is the first structural evidence for the Z leads to E isomerization in bilirubin and supports the view that the precursor (photobilirubin IA or IB) is (4E, 15Z)-bilirubin. Brief irradiation of photobilirubin II gives bilirubin, a new compound (photobilirubin III) and unchanged starting material. The various photoisomers are discussed in terms of their inter-relationships and biological fates.

  16. The AME2016 atomic mass evaluation (II). Tables, graphs and references

    NASA Astrophysics Data System (ADS)

    Wang, Meng; Audi, G.; Kondev, F. G.; Huang, W. J.; Naimi, S.; Xu, Xing

    2017-03-01

    This paper is the second part of the new evaluation of atomic masses, AME2016. Using least-squares adjustments to all evaluated and accepted experimental data, described in Part I, we derive tables with numerical values and graphs to replace those given in AME2012. The first table lists the recommended atomic mass values and their uncertainties. It is followed by a table of the influences of data on primary nuclides, a table of various reaction and decay energies, and finally, a series of graphs of separation and decay energies. The last section of this paper lists all references of the input data used in the AME2016 and the NUBASE2016 evaluations (first paper in this issue). AMDC: http://amdc.impcas.ac.cn/ Contents The AME2016 atomic mass evaluation (II). Tables, graphs and referencesAcrobat PDF (293 KB) Table I. The 2016 Atomic mass tableAcrobat PDF (273 KB) Table II. Influences on primary nuclidesAcrobat PDF (160 KB) Table III. Nuclear-reaction and separation energiesAcrobat PDF (517 KB) Graphs of separation and decay energiesAcrobat PDF (589 KB) References used in the AME2016 and the NUBASE2016 evaluationsAcrobat PDF (722 KB)

  17. Microtraps for neutral atoms using superconducting structures in the critical state

    SciTech Connect

    Emmert, A.; Brune, M.; Raimond, J.-M.; Nogues, G.; Lupascu, A.; Haroche, S.

    2009-12-15

    Recently demonstrated superconducting atom chips provide a platform for trapping atoms and coupling them to solid-state quantum systems. Controlling these devices requires a full understanding of the supercurrent distribution in the trapping structures. For type-II superconductors, this distribution is hysteretic in the critical state due to the partial penetration of the magnetic field in the thin superconducting film through pinned vortices. We report here an experimental observation of this memory effect. Our results are in good agreement with the predictions of the Bean model of the critical state without adjustable parameters. The memory effect allows to write and store permanent currents in micron-sized superconducting structures and paves the way toward engineered trapping potentials.

  18. Stable atomic structure of NiTi austenite

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2014-08-01

    Nitinol (NiTi), the most widely used shape-memory alloy, exhibits an austenite phase that has yet to be identified. The usually assumed austenitic structure is cubic B2, which has imaginary phonon modes, hence it is unstable. We suggest a stable austenitic structure that "on average" has B2 symmetry (observed by x-ray and neutron diffraction), but it exhibits finite atomic displacements from the ideal B2 sites. The proposed structure has a phonon spectrum that agrees with that from neutron scattering, has diffraction spectra in agreement with x-ray diffraction, and has an energy relative to the ground state that agrees with calorimetry data.

  19. Exploratory Study of RNA Polymerase II Using Dynamic Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Rhodin, Thor; Umemura, Kazuo; Gad, Mohammed; Jarvis, Suzanne; Ishikawa, Mitsuru; Fu, Jianhua

    2002-03-01

    An exploratory study of the microtopological dimensions and shape features of yeast RNA polymerase II (y-poly II) on freshly cleaved mica was made in phosphate aqueous buffer solution at room temperature following previous work by Hansma and others. The molecules were imaged by stabilization on freshly cleaved mica at a limiting resolution of 10 Å and scanned using dynamical atomic force microscopy with a 10 nm multi-wall carbon nanotube in the resonance frequency modulation mode. They indicated microtopological shape and dimensional features similar to those predicted by electron density plots derived from the X-ray crystallographic model. It is concluded that this is considered primarily a feasibility study with definitive conclusions subject to more detailed systematic measurements of the 3D microtopology. These measurements appear to establish validity of the noncontact atomic force microscopy (nc-AFM) approach into defining the primary microtopology and biochemical functionality of RNA polymerase II. Further nc-AFM studies at higher resolution using dynamical nc-AFM will be required to clearly define the detailed 3D microtopology of RNA polymerase II in anaerobic aqueous environments for both static and dynamic conditions.

  20. Partially Assembled Nucleosome Structures at Atomic Detail.

    PubMed

    Rychkov, Georgy N; Ilatovskiy, Andrey V; Nazarov, Igor B; Shvetsov, Alexey V; Lebedev, Dmitry V; Konev, Alexander Y; Isaev-Ivanov, Vladimir V; Onufriev, Alexey V

    2017-02-07

    The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

  1. Interfacial Atomic Structure of Twisted Few-Layer Graphene.

    PubMed

    Ishikawa, Ryo; Lugg, Nathan R; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi

    2016-02-18

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene.

  2. Structural Basis of Mucopolysaccharidosis Type II and Construction of a Database of Mutant Iduronate 2-Sulfatases

    PubMed Central

    Saito, Seiji; Ohno, Kazuki; Okuyama, Torayuki; Sakuraba, Hitoshi

    2016-01-01

    Mucopolysaccharidosis type II (MPS II, Hunter syndrome) is an X-linked genetic disorder caused by a deficiency of iduronate 2-sulfatase (IDS), and missense mutations comprising about 30% of the mutations responsible for MPS II result in heterogeneous phenotypes ranging from the severe to the attenuated form. To elucidate the basis of MPS II from the structural viewpoint, we built structural models of the wild type and mutant IDS proteins resulting from 131 missense mutations (phenotypes: 67 severe and 64 attenuated), and analyzed the influence of each amino acid substitution on the IDS structure by calculating the accessible surface area, the number of atoms affected and the root-mean-square distance. The results revealed that the amino acid substitutions causing MPS II were widely spread over the enzyme molecule and that the structural changes of the enzyme protein were generally larger in the severe group than in the attenuated one. Coloring of the atoms influenced by different amino acid substitutions at the same residue showed that the structural changes influenced the disease progression. Based on these data, we constructed a database of IDS mutations as to the structures of mutant IDS proteins. PMID:27695081

  3. Zero-Temperature Structures of Atomic Metallic Hydrogen

    NASA Astrophysics Data System (ADS)

    McMahon, Jeffrey; Ceperley, David

    2011-03-01

    Since the first prediction of an atomic metallic phase of hydrogen by Wigner and Huntington over 75 years ago, there have been many theoretical efforts aimed at determining the crystal structures of the zero-temperature phases. We present results from ab initio random structure searching with density functional theory performed to determine the ground state structures from 500 GPa to 5 TPa. We estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (rs = 1.225), which then remains stable to 2.5 TPa (rs = 0.969). At higher pressures, hydrogen stabilizes in an . . . ABCABC . . . planar structure that is remarkably similar to the ground state of lithium, which compresses to the face-centered cubic lattice beyond 5 TPa (rs < 0.86). Our results provide a complete ab initio description of the atomic metallic crystal structures of hydrogen, resolving one of the most fundamental and long outstanding issues concerning the structures of the elements.

  4. Atomic scale structure investigations of epitaxial Fe/Cr multilayers

    NASA Astrophysics Data System (ADS)

    Kąc, M.; Morgiel, J.; Polit, A.; Zabila, Y.; Marszałek, M.

    2014-06-01

    Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2-3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe-Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.

  5. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

    Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre; Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J.

    2015-11-15

    Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolution view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.

  6. The structures of the crystalline phase and columnar mesophase of rhodium (II) heptanoate and of its binary mixture with copper (II) heptanoate probed by EXAFS

    NASA Astrophysics Data System (ADS)

    Inb-Elhaj, M.; Guillon, D.; Skoulios, A.; Maldivi, P.; Giroud-Godquin, A. M.; Marchon, J.-C.

    1992-12-01

    EXAFS was used to investigate the local structure of the polar spines of rhodium (II) soaps in the columnar liquid crystalline state. It was also used to ascertain the degree of blending of the cores in binary mixtures of rhodium (II) and copper (II) soaps. For the pure rhodium soaps, the columns are shown to result from the stacking of binuclear metal-metal bonded dirhodium tetracarboxylate units bonded to one another by apical ligation of the metal atom of each complex with one of the oxygen atoms of the adjacent molecule. Mixtures of rhodium (II) and copper (II) soaps give a hexagonal columnar mesophase in which pure rhodium and pure copper columns are randomly distributed.

  7. Magnetism and surface structure of atomically controlled ultrathin metal films.

    SciTech Connect

    Shiratsuchi, Yu.; Yamamoto, M.; Bader, S. D.; Materials Science Division; Osaka Univ.

    2007-01-01

    We review the correlation of magnetism and surface structure in ultrathin metal films, including the tailoring of novel magnetic properties using atomic scale control of the nanostructure. We provide an overview of modern fabrication and characterization techniques used to create and explore these fascinating materials, and highlight important phenomena of interest. We also discuss techniques that control and characterize both the magnetic and structural properties on an atomic scale. Recent advances in the development and applications of these techniques allow nanomagnetism to be investigated in an unprecedented manner. A system cannot necessarily retain a two-dimensional structure as it enters the ultrathin region, but it can transform into a three-dimensional, discontinuous structure due to the Volmer-Weber growth mechanism. This structural transformation can give rise to superparamagnetism. During this evolution, competing factors such as interparticle interactions and the effective magnetic anisotropy govern the magnetic state. These magnetic parameters are influenced by the nanostructure of the film. In particular, controlling the magnetic anisotropy is critical for determining the magnetic properties. Surface effects play especially important roles in influencing both the magnitude and direction of the magnetic anisotropy in ultrathin films. By properly altering the surface structure, the strength and direction of the magnetic anisotropy are controlled via spin-orbit and/or dipole interactions.

  8. Ground-state structures of atomic metallic hydrogen.

    PubMed

    McMahon, Jeffrey M; Ceperley, David M

    2011-04-22

    Ab initio random structure searching using density functional theory is used to determine the ground-state structures of atomic metallic hydrogen from 500 GPa to 5 TPa. Including proton zero-point motion within the harmonic approximation, we estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (r(s)=1.23) that remains stable to 1 TPa (r(s)=1.11). At higher pressures, hydrogen stabilizes in an …ABCABC… planar structure that is similar to the ground state of lithium, but with a different stacking sequence. With increasing pressure, this structure compresses to the face-centered cubic lattice near 3.5 TPa (r(s)=0.92).

  9. A one-dimensional chain structure based on unusual tetranuclear manganese(II) clusters.

    PubMed

    Che, Guang Bo; Wang, Jian; Liu, Chun Bo; Li, Xiu Ying; Liu, Bo

    2008-11-01

    The title coordination polymer, poly[bis(mu(4)-biphenyl-2,2'-dicarboxylato)(dipyrido[3,2-a:2',3'-c]phenazine)manganese(II)], [Mn(2)(C(14)H(8)O(4))(2)(C(18)H(10)N(4))](n), was obtained through the reaction of MnCl(2).4H(2)O, biphenyl-2,2'-dicarboxylic acid (H(2)dpdc) and dipyrido[3,2-a:2',3'-c]phenazine (L) under hydrothermal conditions. The asymmetric unit contains two crystallographically unique Mn(II) ions, one unique L ligand and two unique dpdc ligands. One Mn ion is six-coordinated by four O atoms from three different dpdc ligands and two N atoms from one L ligand, adopting a distorted octahedral coordination geometry. The distortions from ideal octahedral geometry are largely due to the presence of chelating ligands and the resulting acute N-Mn-N and O-Mn-O angles. The second Mn ion is coordinated in a distorted trigonal bipyramidal fashion by five O atoms from four distinct dpdc ligands. Four Mn(II) ions are bridged by the carboxylate groups of the dpdc ligands to form an unusual tetranuclear Mn(II) cluster. Clusters are further connected by the aromatic backbone of the dicarboxylate ligands, forming a one-dimensional chain structure along the b axis. The title compound is the first example of a chain structure based on a tetranuclear Mn(II) cluster.

  10. Multi-million atom electronic structure calculations for quantum dots

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

    Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined

  11. Atomic- Resolution Crystal Structure of the Antiviral Lectin Scytovirin

    SciTech Connect

    Moulaei,T.; Botos, I.; Ziolkowska, N.; Bokesch, H.; Krumpe, L.; McKee, T.; O'Keefe, B.; Dauter, Z.; Wlodawer, A.

    2007-01-01

    The crystal structures of the natural and recombinant antiviral lectin scytovirin (SVN) were solved by single-wavelength anomalous scattering and refined with data extending to 1.3 Angstroms and 1.0 Angstroms resolution, respectively. A molecule of SVN consists of a single chain 95 amino acids long, with an almost perfect sequence repeat that creates two very similar domains (RMS deviation 0.25 Angstroms for 40 pairs of Ca atoms). The crystal structure differs significantly from a previously published NMR structure of the same protein, with the RMS deviations calculated separately for the N- and C-terminal domains of 5.3 Angstroms and 3.7 Angstroms, respectively, and a very different relationship between the two domains. In addition, the disulfide bonding pattern of the crystal structures differs from that described in the previously published mass spectrometry and NMR studies.

  12. Structure of a Quantized Vortex in Fermi Atom Gas

    SciTech Connect

    Machida, Masahiko; Koyama, Tomio

    2006-09-07

    In atomic Fermi gases, the pairing character changes from BCS-like to BEC-like when one decreases the threshold energy of the Feshbach resonance. With this crossover, the system enters the strong-coupling regime through the population enhancement of diatom molecules, and the vortex structure becomes much different from well-known core structures in BCS superfluid since the superfluid order parameter is given by a sum of BCS pairs and BEC molecular condensates. In this paper, we study the structure of a vortex by numerically solving the generalized Bogoliubov-de Gennes equation derived from the fermion-boson model and clarify how the vortex structure changes with the threshold energy of the Feshbach resonance. We find that the diatom boson condensate enhances the matter density depletion inside the vortex core and the discreteness of localized quasi-particle spectrum.

  13. Structural properties of reciprocal form factor in neutral atoms and singly charged ions.

    PubMed

    Romera, E; Angulo, J C

    2004-04-22

    Structural characteristics of the spherically averaged internally folded density or reciprocal form factor Br are studied within the Hartree-Fock framework for 103 neutral atoms, 54 singly charged cations, and 43 anions in their ground state. The function Br is classified throughout the Periodic Table into three types: (i) monotonic decrease from the origin, (ii) maximum at r=0 and a negative minimum at r>0, and (iii) a local maximum at r=0 and a pair maximum-minimum out of the origin. A detailed study of the corresponding properties for individual subshells as well as their relative weight for the total Br is also carried out. For completeness, the analytical Br for hydrogenlike atoms in both ground and excited states is also analyzed.

  14. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    SciTech Connect

    Thurmer, Konrad; Feibelman, Peter J.

    2014-09-01

    We applied Scanning Probe Microscopy and Density Functional Theory (DFT) to discover the basics of how adsorbates wet insulating substrates, addressing a key question in geochemistry. To allow experiments on insulating samples we added Atomic Force Microscopy (AFM) capability to our existing UHV Scanning Tunneling Microscope (STM). This was accomplished by integrating and debugging a commercial qPlus AFM upgrade. Examining up-to-40-nm-thick water films grown in vacuum we found that the exact nature of the growth spirals forming around dislocations determines what structure of ice, cubic or hexagonal, is formed at low temperature. DFT revealed that wetting of mica is controlled by how exactly a water layer wraps around (hydrates) the K+ ions that protrude from the mica surface. DFT also sheds light on the experimentally observed extreme sensitivity of the mica surface to preparation conditions: K atoms can easily be rinsed off by water flowing past the mica surface.

  15. Atomic Clocks and Variations of the FIne Structure Constant

    NASA Technical Reports Server (NTRS)

    Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute

    1995-01-01

    We describe a new test for possible variations of the fine structure constant alpha by comparisons of rates between clocks based on hyperfine transitions in alkali atoms with different atomic number Z. H-maser, Cs, and Hg(+) clocks have a different dependence on alpha via relativistic contributions of order (Z-alpha)(sup 2). Recent H-maser vs Hg(+) clock comparison data improve laboratory limits on a time variation by 100-fold to give dot-alpha less than or equal to 3.7 x 10(exp -14)/yr. Future laser cooled clocks (Be(+), Rb, Cs, Hg(+), etc.), when compared, will yield the most sensitive of all tests for dot-alpha/alpha.

  16. Structural Transition in Atomic Chains Driven by Transient Doping

    NASA Astrophysics Data System (ADS)

    Polei, S.; Snijders, P. C.; Erwin, S. C.; Himpsel, F. J.; Meiwes-Broer, K.-H.; Barke, I.

    2013-10-01

    A reversible structural transition is observed on Si(553)-Au by scanning tunneling microscopy, triggered by electrons injected from the tip into the surface. The periodicity of atomic chains near the step edges changes from the 1×3 ground state to a 1×2 excited state with increasing tunneling current. The threshold current for this transition is reduced at lower temperatures. In conjunction with first-principles density-functional calculations it is shown that the 1×2 phase is created by temporary doping of the atom chains. Random telegraph fluctuations between two levels of the tunneling current provide direct access to the dynamics of the phase transition, revealing lifetimes in the millisecond range.

  17. Molecular structures, charge distributions, and vibrational analyses of the tetracoordinate Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine investigated by density functional theory in comparison with experiments

    NASA Astrophysics Data System (ADS)

    Bardakçı, Tayyibe; Kumru, Mustafa; Altun, Ahmet

    2016-07-01

    The Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine have been studied with B3LYP calculations by using def2-TZVP basis set at the metal atoms and using def2-TZVP and 6-311G+(d,p) basis sets at the remaining atoms. Both basis set combinations give analogous results, which validate the use of quickly converging 6-311G+(d,p) basis set in future studies. The molecular structures, atomic charge and spin distributions, and harmonic vibrational frequencies of the complexes have been calculated. The Zn, Cd and Hg complexes have been found to have distorted tetrahedral environments around the metal atoms whereas Cu complex has a square planar geometry. The NBO charge analysis have been found more accurate and less misleading compared with the Mulliken scheme. The present vibrational spectra calculations allow accurate assignment of the vibrational bands, which otherwise assigned tentatively in previous experimental-only studies.

  18. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.

  19. Atomic resolution structure of Erwinia chrysanthemi L-asparaginase.

    PubMed

    Lubkowski, Jacek; Dauter, Miroslawa; Aghaiypour, Khosrow; Wlodawer, Alexander; Dauter, Zbigniew

    2003-01-01

    An X-ray structure of L-asparaginase from Erwinia chrysanthemi (ErA) has been refined at 1 A resolution to an R factor of below 0.1, using data collected on a synchrotron source. With four molecules of the enzyme consisting of 327 amino acids each, this crystal contains one of the largest asymmetric units of a protein refined to date at atomic resolution. Previously, structures of ErA and of related enzymes from other bacterial sources have been refined at resolutions not exceeding 1.7 A; thus, the present structure represents a very significant improvement in the quality of the available models of these proteins and should provide a good basis for future studies of the conformational variability of proteins, identification of subtle conformational features and corroboration of the stereochemical libraries, amongst other things. L-Asparaginases, which are enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 y as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia, although the details of the enzymatic reaction and substrate specificity have not yet been completely elucidated. This atomic resolution structure is a step in that direction.

  20. Atomic-Scale Visualization of Quasiparticle Interference on a Type-II Weyl Semimetal Surface

    NASA Astrophysics Data System (ADS)

    Zheng, Hao; Bian, Guang; Chang, Guoqing; Lu, Hong; Xu, Su-Yang; Wang, Guangqiang; Chang, Tay-Rong; Zhang, Songtian; Belopolski, Ilya; Alidoust, Nasser; Sanchez, Daniel S.; Song, Fengqi; Jeng, Horng-Tay; Yao, Nan; Bansil, Arun; Jia, Shuang; Lin, Hsin; Hasan, M. Zahid

    2016-12-01

    We combine quasiparticle interference simulation (theory) and atomic resolution scanning tunneling spectromicroscopy (experiment) to visualize the interference patterns on a type-II Weyl semimetal Mox W1 -xTe2 for the first time. Our simulation based on first-principles band topology theoretically reveals the surface electron scattering behavior. We identify the topological Fermi arc states and reveal the scattering properties of the surface states in Mo0.66 W0.34 Te2 . In addition, our result reveals an experimental signature of the topology via the interconnectivity of bulk and surface states, which is essential for understanding the unusual nature of this material.

  1. Designing a heterotrinuclear Cu(II)-Ni(II)-Cu(II) complex from a mononuclear Cu(II) Schiff base precursor with dicyanamide as a coligand: synthesis, crystal structure, thermal and photoluminescence properties.

    PubMed

    Hopa, Cigdem; Cokay, Ismail

    2016-08-01

    Schiff bases are considered `versatile ligands' in coordination chemistry. The design of polynuclear complexes has become of interest due to their facile preparations and varied synthetic, structural and magnetic properties. The reaction of the `ligand complex' [CuL] {H2L is 2,2'-[propane-1,3-diylbis(nitrilomethanylylidene)]diphenol} with Ni(OAc)2·4H2O (OAc is acetate) in the presence of dicyanamide (dca) leads to the formation of bis(dicyanamido-1κN(1))bis(dimethyl sulfoxide)-2κO,3κO-bis{μ-2,2'-[propane-1,3-diylbis(nitrilomethanylylidene)]diphenolato}-1:2κ(6)O,O':O,N,N',O';1:3κ(6)O,O':O,N,N',O'-dicopper(II)nickel(II), [Cu2Ni(C17H16N2O2)2(C2N3)2(C2H6OS)2]. The complex shows strong absorption bands in the frequency region 2155-2269 cm(-1), which clearly proves the presence of terminal bonding dca groups. A single-crystal X-ray study revealed that two [CuL] units coordinate to an Ni(II) atom through the phenolate O atoms, with double phenolate bridges between Cu(II) and Ni(II) atoms. Two terminal dca groups complete the distorted octahedral geometry around the central Ni(II) atom. According to differential thermal analysis-thermogravimetric analysis (DTA-TGA), the title complex is stable up to 423 K and thermal decomposition starts with the release of two coordinated dimethyl sulfoxide molecules. Free H2L exhibits photoluminescence properties originating from intraligand (π-π*) transitions and fluorescence quenching is observed on complexation of H2L with Cu(II).

  2. Synthesis and structural characterisation of iron(II) and copper(II) diphosphates containing flattened metal oxotetrahedra

    SciTech Connect

    Keates, Adam C.; Wang, Qianlong; Weller, Mark T.

    2014-02-15

    Single crystal and bulk polycrystalline forms of K{sub 2}MP{sub 2}O{sub 7} (M=Fe(II), Cu(II)) have been synthesised and their structures determined from single crystal X-ray diffraction data. Both compounds crystallize in the tetragonal system, space group P-42{sub 1}m. Their structures are formed from infinite sheets of linked oxopolyhedra of the stoichiometry [MP{sub 2}O{sub 7}]{sup 2−} with potassium cations situated between the layers. The MO{sub 4} tetrahedra share oxygen atoms with [P{sub 2}O{sub 7}]{sup 4−} diphosphate groups and the potassium ions have KO{sub 8} square prismatic geometry. In both compounds the M(II) centre has an unusual strongly flattened, tetrahedral coordination to oxygen, as a result of the Jahn–Teller (JT) effect for the high spin d{sup 6} Fe(II) and p-orbital mixing or a second order JT effect for d{sup 9} Cu(II) centres in four fold coordination. The uncommon transition metal ion environments found in these materials are reflected in their optical absorption spectra and magnetism data. - Graphical abstract: The structures of the tetragonal polymorphs of K{sub 2}MP{sub 2}O{sub 7}, M=Cu(II), Fe(II), consist of infinite sheets of stoichiometry [MP{sub 2}O{sub 7}]{sup 2−}, formed from linked pyrophosphate groups and MO{sub 4} tetrahedra, separated by potassium ions. In both compounds the unusual tetrahedral coordination of the M(II) centre is strongly flattened as a result of Jahn–Teller (JT) effects for high spin, d{sup 6} Fe(II) and p-orbital mixing and second-order JT effects for d{sup 9} Cu(II). Display Omitted - Highlights: • Tetrahedral copper and iron(II) coordinated by oxygen. • New layered phosphate structure. • Jahn–Teller and d{sup 10} distorted coordinations.

  3. Editorial . Quantum fluctuations and coherence in optical and atomic structures

    NASA Astrophysics Data System (ADS)

    Eschner, Jürgen; Gatti, Alessandra; Maître, Agnès; Morigi, Giovanna

    2003-03-01

    From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics

  4. Synthesis, structural and electrochemical properties of nickel(II) sulfamethazine complex with diethylenetriamine ligand.

    PubMed

    Bulut, İclal; Öztürk, Filiz; Bulut, Ahmet

    2015-03-05

    In this study, [Ni(dien)2]⋅smz2⋅(Hsmz: sulfamethazine and dien: diethylenetriamine) complex has been synthesized and its crystal structure has been determined by X-ray diffraction technique. The title complex crystallizes in orthorhombic system with space group Pbnb [a=8.556(5), b=16.228(5), c=28.209(5)Å, V=3917(3)Å(3) and Z=4]. The nickel(II) ion has distorted octahedral coordination geometry. The metal atom, which rides on a crystallographic center of symmetry, is coordinated by six nitrogen atoms of two dien ligands to form a discrete [Ni(dien)2](2+) unit, which captures two sulfamethazine ions, each through intermolecular hydrogen bonds. The powder EPR spectrum of Cu(2+) doped Ni(II) complex was recorded at room temperature. The vibrational investigation has been carried out by considering the characteristic bands related to the functional groups of the complex. The electrochemical behavior of Ni(II) ions in the presence and in the absence of smz and dien were studied by square wave and cyclic voltammetry. A well-defined irreversible peak at -1.112V different from those of the Ni(II)-smz (-0.876V) and the Ni(II)-dien complex (-1.064V) was observed in the solution containing Ni(II) ions, which was attributed to the formation of the new mixed ligand complex of Ni(II) with smz and dien.

  5. Refinement of Atomic Structures Against cryo-EM Maps.

    PubMed

    Murshudov, G N

    2016-01-01

    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.

  6. Understanding the structure of the first atomic contact in gold.

    PubMed

    Sabater, Carlos; Caturla, María José; Palacios, Juan José; Untiedt, Carlos

    2013-05-29

    : We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics.

  7. Atomic Structure of the Stoichiometric GaAs(114) Surface.

    PubMed

    Márquez; Kratzer; Geelhaar; Jacobi; Scheffler

    2001-01-01

    The stoichiometric GaAs(114) surface has been prepared using molecular beam epitaxy followed by annealing in ultrahigh vacuum. Based on in situ scanning tunneling microscopy measurements and first-principles electronic-structure calculations, we determine the surface reconstruction which we call alpha2(2x1). Contrary to what is expected for a high-index surface, it is surprisingly elementary. The (2x1) unit cell contains two As dimers and two rebonded Ga atoms. The surface energy is calculated as 53 meV/Å(2), which falls well within the range of low-index GaAs surface energies.

  8. Chaotic dynamics and fractal structures in experiments with cold atoms

    NASA Astrophysics Data System (ADS)

    Daza, Alvar; Georgeot, Bertrand; Guéry-Odelin, David; Wagemakers, Alexandre; Sanjuán, Miguel A. F.

    2017-01-01

    We use tools from nonlinear dynamics for the detailed analysis of cold-atom experiments. A powerful example is provided by the recent concept of basin entropy, which allows us to quantify the final-state unpredictability that results from the complexity of the phase-space geometry. We show here that this enables one to reliably infer the presence of fractal structures in phase space from direct measurements. We illustrate the method with numerical simulations in an experimental configuration made of two crossing laser guides that can be used as a matter-wave splitter.

  9. Direct observation of a long-lived single-atom catalyst chiseling atomic structures in graphene.

    PubMed

    Wang, Wei Li; Santos, Elton J G; Jiang, Bin; Cubuk, Ekin Dogus; Ophus, Colin; Centeno, Alba; Pesquera, Amaia; Zurutuza, Amaia; Ciston, Jim; Westervelt, Robert; Kaxiras, Efthimios

    2014-02-12

    Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberration-corrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.

  10. Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

    SciTech Connect

    Wang, G.-F. E-mail: s-shuwen@163.com; Zhang, X.; Sun, S.-W.; Sun, H.; Ma, H.-X.

    2015-12-15

    The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [k{sup 3}-N, N',N''-Tp{sup t-Bu}, {sup Me}NiI] (1) and [k{sup 3}-N,N',N''-Tp{sup t-Bu}, {sup Me}NiNO{sub 3}] (2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms from a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.

  11. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    PubMed

    Colvin, Michael T; Silvers, Robert; Ni, Qing Zhe; Can, Thach V; Sergeyev, Ivan; Rosay, Melanie; Donovan, Kevin J; Michael, Brian; Wall, Joseph; Linse, Sara; Griffin, Robert G

    2016-08-03

    Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation.

  12. Atomic Force Microscopy for Investigation of Ribosome-inactivating Proteins' Type II Tetramerization

    NASA Astrophysics Data System (ADS)

    Savvateev, M.; Kozlovskaya, N.; Moisenovich, M.; Tonevitsky, A.; Agapov, I.; Maluchenko, N.; Bykov, V.; Kirpichnikov, M.

    2003-12-01

    Biology of the toxins violently depends on their carbohydrate-binding centres' organization. Toxin tetramerization can lead to both increasing of lectin-binding centres' number and changes in their structural organization. A number and three-dimensional localization of such centres per one molecule strongly influence on toxins' biological properties. Ricin was used to obtain the AFM images of natural dimeric RIPsII structures as far as ricinus agglutinin was used for achievement of AFM images of natural tetrameric RIPsII forms. It is well-known that viscumin (60 kDa) has a property to form tetrameric structures dependently on ambient conditions and its concentration. Usage of the model dimer-tetramer based on ricin-agglutinin allowed to identify viscumin tetramers in AFM scans and to differ them from dimeric viscumin structures. Quantification analysis produced with the NT-MDT software allowed to estimate the geometrical parameters of ricin, ricinus agglutinin and viscumin molecules.

  13. Atomic scale modelling of hexagonal structured metallic fission product alloys.

    PubMed

    Middleburgh, S C; King, D M; Lumpkin, G R

    2015-04-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)-making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance.

  14. Atomic scale modelling of hexagonal structured metallic fission product alloys

    PubMed Central

    Middleburgh, S. C.; King, D. M.; Lumpkin, G. R.

    2015-01-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance. PMID:26064629

  15. A near atomic structure of the active human apoptosome.

    PubMed

    Cheng, Tat Cheung; Hong, Chuan; Akey, Ildikó V; Yuan, Shujun; Akey, Christopher W

    2016-10-04

    In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.

  16. 158 micron forbidden C II mapping of NGC 6946 - Probing the atomic medium

    NASA Technical Reports Server (NTRS)

    Madden, S. C.; Geis, N.; Genzel, R.; Herrmann, F.; Jackson, J.; Poglitsch, A.; Stacey, G. J.; Townes, C. H.

    1993-01-01

    A well-sampled map (23 x 17 kpc) of the strong 158 micron forbidden C II cooling line in the Scd galaxy NGC 6946 at 55 arcsec resolution is presented which was taken with the MPE/UCB Far-infrared Imaging Fabry-Perot Interferometer (FIFI) in the Kuiper Airborne Observatory. It is concluded that the line emission in NGC 6946 is present in three spatially distinct components including nucleus, spiral arms, and extended region. An extended emission region is a source of most of the forbidden C II luminosity in NGC 6946. The 1 arcmin nuclear component has a line luminosity of 1.5 x 10 exp 7 solar luminosity and contributes 0.15 percent of the galaxy's total FIR luminosity. An extended component of forbidden C II emission is found to exist past the molecular extent of the galaxy and to be present to at least the full dimensions of the map. This component is attributed to a mixture of neutral and atomic clouds.

  17. Psychological Action and Structure in "Richard II."

    ERIC Educational Resources Information Center

    Toole, William B., III

    1978-01-01

    Explores the theme that the suffering arising from Richard II's loss of power, a power that consisted more of appearance than of intrinsic worth, led him to spiritual growth and the development of real value as a person. (MB)

  18. First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

    SciTech Connect

    Dave, Mudra R.; Sharma, A. C.

    2015-06-24

    The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

  19. Cloud point extraction and flame atomic absorption spectrometric determination of cadmium(II), lead(II), palladium(II) and silver(I) in environmental samples.

    PubMed

    Ghaedi, Mehrorang; Shokrollahi, Ardeshir; Niknam, Khodabakhsh; Niknam, Ebrahim; Najibi, Asma; Soylak, Mustafa

    2009-09-15

    The phase-separation phenomenon of non-ionic surfactants occurring in aqueous solution was used for the extraction of cadmium(II), lead(II), palladium(II) and silver(I). The analytical procedure involved the formation of understudy metals complex with bis((1H-benzo [d] imidazol-2yl)ethyl) sulfane (BIES), and quantitatively extracted to the phase rich in octylphenoxypolyethoxyethanol (Triton X-114) after centrifugation. Methanol acidified with 1molL(-1) HNO(3) was added to the surfactant-rich phase prior to its analysis by flame atomic absorption spectrometry (FAAS). The concentration of BIES, pH and amount of surfactant (Triton X-114) was optimized. At optimum conditions, the detection limits of (3 sdb/m) of 1.4, 2.8, 1.6 and 1.4 ng mL(-1) for Cd(2+), Pb(2+), Pd(2+) and Ag(+) along with preconcentration factors of 30 and enrichment factors of 48, 39, 32 and 42 for Cd(2+), Pb(2+), Pd(2+) and Ag(+), respectively, were obtained. The proposed cloud point extraction has been successfully applied for the determination of metal ions in real samples with complicated matrix such as radiology waste, vegetable, blood and urine samples.

  20. Crystal structures of copper(II) and nickel(II) nitrate and chloride complexes with 4-bromo-2-[(2-hydroxyethylimino)-methyl]phenol

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Filippova, I. G.; Bocelli, G.; Gulea, A. P.

    2008-07-15

    The crystal structures of {l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquacopper(II) nitrate hemihydrate (I), chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}copper hemihydrate (II), and chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquanickel (III) are determined using X-ray diffraction. Crystals of compound I are formed by cationic complexes, nitrate ions, and solvate water molecules. In the cation, the copper atom coordinates the singly deprotonated molecule of tridentate azomethine and the water molecule. The copper complexes are joined into centrosymmetric dimers by the O{sub w}-H...O hydrogen bonds. The crystal structure of compound II is composed of binuclear copper complexes and solvate water molecules. The copper atom coordinates the O,N,O ligand molecule and the chlorine ion, which fulfills a bridging function. The coordination polyhedron of the metal atom is a distorted tetragonal bipyramid in which the vertex is occupied by the chlorine atom of the neighboring complex in the dimer. Compound III is a centrosymmetric dimer complex. The coordination polyhedra of two nickel atoms related via the inversion center are distorted octahedra shared by the edge.

  1. Magnetic Structures of Heterometallic M(II)-M(III) Formate Compounds.

    PubMed

    Mazzuca, Lidia; Cañadillas-Delgado, Laura; Rodríguez-Velamazán, J Alberto; Fabelo, Oscar; Scarrozza, Marco; Stroppa, Alessandro; Picozzi, Silvia; Zhao, Jiong-Peng; Bu, Xian-He; Rodríguez-Carvajal, Juan

    2017-01-03

    A study of the magnetic structure of the [NH2(CH3)2]n[Fe(III)M(II)(HCOO)6]n niccolite-like compounds, with M(II) = Co(II) (2) and Mn(II) (3) ions, has been carried out using neutron diffraction and compared with the previously reported Fe(II)-containing compound (1). The inclusion of two different metallic atoms into the niccolite-like structure framework leads to the formation of isostructural compounds with very different magnetic behaviors due to the compensation or not of the different spins involved in each lattice. Below TN, the magnetic order in these compounds varies from ferrimagnetic behavior for 1 and 2 to an antiferromagnetic behavior with a weak spin canting for 3. Structure refinements of 2 and 3 at low temperature (45 K) have been carried out combining synchrotron X-ray and high-resolution neutron diffraction in a multipattern approach. The magnetic structures have been determined from the difference patterns between the neutron data in the paramagnetic and the magnetically ordered regions. These difference patterns have been analyzed using a simulated annealing protocol and symmetry analysis techniques. The obtained magnetic structures have been further rationalized by means of ab initio DFT calculations. The direction of the magnetic moment of each compound has been determined. The easy axis of the M(II) for compound 1 (Fe(II)) is along the c axis; for compound 2 (Co(II)), the moments are mainly within the ab plane; finally, for compound 3 (Mn(II)), the calculations show that the moments have components both in the ab plane and along the c axis.

  2. Synthesis, structural and magnetic characterisation of iron(II/III), cobalt(II) and copper(II) cluster complexes of the polytopic ligand: N-(2-pyridyl)-3-carboxypropanamide.

    PubMed

    Russell, Mark E; Hawes, Chris S; Ferguson, Alan; Polson, Matthew I J; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S; Kruger, Paul E

    2013-10-07

    Herein we describe the synthesis, structural and magnetic characterisation of three transition metal cluster complexes that feature the polytopic ligand N-(2-pyridyl)-3-carboxypropanamide (H2L): [Fe3(III)Fe2(II)(HL)6(O)(H2O)3][ClO4]5·3MeCN·4H2O, 1, [Co8(HL)8(O)(OH)4(MeOH)3(H2O)]-[ClO4]3·5MeOH·2H2O, 2, and [Cu6(L(ox))4(MeOH)(H2O)3]·MeOH, 3. Complex 1 is a mixed valence penta-nuclear iron cluster containing the archetypal {Fe3(III)O} triangular basic carboxylate cluster at its core, with two Fe(II) ions above and below the core coordinated to three bidentate pyridyl-amide groups. The structure of the octanuclear Co(II) complex, 2, is based upon a central Co4 square with the remaining four Co(II) centres at the 'wing-tips' of the complex. The cluster core is replete with bridging oxide, hydroxide and carboxylate groups. Cluster 3 contains an oxidised derivative of the ligand, L(ox), generated in situ through hydroxylation of an α-carbon atom. This hexanuclear cluster has a 'barrel-like' core and contains Cu(II) ions in both square planar and square-based pyramidal geometries. Bridging between Cu(II) centres is furnished by alkoxide and carboxylate groups. Magnetic studies on 1-3 reveals dominant antiferro-magnetic interactions for 1 and 2, leading to small non-zero spin ground states, while 3 shows ferro-magnetic exchange between the Cu(II) centres to give an S = 3 spin ground state.

  3. Syntheses, characterizations and structures of NO donor Schiff base ligands and nickel(II) and copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Şenol, Cemal; Hayvali, Zeliha; Dal, Hakan; Hökelek, Tuncer

    2011-06-01

    New Schiff base derivatives ( L 1 and L 2) were prepared by the condensation of 2-hydroxy-3-methoxybenzaldehyde ( o-vanillin) and 3-hydroxy-4-methoxybenzaldehyde ( iso-vanillin) with 5-methylfurfurylamine. Two new complexes [Ni(L 1) 2] and [Cu(L 1) 2] have been synthesized with bidentate NO donor Schiff base ligand ( L 1). The Ni(II) and Cu(II) atoms in each complex are four coordinated in a square planar geometry. Schiff bases ( L 1 and L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] were characterized by elemental analyses, FT-IR, UV-vis, mass and 1H, 13C NMR spectroscopies. The crystal structures of the ligand ( L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] have also been determined by using X-ray crystallographic technique.

  4. Structure of self-assembled Mn atom chains on Si(001)

    NASA Astrophysics Data System (ADS)

    Villarreal, Renan; Longobardi, Maria; Koester, Sigrun A.; Kirkham, Christopher J.; Bowler, David; Renner, Christoph

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy and density functional theory we find that a simple necklace-like chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modelling the electronic and magnetic properties of Mn atom chains on Si(001).

  5. Structure of Self-Assembled Mn Atom Chains on Si(001)

    NASA Astrophysics Data System (ADS)

    Villarreal, R.; Longobardi, M.; Köster, S. A.; Kirkham, Ch. J.; Bowler, D.; Renner, Ch.

    2015-12-01

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001).

  6. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

    Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

    2014-01-01

    The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

  7. The Atomic scale structure of liquid metal-electrolyte interfaces

    NASA Astrophysics Data System (ADS)

    Murphy, B. M.; Festersen, S.; Magnussen, O. M.

    2016-07-01

    Electrochemical interfaces between immiscible liquids have lately received renewed interest, both for gaining fundamental insight as well as for applications in nanomaterial synthesis. In this feature article we demonstrate that the atomic scale structure of these previously inaccessible interfaces nowadays can be explored by in situ synchrotron based X-ray scattering techniques. Exemplary studies of a prototypical electrochemical system - a liquid mercury electrode in pure NaCl solution - reveal that the liquid metal is terminated by a well-defined atomic layer. This layering decays on length scales of 0.5 nm into the Hg bulk and displays a potential and temperature dependent behaviour that can be explained by electrocapillary effects and contributions of the electronic charge distribution on the electrode. In similar studies of nanomaterial growth, performed for the electrochemical deposition of PbFBr, a complex nucleation and growth behaviour is found, involving a crystalline precursor layer prior to the 3D crystal growth. Operando X-ray scattering measurements provide detailed data on the processes of nanoscale film formation.

  8. Defects in p-GaN and their atomic structure

    SciTech Connect

    Liliental-Weber, Z.; Tomaszewicz, T.; Zakharov, D.; Jasinski, J.; and O'Keefe, M.

    2004-10-08

    In this paper defects formed in p-doped GaN:Mg grown with Ga polarity will be discussed. The atomic structure of these characteristic defects (Mg-rich hexagonal pyramids and truncated pyramids) in bulk and thin GaN:Mg films grown with Ga polarity was determined at atomic resolution by direct reconstruction of the scattered electron wave in a transmission electron microscope. Small cavities were present inside the defects. The inside walls of the cavities were covered by GaN which grew with reverse polarity compared to the matrix. It was proposed that lateral overgrowth of the cavities restores matrix polarity on the defect base. Exchange of Ga and N sublattices within the defect compared to the matrix lead to a 0.6 {+-} 0.2 {angstrom} displacement between the Ga sublattices of these two areas. A [1{und 1}00]/3 shift with change from AB stacking in the matrix to BC within the entire pyramid is observed

  9. Crystal structure of catena-poly[di­ammonium [di-μ-oxalato-cuprate(II)

    PubMed Central

    Dickie, Diane A.; Kemp, Richard A.

    2016-01-01

    The structure of the title compound, {(NH4)2[Cu(C2O4)2]}n, at 100 K has monoclinic (P21/c) symmetry with the CuII atom on an inversion center. The compound has a polymeric structure due to long Cu⋯O inter­actions which create [Cu(C2O4)2] chains along the a axis. The structure also displays inter­molecular N—H⋯O hydrogen bonding, which links these chains into a three-dimensional network. PMID:27980829

  10. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

    SciTech Connect

    Shelobolina, Evgenya S.; Xu, Huifang; Konishi, Hiromi; Kukkadapu, Ravi K.; Wu, Tao; Blothe, Marco; Roden, Eric E.

    2012-06-08

    Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through production of organic ligands and acids, and through uptake of products of weathering. Here we show that a lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture (Straub, 6 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Moessbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 107 cells were produced per {micro}mol Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including decrease in unit cell b-dimension toward dioctahedral levels and iron and potassium release. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms may be directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.

  11. Structural basis for exon recognition by a group II intron

    SciTech Connect

    Toor, Navtej; Rajashankar, Kanagalaghatta; Keating, Kevin S.; Pyle, Anna Marie

    2008-11-18

    Free group II introns are infectious retroelements that can bind and insert themselves into RNA and DNA molecules via reverse splicing. Here we report the 3.4-A crystal structure of a complex between an oligonucleotide target substrate and a group IIC intron, as well as the refined free intron structure. The structure of the complex reveals the conformation of motifs involved in exon recognition by group II introns.

  12. Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

    SciTech Connect

    Gabdulkhakov, A. G. Dontsova, M. V.; Saenger, W.

    2011-11-15

    Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of the refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.

  13. Atomically Resolved Structural and Chemical Investigation of Single MXene Sheets.

    PubMed

    Karlsson, Linda H; Birch, Jens; Halim, Joseph; Barsoum, Michel W; Persson, Per O Å

    2015-08-12

    The properties of two-dimensional (2D) materials depend strongly on the chemical and electrochemical activity of their surfaces. MXene, one of the most recent additions to 2D materials, shows great promise as an energy storage material. In the present investigation, the chemical and structural properties of individual Ti3C2 MXene sheets with associated surface groups are investigated at the atomic level by aberration corrected STEM-EELS. The MXene sheets are shown to exhibit a nonuniform coverage of O-based surface groups which locally affect the chemistry. Additionally, native point defects which are proposed to affect the local surface chemistry, such as oxidized titanium adatoms (TiOx), are identified and found to be mobile.

  14. Phase Space Structures Explain Hydrogen Atom Roaming in Formaldehyde Decomposition.

    PubMed

    Mauguière, Frédéric A L; Collins, Peter; Kramer, Zeb C; Carpenter, Barry K; Ezra, Gregory S; Farantos, Stavros C; Wiggins, Stephen

    2015-10-15

    We re-examine the prototypical roaming reaction--hydrogen atom roaming in formaldehyde decomposition--from a phase space perspective. Specifically, we address the question "why do trajectories roam, rather than dissociate through the radical channel?" We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs, we show that in the roaming region, there is an unstable periodic orbit whose stable and unstable manifolds define a conduit that both encompasses all roaming trajectories exiting the formaldehyde well and shepherds them toward the H2···CO well.

  15. Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons

    PubMed Central

    Huang, Han; Wei, Dacheng; Sun, Jiatao; Wong, Swee Liang; Feng, Yuan Ping; Neto, A. H. Castro; Wee, Andrew Thye Shen

    2012-01-01

    Graphene has attracted much interest in both academia and industry. The challenge of making it semiconducting is crucial for applications in electronic devices. A promising approach is to reduce its physical size down to the nanometer scale. Here, we present the surface-assisted bottom-up fabrication of atomically precise armchair graphene nanoribbons (AGNRs) with predefined widths, namely 7-, 14- and 21-AGNRs, on Ag(111) as well as their spatially resolved width-dependent electronic structures. STM/STS measurements reveal their associated electron scattering patterns and the energy gaps over 1 eV. The mechanism to form such AGNRs is addressed based on the observed intermediate products. Our results provide new insights into the local properties of AGNRs, and have implications for the understanding of their electrical properties and potential applications. PMID:23248746

  16. Angular momentum algebra for symbolic expansions in atomic structure theory

    NASA Astrophysics Data System (ADS)

    Matulioniene, Rasa

    Computer programs based on multiconfiguration methods have become standard tools in atomic structure theory. Reliable predictions of atomic properties require very large configuration expansions. The computational resources required often exceed the capabilities of conventional computers. There is a need to restructure existing computer programs to take advantage of modern high-performance computational technology. This dissertation deals with one important aspect of the effort to implement two widely used atomic structure packages (MCHF and GRASP92) on distributed memory parallel computers: the method for handling the angular momentum algebra. In the existing algorithms, the angular integrations required for the Hamiltonian matrix elements are computed for each pair of configurations, even though the results may be identical or very similar for all configurations of a given type. This redundancy leads to a significant increase in computer resource requirements, because the angular matrix elements, which are repeatedly reused in the calculation, need to be stored in computer memory or on disk. At present, the size (and, therefore, accuracy) of the calculations is limited by the large amounts of angular data produced. The aim of the research reported in this dissertation is to provide the theoretical basis for a computational method to curtail the growth of stored angular data with the size of the calculation. The multiconfiguration basis is often generated by one- and two-particle replacements from a reference set to correlation orbitals. The redundancy in the stored angular data could be removed by reformulating the algorithm to treat simultaneously all angular matrix elements that differ only in the quantum numbers of the correlation orbitals. To accomplish this, we expand N- electron matrix elements of a general symmetric two-body scalar operator, an example of which is the Hamiltonian, in terms of two-electron matrix elements. Using diagrammatic methods of

  17. Atomic structure of InSb(001) and GaAs(001) surfaces imaged with noncontact atomic force microscopy.

    PubMed

    Kolodziej, J J; Such, B; Szymonski, M; Krok, F

    2003-06-06

    Noncontact atomic force microscopy (NC-AFM) has been used to study the c(8x2) InSb(001) and the c(8x2) GaAs(001) surfaces prepared by sputter cleaning and annealing. Atomically resolved tip-surface interaction maps display different characteristic patterns depending on the tip front atom type. It is shown that representative AFM maps can be interpreted consistently with the most recent structural model of A(III)B(V)(001) surface, as corresponding to the A(III) sublattice, to the B(V) sublattice, or to the combination of both sublattices.

  18. Formation and atomic structure of boron nitride nanotubes with a cup-stacked structure

    NASA Astrophysics Data System (ADS)

    Oku, Takeo; Koi, Naruhiro; Suganuma, Katsuaki; Belosludov, Rodion V.; Kawazoe, Yoshiyuki

    2007-08-01

    Boron nitride (BN) nanotubes were synthesized by annealing Fe 4N/B powder at 1000 ∘C for 1 h in a nitrogen gas atmosphere, and large amounts of BN nanotubes with a cup-stacked structure were obtained after a purification process. The atomic structures of the cup-stacked BN nanotubes were investigated by high-resolution electron microscopy as well as molecular mechanics calculations, and compared with double walled BN nanotubes. The present results indicate that the cup-stacked structure with a cone angle of 20 ∘ is more stable than the structure with an angle of 38 ∘ and ordinary nanotube structures.

  19. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    NASA Astrophysics Data System (ADS)

    Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

    2013-05-01

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (H L) with cobalt(II) acetate gives the coordination compound [Co L 2] · CHCl3 ( I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds H L, L, and Co L 2 are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  20. First Optical Hyperfine Structure Measurement in an Atomic Anion

    SciTech Connect

    Fischer, A.; Canali, C.; Warring, U.; Kellerbauer, A.; Fritzsche, S.

    2010-02-19

    We have investigated the hyperfine structure of the transition between the 5d{sup 7}6s{sup 2} {sup 4}F{sub 9/2}{sup e} ground state and the 5d{sup 6}6s{sup 2}6p {sup 6}D{sub J}{sup o} excited state in the negative osmium ion by high-resolution collinear laser spectroscopy. This transition is unique because it is the only known electric-dipole transition in atomic anions and might be amenable to laser cooling. From the observed hyperfine structure in {sup 187}Os{sup -} and {sup 189}Os{sup -} the yet unknown total angular momentum of the bound excited state was found to be J=9/2. The hyperfine structure constants of the {sup 4}F{sub 9/2}{sup e} ground state and the {sup 6}D{sub 9/2}{sup o} excited state were determined experimentally and compared to multiconfiguration Dirac-Fock calculations. Using the knowledge of the ground and excited state angular momenta, the full energy level diagram of {sup 192}Os{sup -} in an external magnetic field was calculated, revealing possible laser cooling transitions.

  1. On the atomic structure of cocaine in solution.

    PubMed

    Johnston, Andrew J; Busch, Sebastian; Pardo, Luis Carlos; Callear, Samantha K; Biggin, Philip C; McLain, Sylvia E

    2016-01-14

    Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.

  2. The atomic structure of niobium and tantalum containing borophosphate glasses.

    PubMed

    Wetherall, K M; Doughty, P; Mountjoy, G; Bettinelli, M; Speghini, A; Casula, M F; Cesare-Marincola, F; Locci, E; Newport, R J

    2009-09-16

    A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content, where M is either niobium or tantalum. The glasses are found to consist of tetrahedral borate and phosphate with octahedral MO(6). As expected, B and P play the roles of tetrahedral network formers. At low M content there are isolated MO(6) units with [Formula: see text] and [Formula: see text] linkages that contribute to the glass network. As the M content increases, the number of [Formula: see text] links increases, and at the highest M content each MO(6) unit is connected to several others. The octahedra become significantly distorted as the niobium content increases, an effect that is not seen for tantalum.

  3. The grasp2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; He, X.; Froese Fischer, C.; Grant, I. P.

    2007-10-01

    This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel

  4. Thermal equilibrium/disequilibrium features in the excited-state temperature of atomic helium in MAP-II divertor simulator

    NASA Astrophysics Data System (ADS)

    Kado, S.

    2015-08-01

    Doppler-Stark spectrometry and laser Thomson scattering diagnostics for helium plasmas were applied to the MAP-II (material and plasma) steady-state linear divertor simulator at the University of Tokyo. In recombining plasmas, as the volumetric recombination proceeded, atomic, ionic and electron temperatures converged to the same values, which indicated the achievement of thermal equilibrium. On the other hand, in ionizing plasmas, in addition to the collisional heating of bulk atoms, excess heating of atoms in the high principal quantum number states (above Griem's boundary) was observed. This disequilibrium feature can be attributed to the presence of two prevailing conditions: that the characteristic time of the charge-exchange process of the atoms with ions in the system became shorter than the lifetime of the excited atoms spent above Griem's boundary, and that the population influx from above Griem's boundary is considerably larger than that from below the boundary.

  5. Cation-Poor Complex Metallic Alloys in Ba(Eu)-Au-Al(Ga) Systems: Identifying the Keys that Control Structural Arrangements and Atom Distributions at the Atomic Level.

    PubMed

    Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; Pecharsky, Vitalij; Miller, Gordon J; Mudring, Anja-Verena

    2015-11-02

    Four complex intermetallic compounds BaAu(6±x)Ga(6±y) (x = 1, y = 0.9) (I), BaAu(6±x)Al(6±y) (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104-112, Fm3̅c), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution ("coloring scheme"). Chemical bonding analyses for two different "EuAu6Tr6" models reveal maximization of the number of heteroatomic Au-Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the "EuAu6Tr6" models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. The effective moments of 8.3 μB/f.u., determined from Curie-Weiss fits, point to divalent oxidation states for europium in both III and IV.

  6. THE FORMATION OF IRIS DIAGNOSTICS. I. A QUINTESSENTIAL MODEL ATOM OF Mg II AND GENERAL FORMATION PROPERTIES OF THE Mg II h and k LINES

    SciTech Connect

    Leenaarts, J.; Pereira, T. M. D.; Carlsson, M.; De Pontieu, B.; Uitenbroek, H. E-mail: tiago.pereira@astro.uio.no E-mail: bdp@lmsal.com

    2013-08-01

    NASA's Interface Region Imaging Spectrograph (IRIS) space mission will study how the solar atmosphere is energized. IRIS contains an imaging spectrograph that covers the Mg II h and k lines as well as a slit-jaw imager centered at Mg II k. Understanding the observations will require forward modeling of Mg II h and k line formation from three-dimensional (3D) radiation-MHD models. This paper is the first in a series where we undertake this forward modeling. We discuss the atomic physics pertinent to h and k line formation, present a quintessential model atom that can be used in radiative transfer computations, and discuss the effect of partial redistribution (PRD) and 3D radiative transfer on the emergent line profiles. We conclude that Mg II h and k can be modeled accurately with a four-level plus continuum Mg II model atom. Ideally radiative transfer computations should be done in 3D including PRD effects. In practice this is currently not possible. A reasonable compromise is to use one-dimensional PRD computations to model the line profile up to and including the central emission peaks, and use 3D transfer assuming complete redistribution to model the central depression.

  7. Twinned low-temperature structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate.

    PubMed

    Lutz, Martin

    2010-11-01

    Tris(ethylenediamine)zinc(II) sulfate, [Zn(C(2)H(8)N(2))(3)]SO(4), (I), undergoes a reversible solid-solid phase transition during cooling, accompanied by a lowering of the symmetry from high-trigonal P31c to low-trigonal P3 and by merohedral twinning. The molecular symmetries of the cation and anion change from 32 (D(3)) to 3 (C(3)). This lower symmetry allows an ordered sulfate anion and generates in the complex cation two independent N atoms with significantly different geometries. The twinning is the same as in the corresponding Ni complex [Jameson et al. (1982). Acta Cryst. B38, 3016-3020]. The low-temperature phase of tris(ethylenediamine)copper(II) sulfate, [Cu(C(2)H(8)N(2))(3)]SO(4), (II), has only triclinic symmetry and the unit-cell volume is doubled with respect to the room-temperature structure in P31c. (II) was refined as a nonmerohedral twin with five twin domains. The asymmetric unit contains two independent formula units, and all cations and anions are located on general positions with 1 (C(1)) symmetry. Both molecules of the Cu complex are in elongated octahedral geometries because of the Jahn-Teller effect. This is in contrast to an earlier publication, which describes the complex as a compressed octahedron [Bertini et al. (1979). J. Chem. Soc. Dalton Trans. pp. 1409-1414].

  8. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  9. An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

    PubMed Central

    Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

    2012-01-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  10. Crystal structure of cis-diamminebis(nitrito-κN)platinum(II).

    PubMed

    Kahlenberg, Volker; Gelbrich, Thomas; Tessadri, Richard; Klauser, Frederik

    2015-04-01

    Single crystals of cis-[Pt(NO2)2(NH3)2], were obtained by means of hyper-saturation directly out of a plating electrolyte. The square-planar coordination environment of the divalent Pt(II) atom is formed by four N atoms belonging to two ammine and two monodentate nitrite ligands. The ligands adopt a cis configuration. The crystal structure contains stacks of close-packed mol-ecules which run parallel to [001]. There are nine crystallographically independent inter-molecular N-H⋯O hydrogen bonds, resulting in a hydrogen-bonded hxl-type framework in which each mol-ecule serves as an eight-connected node. Four of the nine distinct hydrogen bonds connect complexes which belong to the same close-packed column parallel to [001]. In contrast to the previously reported crystal structure of the trans isomer, the title structure does not display intra-molecular hydrogen bonding.

  11. In Situ D-periodic Molecular Structure of Type II Collagen

    SciTech Connect

    Antipova, Olga; Orgel, Joseph P.R.O.

    2010-05-06

    Collagens are essential components of extracellular matrices in multicellular animals. Fibrillar type II collagen is the most prominent component of articular cartilage and other cartilage-like tissues such as notochord. Its in situ macromolecular and packing structures have not been fully characterized, but an understanding of these attributes may help reveal mechanisms of tissue assembly and degradation (as in osteo- and rheumatoid arthritis). In some tissues such as lamprey notochord, the collagen fibrillar organization is naturally crystalline and may be studied by x-ray diffraction. We used diffraction data from native and derivative notochord tissue samples to solve the axial, D-periodic structure of type II collagen via multiple isomorphous replacement. The electron density maps and heavy atom data revealed the conformation of the nonhelical telopeptides and the overall D-periodic structure of collagen type II in native tissues, data that were further supported by structure prediction and transmission electron microscopy. These results help to explain the observed differences in collagen type I and type II fibrillar architecture and indicate the collagen type II cross-link organization, which is crucial for fibrillogenesis. Transmission electron microscopy data show the close relationship between lamprey and mammalian collagen fibrils, even though the respective larger scale tissue architecture differs.

  12. First Structural Steel Erected at NSLS-II

    ScienceCinema

    None

    2016-07-12

    Ten steel columns were incorporated into the ever-growing framework for the National Synchrotron Light Source II last week, the first structural steel erected for the future 400,000-square-foot facility.

  13. First Structural Steel Erected at NSLS-II

    SciTech Connect

    2009-09-14

    Ten steel columns were incorporated into the ever-growing framework for the National Synchrotron Light Source II last week, the first structural steel erected for the future 400,000-square-foot facility.

  14. On structural patterns in H II regions

    SciTech Connect

    Feibelman, W.A. )

    1989-05-01

    High-resolution photographs of H II regions show that a large number of stars embedded in the nebulosities appear to be surrounded by emply spaces. This phenomenon seems to be quite common but has escaped attention up to now. The effect is not a photographic one, nor does it arise in the half-tone reproduction processes employed in publications, but no satisfactory explanation is apparent. 9 refs.

  15. Tooth structure studied using the atomic force microscope

    NASA Astrophysics Data System (ADS)

    Kasas, Sandor; Berdal, Ariane; Celio, Marco R.

    1993-06-01

    We used the atomic force microscope (AFM) to observe structure of the tooth, both rat and human. The rigidity and the surface flatness of thin sections of this mineralized tissue, allow us to attain good resolution with the AFM. As enamel contains uniquely large crystals of hydroxyapatite it can be investigated at high resolution. Tooth enamel and thin slices of undecalcified developing tooth germs from 2 - 12 day old rats were observed, embedded in acrylic resin (Lowicryl K4M). In addition, as orthophosphoric acid is widely used clinically to etch tooth enamel before restoring with composites, we studied its action at pH2 on the tooth surface during 1 hour of exposition. Hydroxyapatite crystals and collagen fibers were seen in the tooth slices observed in air, and the classical structure of the enamel was visible. The etched enamel surface under liquid, showed dramatic differences to that imaged in air. Modifications to the surface were also seen during exposure to the acid.

  16. Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Dihydroartemisinic acid (DHAA, C15H24O2, five chiral centers) is a precursor in proposed low-cost synthetic routes to the antimalarial drug artemisinin. In one reaction process being considered in pharmaceutical production, DHAA is formed from an enantiopure sample of artemisinic acid through hydrogenation of the alkene. This reaction needs to properly set the stereochemistry of the asymmetric carbon for the synthesis to produce artemisinin. A recrystallization process can purify the diastereomer mixture of the hydrogenation reaction if the unwanted epimer is produced in less than 10% abundance. There is a need in the process analytical chemistry to rapidly (less than 1 min) measure the diastereomer excess and current solutions, such a HPLC, lack the needed measurement speed. The rotational spectrum of DHAA has been measured at 300:1 signal-to-noise ratio in a chirped-pulsed Fourier transform microwave spectrometer operating from 2-8 GHz using simple heating of the compound. The 13C isotope analysis provides a carbon atom structure that confirms the diastereomer. This structure is in excellent agreement with quantum chemistry calculations at the B2PLYPD3/ 6-311++G** level of theory. The DHAA spectrum is expected to be fully resolved from the unwanted diastereomer raising the potential for fast diastereomer excess measurement by rotational spectroscopy in the pharmaceutical production process.

  17. An atomic structure of human γ-secretase

    PubMed Central

    Lu, Peilong; Ma, Dan; Sun, Linfeng; Zhou, Rui; Scheres, Sjors H.W.; Shi, Yigong

    2015-01-01

    Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer’s disease (AD), with most AD-derived mutations mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human γ-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy. AD-derived mutations in PS1 affect residues at two hotspots, each located at the center of a distinct four transmembrane segment (TM) bundle. TM2, and to a lesser extent TM6, exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain (ECD) following substrate recruitment. Aph-1 serves as a scaffold, anchoring the lone TM from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of γ-secretase function. PMID:26280335

  18. An atomic structure of human γ-secretase

    NASA Astrophysics Data System (ADS)

    Bai, Xiao-Chen; Yan, Chuangye; Yang, Guanghui; Lu, Peilong; Ma, Dan; Sun, Linfeng; Zhou, Rui; Scheres, Sjors H. W.; Shi, Yigong

    2015-09-01

    Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human γ-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy. Mutations derived from Alzheimer's disease affect residues at two hotspots in PS1, each located at the centre of a distinct four transmembrane segment (TM) bundle. TM2 and, to a lesser extent, TM6 exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain after substrate recruitment. Component protein APH-1 serves as a scaffold, anchoring the lone transmembrane helix from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of γ-secretase function.

  19. Atomic Structure Refinement of Pbnm-type Perovskite Oxide Films

    NASA Astrophysics Data System (ADS)

    Choquette, Amber; Smith, Cole; May, Steve

    Complex ABO3 oxide heterostructures are of interest due to their wide variety of electronic, optical, and magnetic properties. One of the controlling factors to these functionalities is the distortions and rotations of the corner-connected BO6 octahedral network. This BO6 octahedra network directly couples to the electronic bandwidth of these materials, but the inability to determine the full atomic structure in thin films has inhibited quantitative understanding of how factors such as epitaxial strain alter the octahedral rotations in this broad class of materials. Earlier work of has demonstrate that half-order diffraction peaks can be used to quantify octahedral rotations in thin strained films. Here, we build on this approach to solve for both the oxygen and A-site positions in films of the commonly occurring Pbnm structure type. We present on epitaxial RFeO3 heterostructures, where R is a rare earth element, to demonstrate the feasibility of quantifying oxygen and A-site displacements in films using synchrotron diffraction. This work is supported by the National Science Foundation (DMR-1151649).

  20. A near atomic structure of the active human apoptosome

    PubMed Central

    Cheng, Tat Cheung; Hong, Chuan; Akey, Ildikó V; Yuan, Shujun; Akey, Christopher W

    2016-01-01

    In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. DOI: http://dx.doi.org/10.7554/eLife.17755.001 PMID:27697150

  1. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    SciTech Connect

    Chen, Liqing Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  2. Atomic Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S2.

    ERIC Educational Resources Information Center

    Inner London Education Authority (England).

    This unit on atomic structure is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. Level one focuses on the atomic nucleus. Level two focuses on the arrangement of extranuclear electrons, approaching atomic orbitals through both electron bombardment and spectra.…

  3. Crystal structures of copper(II) nitrate complexes containing 4,4'-bipyridyl and halogen-substituted 2-[(2-hydroxyethylimino)methyl]phenols

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Petrenko, P. A.; Popovski, L. G.; Simonov, Yu. A.; Bocelli, G.; Gulea, A. P.

    2009-03-15

    The crystal structures of ({mu}-4,4'-bipyridyl)-di{l_brace}nitrato-2,4-dibromo-6-[(2-hydroxyethylimino)methyl] phenolo (1-)copper{r_brace} (I), ({mu}-4,4'-bipyridyl)-di{l_brace}nitrato-2,4-dichloro-6-[(2-hydroxyethylimino)methyl] phenolo(1-)copper{r_brace} (II), and ({mu}-4,4'-bipyridyl)-{l_brace}4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(2-) copper-nitrato-4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(1-)copper{r_brace} tetrahydrate (III) are determined. The crystal structures of compounds I and II contain binuclear complexes, in which each copper atom is coordinated by the singly deprotonated tridentate molecule of the corresponding azomethine, the monodentate nitrate ion, and bipyridyl that plays the role of a bridge between the central atoms. In the structures of compounds I and II, the coordination polyhedra of the copper atoms are slightly distorted tetragonal pyramids. The pyramid base is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. The axial vertices of the pyramids are occupied by the oxygen atoms of the monodentate nitrato groups. The crystal structure of compound III involves tetranuclear complexes in which the coordination polyhedra of the central copper atoms are (4 + 1 + 1) bipyramids. The base of these bipyramids is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. One apical vertex is occupied by the bridging phenol oxygen atom of the nearest complex. The sixth coordination site of the first copper atom is occupied by the chlorine atom of the salicylidene fragment of the neighboring complex related to the initial complex through the center of symmetry. In turn, the sixth coordination site of the second copper atom is occupied by the oxygen atom of the monodentate nitrato group.

  4. Atomic structure and surface defects at mineral-water interfaces probed by in situ atomic force microscopy.

    PubMed

    Siretanu, Igor; van den Ende, Dirk; Mugele, Frieder

    2016-04-21

    Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.

  5. Structure and evolution of fossil H II regions

    NASA Technical Reports Server (NTRS)

    Mccray, R.; Schwarz, J.

    1971-01-01

    The structure and evolution of a fossil H II region created by a burst of ionizing radiation from a supernova is considered. The cooling time scale for the shell is about 10 to the 6th power years. Superposition of million-year-old fossil H II regions may account for the temperature and ionization of the interstellar medium. Fossil H II regions are unstable to growth of thermal condensations. Highly ionized filamentary structures form and dissipate in about 10,000 years. Partially ionized clouds form and dissipate in about 10 to the 6th power years.

  6. Entangling strings of neutral atoms in 1D atomic pipeline structures.

    PubMed

    Dorner, U; Fedichev, P; Jaksch, D; Lewenstein, M; Zoller, P

    2003-08-15

    We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.

  7. Palladium(II) and platinum(II) complexes containing benzimidazole ligands: Molecular structures, vibrational frequencies and cytotoxicity

    NASA Astrophysics Data System (ADS)

    Abdel Ghani, Nour T.; Mansour, Ahmed M.

    2011-04-01

    (1H-benzimidazol-2-ylmethyl)-(4-methoxyl-phenyl)-amine (L 1), (1H-benzimidazol-2-ylmethyl)-(4-methyl-phenyl)-amine (L 2) and their Pd(II) and Pt(II) complexes have been synthesized as potential anticancer compounds and their structures were elucidated using a variety of physico-chemical techniques. Theoretical calculations invoking geometry optimization, vibrational assignments, 1H NMR, charge distribution and molecular orbital description HOMO and LUMO were done using density functional theory. Natural bond orbital analysis (NBO) method was performed to provide details about the type of hybridization and the nature of bonding in the studied complexes. Strong coordination bonds (LP(1)N11 → σ *(M sbnd Cl22)) and (LP(1)N21 → σ *(M sbnd Cl23)) (M = Pd or Pt) result from donation of electron density from a lone pair orbital on the nitrogen atoms to the acceptor metal molecular orbitals. The experimental results and the calculated molecular parameters revealed square-planar geometries around the metallic centre through the pyridine-type nitrogen of the benzimidazole ring and secondary amino group and two chlorine atoms. The activation thermodynamic parameters were calculated using non-isothermal methods. The synthesized ligands, in comparison to their metal complexes were screened for their antibacterial activity. In addition, the studied complexes showed activity against three cell lines of different origin, breast cancer (MCF-7), Colon Carcinoma (HCT) and human heptacellular carcinoma (Hep-G2) comparable to cis-platin.

  8. Which One Is Better? Jigsaw II versus Jigsaw IV on the Subject of the Building Blocks of Matter and Atom

    ERIC Educational Resources Information Center

    Turkmen, Hakan; Buyukaltay, Didem

    2015-01-01

    In this study, the effect of using Jigsaw II and Jigsaw IV techniques on the subject of "Atoms-The Basic Unit of Matter" in science course of 6th grade on academic achievement was examined. Pre-test post-test control group research was used in the study. Study population is all secondary schools in Turgutlu district of Manisa province…

  9. An atomic-force-microscopy study of the structure of surface layers of intact fibroblasts

    NASA Astrophysics Data System (ADS)

    Khalisov, M. M.; Ankudinov, A. V.; Penniyaynen, V. A.; Nyapshaev, I. A.; Kipenko, A. V.; Timoshchuk, K. I.; Podzorova, S. A.; Krylov, B. V.

    2017-02-01

    Intact embryonic fibroblasts on a collagen-treated substrate have been studied by atomic-force microscopy (AFM) using probes of two types: (i) standard probes with tip curvature radii of 2-10 nm and (ii) special probes with a calibrated 325-nm SiO2 ball radius at the tip apex. It is established that, irrespective of probe type, the average maximum fibroblast height is on a level of 1.7 μm and the average stiffness of the probe-cell contact amounts to 16.5 mN/m. The obtained AFM data reveal a peculiarity of the fibroblast structure, whereby its external layers move as a rigid shell relative to the interior and can be pressed inside to a depth dependent on the load only.

  10. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; Gaigalas, G.; Bieroń, J.; Fischer, C. Froese; Grant, I. P.

    2013-09-01

    , Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine structure parameters, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A

  11. General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

  12. Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

    SciTech Connect

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-17

    In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

  13. Influence of nitrogen-containing chelating ligands on the structures of zinc(II) 4,4'-ethylenedibenzoates.

    PubMed

    Wang, Xiu-Yan; Wang, Jia-Jun; Ng, Seik Weng

    2008-12-01

    The Zn(II) compounds, micro-4,4'-ethylenedibenzoato-bis[acetatoaqua(dipyrido[3,2-a:2',3'-c]phenazine)zinc(II)] dihydrate, [Zn(2)(C(2)H(3)O(2))(2)(C(16)H(10)O(4))(C(18)H(10)N(4))(2)(H(2)O)(2)] x 2H(2)O, (I), and catena-poly[[[aqua(pyrazino[2,3-f][1,10]phenanthroline)zinc(II)]-micro-4,4'-ethylenedibenzoato] N,N-dimethylformamide hemisolvate], {[Zn(C(16)H(10)O(4))(C(14)H(8)N(4))(H(2)O)] x 0.5C(3)H(7)NO}(n), (II), display very different structures because of the influence of the N-donor chelating ligands. In (I), the coordination geometry of each Zn(II) centre is distorted octahedral, involving two N atoms from one dipyrido[3,2-a:2',3'-c]phenazine (L1) ligand, and four O atoms from one bis-chelating acetate anion, one bridging 4,4'-ethylenedibenzoate (bpea) ligand and one water molecule. Adjacent Zn(II) atoms are bridged by one bpea ligand to form a dinuclear complex, and the dinuclear species is centrosymmetric. Two types of pi-pi interactions between neighbouring dinuclear species have been found: one is between the L1 ligands, and the second is between the L1 and bpea ligands. In this way, an interesting two-dimensional supramolecular layer is formed. The layers are further linked by O-H...O and O-H...N hydrogen bonds, generating a three-dimensional supramolecular network. In (II), each Zn(II) atom is square-pyramidally coordinated by two N atoms from one pyrazino[2,3-f][1,10]phenanthroline ligand, three O atoms from two different bpea ligands and one water molecule. The two bpea dianions are situated across inversion centres. The bpea dianions bridge neighbouring Zn(II) centres, giving a one-dimensional chain structure in the ab plane. As in (I), two types of pi-pi interactions between neighbouring chains complete a three-dimensional supramolecular structure. The results indicate that the structures of the N-donor chelating ligands are the dominant factors determining the final supramolecular structures of the two compounds.

  14. Electronically excited rubidium atom in helium clusters and films. II. Second excited state and absorption spectrum.

    PubMed

    Leino, Markku; Viel, Alexandra; Zillich, Robert E

    2011-01-14

    Following our work on the study of helium droplets and film doped with one electronically excited rubidium atom Rb(∗) ((2)P) [M. Leino, A. Viel, and R. E. Zillich, J. Chem. Phys. 129, 184308 (2008)], we focus in this paper on the second excited state. We present theoretical studies of such droplets and films using quantum Monte Carlo approaches. Diffusion and path integral Monte Carlo algorithms combined with a diatomics-in-molecule scheme to model the nonpair additive potential energy surface are used to investigate the energetics and the structure of Rb(∗)He(n) clusters. Helium films as a model for the limit of large clusters are also considered. As in our work on the first electronic excited state, our present calculations find stable Rb(∗)He(n) clusters. The structures obtained are however different with a He-Rb(∗)-He exciplex core to which more helium atoms are weakly attached, preferentially on one end of the core exciplex. The electronic absorption spectrum is also presented for increasing cluster sizes as well as for the film.

  15. Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

    PubMed

    Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-02-08

    Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.

  16. Million Atom Pseudopotential Manybody Theory of Electronic Structure and Spectroscopy of Semiconductor Quantum Dots

    NASA Astrophysics Data System (ADS)

    Zunger, Alex

    2003-03-01

    Semiconductor Quantum Dots that are of sufficient structural quality (good crystallinity, surface passivation, size uniformity) to produce ultra sharp spectroscopic lines worthy of a detailed theoretical effort tend to be rather BIG, containing thousands to million atoms. Yet, in this size regime, the only theoretical methods available are effective-mass based, particle-in-a-box approaches, that neglect multi-band and inter-valley coupling, leading to significant qualitative errors.(A. Zunger,Phys. Stat. Sol. (a) 190), 467 (2002). While LDA-based methods are capable of solving the Single-Particle problem even for ˜1,000 atom dots, the all important many-body problem can be currently addressed only for considerably smaller dots. I will present here a computational alternative which addresses both the single-particle and the Manybody parts of the problem for 10^3 to 10^6 atom dots .The method is applicable both to ``free Standing" (e.g. colloidal) dots of CdSe, InP, InAs and Si, as well as to the strained, ``self-assembled" epitaxial dots of, e.g., InGaAs/GaAs. It is based on a ``Linear Combination of Bulk Bands" (LCBB) approach that expands the dot states in terms of plane wave based (pseudopotential) Bloch states throughout the Brillouin zone. The manybody part is treated via Configuration Interaction. I will illustrate how this method addresses some of the recent striking experimental observations on semiconductor quantum dots:(i) Scaling laws for band gaps and exchange interactions (ii) Rapid Auger transitions in colloidal dots (iii) Coulomb Blocade and Spin Blockade in colloidal dots (iv) Charged Excitons (e.g. Trions) in Self-assembled dots, and (v) excitonic Fine-Structure in self assembled dots.

  17. Functionalized cotton via surface-initiated atom transfer radical polymerization for enhanced sorption of Cu(II) and Pb(II).

    PubMed

    Zheng, Y Q; Deng, Shubo; Niu, Li; Xu, F J; Chai, M Y; Yu, Gang

    2011-09-15

    The surface-initiated atom transfer radical polymerization (ATRP) was used to successfully prepare the aminated cotton and polyacrylic acid sodium (P(AA-Na))-grafted cotton for the efficient removal of Cu(II) and Pb(II) from aqueous solution in this study. The modified cotton surfaces were characterized by scanning electron microscopy (SEM), Fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS). The grafted long polymers with high density of amine and carboxyl groups on the cotton surfaces were responsible for the enhanced adsorption of heavy metals. The sorption behaviors including sorption kinetics, isotherms and pH effect were investigated. The sorption equilibrium of Cu(II) and Pb(II) was achieved within 1h on the P(AA-Na)-grafted cotton, much faster than 8h on the aminated cotton. According to the Langmuir fitting, the maximum sorption capacities of Cu(II) and Pb(II) on the P(AA-Na)-grafted cotton were 2.45 and 2.44 mmol/g, respectively, higher than many adsorbents reported in the literature. The P(AA-Na)-grafted cotton had better adsorption behaviors for Cu(II) and Pb(II) than the aminated cotton.

  18. Does atomic polarizability play a role in hydrogen radio recombination spectra from Galactic H II regions?

    NASA Astrophysics Data System (ADS)

    Hey, J. D.

    2013-09-01

    Since highly excited atoms, which contribute to the radio recombination spectra from Galactic H II regions, possess large polarizabilities, their lifetimes are influenced by ion (proton)-induced dipole collisions. It is shown that, while these ion-radiator collisional processes, if acting alone, would effectively limit the upper principal quantum number attainable for given plasma parameters, their influence is small relative to that of electron impacts within the framework of line broadening theory. The present work suggests that ion-permanent dipole interactions (Hey et al 2004 J. Phys. B: At. Mol. Opt. Phys. 37 2543) would also be of minor importance in limiting the occupation of highly excited states. On the other hand, the ion-induced dipole collisions are essential for ensuring equipartition of energy between atomic and electron kinetic distributions (Hey et al 1999 J. Phys. B: At. Mol. Opt. Phys. 32 3555; 2005 J. Phys. B: At. Mol. Opt. Phys. 38 3517), without which Voigt profile analysis to extract impact broadening widths would not be possible. Electron densities deduced from electron impact broadening of individual lines (Griem 1967 Astrophys. J. 148 547; Watson 2006 J. Phys. B: At. Mol. Opt. Phys. 39 1889) may be used to check the significance of the constraints arising from the present analysis. The spectra of Bell et al (2000 Publ. Astron. Soc. Pac. 112 1236; 2011 Astrophys. Space Sci. 333 377; 2011 Astrophys. Space Sci. 335 451) for Orion A and W51 in the vicinity of 6.0 and 17.6 GHz are examined in this context, and also in terms of a possible role of the background ion microfield in reducing the near-elastic contributions to the electron impact broadening below the predictions of theory (Hey 2012 J. Phys. B: At. Mol. Opt. Phys. 45 065701). These spectra are analysed, subject to the constraint that calculated relative intensities of lines, arising from upper states in collisional-radiative equilibrium, should be consistent with those obtained from

  19. Atomic structure of intracellular amorphous calcium phosphate deposits.

    PubMed

    Betts, F; Blumenthal, N C; Posner, A S; Becker, G L; Lehninger, A L

    1975-06-01

    The radial distribution function calculated from x-ray diffraction of mineralized cytoplasmic structures isolated from the hepatopancreas of the blue crab (Callinectes sapidus) is very similar to that previously found for synthetic amorphous calcium phosphate. Both types of mineral apparently have only short-range atomic order, represented as a neutral ion cluster of about 10 A in longest dimension, whose probable composition is expressed by the formula Ca9(PO4)6. The minor differences observed are attributed to the presence in the biological mineral of significant amounts of Mg-2+ and ATP. Synthetic amorphous calcium phosphate in contact with a solution containing an amount of ATP equivalent to that of the biological mineral failed to undergo conversion to the thermodynamically more stable hydroxyapatite. The amorphous calcium phosphate of the cytoplasmic mineral granules is similarly stable, and does not undergo conversion to hydroxyapatite, presumably owing to the presence of ATP and Mg-2+, known in inhibitors of the conversion process. The physiological implications of mineral deposits consisting of stabilized calcium phosphate ion clusters are discussed.

  20. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

    Guo, Yu; Zhou, Si; Zhang, Junfeng; Bai, Yizhen; Zhao, Jijun

    2016-06-01

    Grain boundary (GB) is one main type of defects in two-dimensional (2D) crystals, and has significant impact on the physical properties of 2D materials. Phosphorene, a recently synthesized 2D semiconductor, possesses a puckered honeycomb lattice and outstanding electronic properties. It is very interesting to know the possible GBs present in this novel material, and how their properties differ from those in the other 2D materials. Based on first-principles calculations, we explore the atomic structure, thermodynamic stability, and electronic properties of phosphorene GBs. A total of 19 GBs are predicted and found to be energetically stable with formation energies much lower than those in graphene. These GBs do not severely affect the electronic properties of phosphorene: the band gap of perfect phosphorene is preserved, and the electron mobilities are only moderately reduced in these defective systems. Our theoretical results provide vital guidance for experimental tailoring the electronic properties of phosphorene as well as the device applications using phosphorene materials.

  1. Calculation of atomic structures and radiative properties of fusion plasmas

    NASA Astrophysics Data System (ADS)

    Jarrah, Walid; Pain, Jean-Christophe; Benredjem, Djamel

    2017-03-01

    The opacity is an important issue in the knowledge of the radiative properties of Inertial Confinement Fusion (ICF) and astrophysical plasmas. In this work we present the opacity of the mixture C+Si, composing the ablator of some ICF capsules. We have used Cowan's code to calculate the atomic structure of carbon and silicon. We also have developed a collisional-radiative model in order to obtain the opacity of the mixture. Line broadening, line shift and ionization potential depression are taken into account in the opacity profile. Comparisons to other calculations are carried out. NLTE and LTE opacity calculations show discrepancies mainly in the range 1900-2000 eV for the bound-bound contribution to the total opacity and in the range 50-350 eV for the bound-free contribution. We have also accounted for photoexcitation and photoionization processes. The corresponding rates are obtained by modeling the Hohlraum radiation by a Planckian distribution at a radiative temperature of 300 eV.

  2. Syntheses, structural characterization and spectroscopic studies of cadmium(II)-metal(II) cyanide complexes with 4-(2-aminoethyl)pyridine

    NASA Astrophysics Data System (ADS)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Hökelek, Tuncer

    2017-02-01

    Three new cadmium(II)-metal(II) cyanide complexes, [Cd(4aepy)2(H2O)2][Ni(CN)4] (1), [Cd(4aepy)2(H2O)2][Pd(CN)4] (2) and [Cd(4aepy)2(H2O)2][Pt(CN)4] (3) [4aepy = 4-(2-aminoethyl)pyridine], have been synthesized and characterized by elemental, thermal, FT-IR and Raman spectral analyses. The crystal structures of 1 and 2 have been determined by single crystal X-ray diffraction technique, in which they crystallize in the monoclinic system and C2/c space group. The M(II) [M(II) = Ni(II), Pd(II) and Pt(II)] ions are coordinated with the carbon atoms of the four cyanide groups in the square planar geometries and the [M(CN)4]2- ions act as counter ions. The Cd(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. 3D supramolecular structures of 1 and 2 were occurred by M⋯π and hydrogen bonding (Nsbnd H⋯N and Osbnd H⋯N) interactions. Vibrational assignments of all the observed bands were given and the spectral properties were also supported the crystal structures of the complexes. A possible decompositions of the complexes were investigated in the temperature range 30-800 °C in the static atmosphere.

  3. Synthesis, structural elucidation and carbon dioxide adsorption on Zn (II) hexacyanoferrate (II) Prussian blue analogue

    NASA Astrophysics Data System (ADS)

    Roque-Malherbe, R.; Lugo, F.; Polanco, R.

    2016-11-01

    In the course of the last years hexacyanoferrates have been widely studied; even though, the adsorption properties of Zn (II) hexacyanoferrate(II) (labelled here Zn-HII) have not been thoroughly considered. In addition, soft porous crystals, i.e., adsorbents that display structural flexibility have been, as well, extensively studied, however this property has not been reported for Zn (II) hexacyanoferrate(II). In this regard, the key questions addressed here were the synthesis and structural characterization of Zn-HII together with the investigation of their low (up to 1 bar) and high pressure (up to 30 bar) adsorption properties, to found if these materials show structural flexibility. Then, to attain the anticipated goals, structural characterizations were made with: X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) and thermo-gravimetric analysis (TGA), simultaneously, with the investigation of the adsorption of carbon dioxide. As a result of the research process we concluded that the Zn-HII displayed Fm3 barm space group framework. Besides, the carbon dioxide adsorption investigation demonstrated the presence of the framework expansion effect together with an extremely high adsorption heat, properties that could be useful for the use of Zn(II) hexacyanoferrate(II) as an excellent adsorbent.

  4. Atomic Structure and Dynamics of Single Platinum Atom Interactions with Monolayer MoS2.

    PubMed

    Li, Huashan; Wang, Shanshan; Sawada, Hidetake; Han, Grace G D; Samuels, Thomas; Allen, Christopher S; Kirkland, Angus I; Grossman, Jeffrey C; Warner, Jamie H

    2017-03-28

    We have studied atomic level interactions between single Pt atoms and the surface of monolayer MoS2 using aberration-corrected annular dark field scanning transmission electron microscopy at an accelerating voltage of 60 kV. Strong contrast from single Pt atoms on the atomically resolved monolayer MoS2 lattice enables their exact position to be determined with respect to the MoS2 lattice, revealing stable binding sites. In regions of MoS2 free from surface contamination, the Pt atoms are localized in S vacancy sites and exhibit dynamic hopping to nearby vacancy sites driven by the energy supplied by the electron beam. However, in areas of MoS2 contaminated with carbon surface layers, the Pt atoms appear at various positions with respect to the underlying MoS2 lattice, including on top of Mo and in off-axis positions. These variations are due to the Pt bonding with the surrounding amorphous carbon layer, which disrupts the intrinsic Pt-MoS2 interactions, leading to more varied positions. Density functional theory (DFT) calculations reveal that Pt atoms on the surface of MoS2 have a small barrier for migration and are stabilized when bound to either a single or double sulfur vacancies. DFT calculations have been used to understand how the catalytic activity of the MoS2 basal plane for hydrogen evolution reaction is influenced by Pt dopants by variation of the hydrogen adsorption free energy. This strong dependence of catalytic effect on interfacial configurations is shown to be common for a series of dopants, which may provide a means to create and optimize reaction centers.

  5. Structures and Properties of Polyurethanes. Part II,

    DTIC Science & Technology

    1979-03-23

    small. Relaxatio" processes in polyurethane elastomers on three following LKeasons must differ from the same in other elastomeric systems the idLge... elastomeric polyurethane fibers is given also in work [22b]. The authors will examine the structure of the linear polyurethane elastomers , formed from rigid...properties of polyuretuane elastomers to a considerable degree depend on structure and aoiecular weight of basic component - polyether/polyester. Stuaied tne

  6. The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

    PubMed

    Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

    2015-06-01

    Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

  7. Imino-phosphine palladium(II) and platinum(II) complexes: synthesis, molecular structures and evaluation as antitumor agents.

    PubMed

    Motswainyana, William M; Onani, Martin O; Madiehe, Abram M; Saibu, Morounke; Thovhogi, Ntevheleni; Lalancette, Roger A

    2013-12-01

    The imino-phosphine ligands L1 and L2 were prepared via condensation reaction of 2-(diphenylphosphino)benzaldehyde with substituted anilines and obtained in very good yields. An equimolar reaction of L1 and L2 with either PdCl2(cod) or PtCl2(cod) gave new palladium(II) and platinum(II) complexes 1-4. The compounds were characterized by elemental analysis, IR, (1)H and (31)P NMR spectroscopy. The molecular structures of 2, 3 and 4 were confirmed by X-ray crystallography. All the three molecular structures crystallized in monoclinic C2/c space system. The coordination geometry around the palladium and platinum atoms in respective structures exhibited distorted square planar geometry at the metal centers. The complexes were evaluated in vitro for their cytotoxic activity against human breast (MCF-7) and human colon (HT-29) cancer cells, and they exhibited growth inhibitory activities and selectivity that were superior to the standard compound cisplatin.

  8. Coordination structure of adsorbed Zn(II) at Water-TiO2 interfaces

    SciTech Connect

    He, G.; Pan, G.; Zhang, M.; Waychunas, G.A.

    2011-01-15

    The local structure of aqueous metal ions on solid surfaces is central to understanding many chemical and biological processes in soil and aquatic environments. Here, the local coordination structure of hydrated Zn(II) at water-TiO{sub 2} interfaces was identified by extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectroscopy combined with density functional theory (DFT) calculations. A nonintegral coordination number of average {approx}4.5 O atoms around a central Zn atom was obtained by EXAFS analysis. DFT calculations indicated that this coordination structure was consistent with the mixture of 4-coordinated bidentate binuclear (BB) and 5-coordinated bidentate mononuclear (BM) metastable equilibrium adsorption (MEA) states. The BB complex has 4-coordinated Zn, while the monodentate mononuclear (MM) complex has 6-coordinated Zn, and a 5-coordinated adsorbed Zn was found in the BM adsorption mode. DFT calculated energies showed that the lower-coordinated BB and BM modes were thermodynamically more favorable than the higher-coordinated MM MEA state. The experimentally observed XANES fingerprinting provided additional direct spectral evidence of 4- and 5-coordinated Zn-O modes. The overall spectral and computational evidence indicated that Zn(II) can occur in 4-, 5-, and 6-oxygen coordinated sites in different MEA states due to steric hindrance effects, and the coexistence of different MEA states formed the multiple coordination environments.

  9. Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 Å resolution.

    PubMed

    Kawakami, Keisuke; Umena, Yasufumi; Kamiya, Nobuo; Shen, Jian-Ren

    2011-01-01

    The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn(4)Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 Å, which yielded a detailed picture of the Mn(4)CaO(5)-cluster for the first time. In the high resolution structure, the Mn(4)CaO(5)-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn(4)CaO(5)-cluster analyzed at 1.9 Å resolution, and compare them with the structures reported previously.

  10. Atomic structure of machined semiconducting chips: An x-ray absorption spectroscopy study

    SciTech Connect

    Paesler, M.; Sayers, D.

    1988-12-01

    X-ray absorption spectroscopy (XAS) has been used to examine the atomic structure of chips of germanium that were produced by single point diamond machining. It is demonstrated that although the local (nearest neighbor) atomic structure is experimentally quite similar to that of single crystal specimens information from more distant atoms indicates the presence of considerable stress. An outline of the technique is given and the strength of XAS in studying the machining process is demonstrated.

  11. Local structures of high-entropy alloys (HEAs) on atomic scales: An overview

    SciTech Connect

    Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; Egami, Takeshi; Liaw, Peter K.

    2015-01-01

    The high-entropy alloys, containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on the atomic level are essential to understand the mechanical behaviors and related mechanisms. This article covers the local structure and stress on the atomic level are reviewed by the pair-distribution function of neutron-diffraction data, ab-initio molecular dynamics simulations, and the atomic probe microscopy.

  12. Optofluidic waveguides: II. Fabrication and structures

    PubMed Central

    Schmidt, Holger

    2011-01-01

    We review fabrication methods and common structures for optofluidic waveguides, defined as structures capable of optical confinement and transmission through fluid filled cores. Cited structures include those based on total internal reflection, metallic coatings, and interference based confinement. Configurations include optical fibers and waveguides fabricated on flat substrates (integrated waveguides). Some examples of optofluidic waveguides that are included in this review are Photonic Crystal Fibers (PCFs) and two-dimensional photonic crystal arrays, Bragg fibers and waveguides, and Anti Resonant Reflecting Optical Waveguides (ARROWs). An emphasis is placed on integrated ARROWs fabricated using a thin-film deposition process, which illustrates how optofluidic waveguides can be combined with other microfluidic elements in the creation of lab-on-a-chip devices. PMID:21603122

  13. Synthesis, Crystal Structure, and Thermal Decomposition of the Cobalt(II) Complex with 2-Picolinic Acid

    PubMed Central

    Li, Di

    2014-01-01

    The cobalt(II) complex of 2-picolinic acid (Hpic), namely, [Co(pic)2(H2O)2] · 2H2O, was synthesized with the reaction of cobalt acetate and 2-picolinic acid as the reactants by solid-solid reaction at room temperature. The composition and structure of the complex were characterized by elemental analysis, infrared spectroscopy, single crystal X-ray diffraction, and thermogravimetry-differential scanning calorimetry (TG-DSC). The crystal structure of the complex belongs to monoclinic system and space group P2(1)/n, with cell parameters of a = 9.8468(7) Å, b = 5.2013(4) Å, c = 14.6041(15) Å, β = 111.745(6)°, V = 747.96(11) Å3, Z = 2, Dc = 1.666 g cm−3, R1 = 0.0297, and wR2 = 0.0831. In the title complex, the Co(II) ion is six-coordinated by two pyridine N atoms and two carboxyl O atoms from two 2-picolinic acid anions, and two O atoms from two H2O molecules, and forming a slightly distorted octahedral geometry. The thermal decomposition processes of the complex under nitrogen include dehydration and pyrolysis of the ligand, and the final residue is cobalt oxalate at about 450°C. PMID:24578654

  14. Synthesis, structure and some properties of a manganese(II) benzoate containing diimine

    NASA Astrophysics Data System (ADS)

    Paul, Pranajit; Roy, Subhadip; Sarkar, Sanjoy; Chowdhury, Shubhamoy; Purkayastha, R. N. Dutta; Raghavaiah, Pallepogu; McArdle, Patrick; Deb, Lokesh; Devi, Sarangthem Indira

    2015-12-01

    A new monomeric manganese(II) benzoate complex containing nitrogen donor 2,2‧-bipyridine, [Mn(OBz)2(bipy)(H2O)] (OBz = benzoate, bipy = 2,2‧-bipyridine) has been synthesized from aqueous methanol medium and characterized by analytical, spectroscopic and single crystal X-ray diffraction studies. The compound exhibits moderate to appreciable antimicrobial activity. The complex crystallizes in space group P21/n. Mn(II) atom is ligated by two N atoms of bipyridine, three O atoms from a monodentate and a bidentate benzoate ligand and a water molecule forming distorted octahedral structure. The coordinated water molecule forms intramolecular hydrogen bonds and links the monomer molecules into hydrogen bonded dimer. The hydrogen bonded dimers are involved in intermolecular C-H···O and π-π stacking interactions. Density functional theory (DFT) computation was carried out to compute the frequencies of relevant vibrational modes and electronic properties, the results are in compliance with the experimentally obtained structural and spectral data.

  15. Atomic layer deposited titanium dioxide coatings on KD-II silicon carbide fibers and their characterization

    NASA Astrophysics Data System (ADS)

    Cao, Shiyi; Wang, Jun; Wang, Hao

    2016-03-01

    To provide oxidation protection and/or to act as an interfacial coating, titanium oxide (TiO2) coatings were deposited on KD-II SiC fibers by employing atomic layer deposition (ALD) technique with tetrakis(dimethylamido)titanium (TDMAT) and water (H2O) as precursors. The average deposition rate was about 0.08 nm per cycle, and the prepared coatings were smooth, uniform and conformal, shielding the fibers entirely. The as-deposited coatings were amorphous regardless of the coating thickness, and changed to anatase and rutile crystal phase after annealing at 600 °C and 1000 °C, respectively. The oxidation measurement suggests that the TiO2 coating enhanced the oxidation resistance of SiC fibers obviously. SiC fibers coated with a 70-nm-thick TiO2 layer retained a relatively high tensile strength of 1.66 GPa even after exposition to air at 1400 °C for 1 h, and thick silica layer was not observed. In contrast, uncoated SiC fibers were oxidized dramatically through the same oxidation treatment, covered with a macro-cracked thick silica film, and the tensile strength was not measurable due to interfilament adhesion. The above results indicate that TiO2 films deposited by ALD are a promising oxidation resistance coating for SiC fibers.

  16. The Structure and Environment of H II Galaxies

    NASA Astrophysics Data System (ADS)

    Telles, Eduardo

    1996-05-01

    H II galaxies are dwarf star forming galaxies found in objective prism surveys through their strong emission lines. They have been targets of extensive studies of their spectroscopic properties such as chemical abundances, physical conditions and kinematics. Little surface photometry work has been done on H II galaxies up to now. This thesis is primarily a CCD surface photometry study of the structural properties, optical colors and a statistical analysis of the environment of H II galaxies. In the chapter "The Morphology of H II Galaxies" I have used a sample of 39 H II galaxies with CCD images for a study of their overall morphology and luminosity profiles. The results show that H II galaxies can be classified in two main types: type I H II galaxies are luminous and have disturbed and irregular outer shapes while type II H II galaxies are less luminous and have regular shapes. The outer parts of profiles of all HIi galaxies are well represented by an exponential as in other types of known dwarf galaxies. In "The Dynamics of H II Galaxies" I have investigated the relation between the linear size of the starburst, luminosity and velocity dispersion. It is found that H II galaxies have similar relations as virialized systems which supports the gravitational origin of their overall kinematics. The possible bi-parametric behavior ("fundamental plane") of H II galaxies is also investigated. However, a conclusive answer to this question still requires more and better data. In "The Colors of H II Galaxies" I have presented a high spatial resolution CCD surface photometry study. The colors of the underlying stellar continuum within the starburst are obtained by removing the flux contribution of the emission lines in the broad band filters. Comparison with recent evolutionary population synthesis models show that the observational errors and the uncertainties in the models are still too large to put strict constraints on their past star formation history. However, the

  17. Unveiling the atomic structure and electronic properties of atomically thin boron sheets on an Ag(111) surface.

    PubMed

    Shu, Haibo; Li, Feng; Liang, Pei; Chen, Xiaoshuang

    2016-09-15

    Two-dimensional (2D) boron sheets (i.e., borophene) have a huge potential as a basic building block in nanoelectronics and optoelectronics; such a situation is greatly promoted by recent experiments on fabrication of borophene on silver substrates. However, the fundamental atomic structure of borophene on the Ag substrate is still under debate, which greatly impedes further exploration of its properties. Herein, the atomic structure and electronic properties of borophene on an Ag(111) surface have been studied using first-principles calculations and ab initio molecular dynamics simulations. Our results reveal that there exist three energetically favorable borophene structures (β5, χ1, and χ2) on the Ag(111) surface and their simulated STM images are in good agreement with experimental results, suggesting the coexistence of boron phases during the growth. All these stable borophene structures have a planar structure with slight surface buckling (∼0.15 Å) and relatively high hexagonal vacancy density (1/6 and 1/5) and exhibit typical metallic conductivity. These findings not only can be applied to solve the experimental controversies about the atomic structure of borophene on the Ag substrate but also provide a theoretical basis for exploring the fundamental properties and applications of 2D boron sheets.

  18. Doubly chloro bridged dimeric copper(II) complex: magneto-structural correlation and anticancer activity.

    PubMed

    Sikdar, Yeasin; Modak, Ritwik; Bose, Dipayan; Banerjee, Saswati; Bieńko, Dariusz; Zierkiewicz, Wiktor; Bieńko, Alina; Das Saha, Krishna; Goswami, Sanchita

    2015-05-21

    We have synthesized and structurally characterized a new doubly chloro bridged dimeric copper(II) complex, [Cu2(μ-Cl)2(HL)2Cl2] (1) based on a Schiff base ligand, 5-[(pyridin-2-ylmethylene)-amino]-pentan-1-ol). Single crystal X-ray diffraction shows the presence of dinuclear copper(II) centres in a square pyramidal geometry linked by obtuse double chloro bridge. The magnetic study illustrated that weak antiferromagnetic interactions (J = -0.47 cm(-1)) prevail in complex 1 which is well supported by magneto-structural correlation. This compound adds to the library of doubly chloro bridged copper(ii) complexes in the regime of spin state cross over. DFT calculations have been conducted within a broken-symmetry (BS) framework to investigate the exchange interaction further which depicts that the approximate spin projection technique yields the best corroboration of the experimental J value. Spin density plots show the presence of an ∼0.52e charge residing on the copper atom along with a substantial charge on bridging and peripheral chlorine atoms. The potential of complex1 to act as an anticancer agent is thoroughly examined on a series of liver cancer cell lines and screening shows the HepG2 cell line exhibits maximum cytotoxicity by phosphatidyl serine exposure in the outer cell membrane associated with ROS generation and mitochondrial depolarization with increasing time in the in vitro model system.

  19. Similarity recognition of molecular structures by optimal atomic matching and rotational superposition.

    PubMed

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

    An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.

  20. Atomic shell structure from the Single-Exponential Decay Detector

    SciTech Connect

    Silva, Piotr de; Korchowiec, Jacek; Wesolowski, Tomasz A.

    2014-04-28

    The density of atomic systems is analysed via the Single-Exponential Decay Detector (SEDD). SEDD is a scalar field designed to explore mathematical, rather than physical, properties of electron density. Nevertheless, it has been shown that SEDD can serve as a descriptor of bonding patterns in molecules as well as an indicator of atomic shells [P. de Silva, J. Korchowiec, and T. A. Wesolowski, ChemPhysChem 13, 3462 (2012)]. In this work, a more detailed analysis of atomic shells is done for atoms in the Li–Xe series. Shell populations based on SEDD agree with the Aufbau principle even better than those obtained from the Electron Localization Function, which is a popular indicator of electron localization. A link between SEDD and the local wave vector is given, which provides a physical interpretation of SEDD.

  1. Racing carbon atoms. Atomic motion reaction coordinates and structural effects on Newtonian kinetic isotope effects.

    PubMed

    Andujar-De Sanctis, Ivonne L; Singleton, Daniel A

    2012-10-19

    Intramolecular (13)C kinetic isotope effects were determined for the dimerization of methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newton's second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity.

  2. Atomic structure measurements and tests of fundamental symmetries in a thallium atomic beam

    NASA Astrophysics Data System (ADS)

    Majumder, Protik; Butts, David; Uhl, Ralph

    2006-05-01

    Using a thallium atomic beam apparatus, we are undertaking a series of laser spectroscopy measurements with the goal of providing precise, independent cross-checks on the accuracy of new calculations of parity nonconservation in thallium, as well as probing possible new symmetry-violating forces. In our apparatus, a diode laser beam interacts transversely with a dense, thallium beam and reveals roughly tenfold Doppler narrowing of the absorption profile. Having completed a new 0.4% measurement of the Stark shift in the 378 nm E1 transition in thallium, we are now studying the M1/E2 1283,m 6P1/2-6P3/2 transition in the atomic beam. To enhance the detectability of this weak transition, we are utilizing both a two-tone frequency modulation method, as well as an entirely new scheme to measure differential optical cavity phase shifts induced by the atoms. In the course of this work, we have developed a new laser stabilization method suitable for locking near this E1-forbidden transition. We use low-field Faraday rotation polarimetry and achieve sub-MHz frequency stability. Future work includes two-step atomic beam excitation and Stark shift experiments in thallium, as well as a search for long-range T-odd, P-even symmetry-violating forces in thallium. Current results will be presented.

  3. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige

    2000-01-01

    Since its invention in 1948, the transistor has revolutionized our everyday life - transistor radios and TV's appeared in the early 1960s, personal computers came into widespread use in the mid-1980s, and cellular phones, laptops, and palm-sized organizers dominated the 1990s. The electronics revolution is based upon transistor miniaturization; smaller transistors are faster, and denser circuitry has more functionality. Transistors in current generation chips are 0.25 micron or 250 nanometers in size, and the electronics industry has completed development of 0.18 micron transistors which will enter production within the next few years. Industry researchers are now working to reduce transistor size down to 0.13 micron - a thousandth of the width of a human hair. However, studies indicate that the miniaturization of silicon transistors will soon reach its limit. For further progress in microelectronics, scientists have turned to nanotechnology to advance the science. Rather than continuing to miniaturize transistors to a point where they become unreliable, nanotechnology offers the new approach of building devices on the atomic scale [see sidebar]. One vision for the next generation of miniature electronics is atomic chain electronics, where devices are composed of atoms aligned on top of a substrate surface in a regular pattern. The Atomic Chain Electronics Project (ACEP) - part of the Semiconductor Device Modeling and Nanotechnology group, Integrated Product Team at the NAS Facility has been developing the theory of understanding atomic chain devices, and the author's patent for atomic chain electronics is now pending.

  4. Electrochemical synthesis and structural characterization of a novel mixed-valence copper(I)-copper(II) complex: {[bis(ethylenediamine)copper(II)] bis[diiodocuprate(I)]}.

    PubMed

    Fotouhi, Lida; Dehghanpour, Saeed; Heravi, Majid M; Ardakani, Mahboobeh Dashti

    2007-07-12

    A novel, mixed-valent copper(I)-copper(II) complex, {[bis(ethylene-diamine)copper(II)] bis[diiodocuprate(I)]} (1), has been prepared by electrochemical dissolution of a sacrificial copper anode in a solution of ethylenediamine (en), I2 and tetraethylammoniumperchlorate (TEAP) as supporting electrolyte in acetonitrile (AcN)and characterized by single-crystal X-ray structure determination. The crystal structure of the complex 1 shows that it consists of a CuI2 polymer formed from I- ligands bridging Cu(I) ions, with a nearly square planar geometry of bivalent Cu(II) atoms chelated by two ethylenediamine ligands. The results also show that direct electrosynthesis of the complex had high current efficiency, purity and electrolysis yield.

  5. Crystal Structure of a Self-Spliced Group II Intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie

    2008-04-10

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  6. Elasticity of some mantle crystal structures. II.

    NASA Technical Reports Server (NTRS)

    Wang, H.; Simmons, G.

    1973-01-01

    The single-crystal elastic constants are determined as a function of pressure and temperature for rutile structure germanium dioxide (GeO2). The data are qualitatively similar to those of rutile TiO2 measured by Manghnani (1969). The compressibility in the c direction is less than one-half that in the a direction, the pressure derivative of the shear constant is negative, and the pressure derivative of the bulk modulus has a relatively high value of about 6.2. According to an elastic strain energy theory, the negative shear modulus derivative implies that the kinetic barrier to diffusion decreases with increasing pressure.

  7. Testing the existence of non-Maxwellian electron distributions in H II regions after assessing atomic data accuracy

    SciTech Connect

    Mendoza, C.; Bautista, M. A. E-mail: manuel.bautista@wmich.edu

    2014-04-20

    The classic optical nebular diagnostics [N II], [O II], [O III], [S II], [S III], and [Ar III] are employed to search for evidence of non-Maxwellian electron distributions, namely κ distributions, in a sample of well-observed Galactic H II regions. By computing new effective collision strengths for all these systems and A-values when necessary (e.g., S II), and by comparing with previous collisional and radiative data sets, we have been able to obtain realistic estimates of the electron-temperature dispersion caused by the atomic data, which in most cases are not larger than ∼10%. If the uncertainties due to both observation and atomic data are then taken into account, it is plausible to determine for some nebulae a representative average temperature while in others there are at least two plasma excitation regions. For the latter, it is found that the diagnostic temperature differences in the high-excitation region, e.g., T{sub e} (O III), T{sub e} (S III), and T{sub e} (Ar III), cannot be conciliated by invoking κ distributions. For the low-excitation region, it is possible in some, but not all, cases to arrive at a common, lower temperature for [N II], [O II], and [S II] with κ ≈ 10, which would then lead to significant abundance enhancements for these ions. An analytic formula is proposed to generate accurate κ-averaged excitation rate coefficients (better than 10% for κ ≥ 5) from temperature tabulations of the Maxwell-Boltzmann effective collision strengths.

  8. Crystal structure of trans-dihydrido­bis[tris­(di­methyl­amino)­phosphane-κP]platinum(II)

    PubMed Central

    Downs, Emma L.; Zakharov, Lev N.; Tyler, David R.

    2015-01-01

    The mol­ecule of the title compound, [PtH2(C6H18N3P)2], has a centrosymmetric square-planar structure in which the PtII atom is bonded to two H and two P atoms in a mutually trans configuration. The PtII atom sits on an inversion center and thus the asymmetric unit contains only half the mol­ecule. The Pt—P and Pt—H distances are 2.2574 (10) and 1.49 (7) Å, respectively. PMID:26029413

  9. First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures

    SciTech Connect

    Evans, Matthew H; Zhang, Xiaoguang; Joannopoulos, J. D.; Pantelides, Sokrates T

    2005-01-01

    Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.

  10. A new tetranuclear copper(II) Schiff base complex containing Cu 4O 4 cubane core: Structural and spectral characterizations

    NASA Astrophysics Data System (ADS)

    Shit, Shyamapada; Rosair, Georgina; Mitra, Samiran

    2011-04-01

    A new tetra-nuclear coordination complex [Cu 4(HL) 4] ( 1) containing Cu 4O 4 cubane core has been synthesized by using Schiff base ligand [(OH)C 6H 4CH dbnd N sbnd C(CH 3)(CH 2OH) 2] (H 3L), obtained by the 1:1 condensation of 2-amino-2-methyl-1,3-propanediol with salicylaldehyde and thoroughly characterized by micro-analytical, FT-IR, UV-Vis, thermal and room temperature magnetic susceptibility measurements. Structural characterization of the complex has been done by single crystal X-ray diffraction analysis. Structural elucidation reveals versatile coordination modes for two identical alkoxo oxygen atoms of the Schiff base ligand; one in its deprotonated form exhibits μ 3-bridging to bind three similar copper(II) centers whilst the protonated one remains as monodentate or non-coordinating. Structural analysis also shows that the Cu 4O 4 cubane core in 1 consists of four μ 3-alkoxo oxygen bridged copper(II) atoms giving an approximately cubic array of alternating oxygen atoms and copper(II) atoms where the metal centers display both distorted square pyramidal and distorted octahedral geometries.

  11. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)2

    NASA Astrophysics Data System (ADS)

    Téllez Soto, C. A.; Costa, A. C.; Versiane, O.; Lemma, T.; Machado, N. C. F.; Mondragón, M. A.; Martin, A. A.

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained.

  12. Atomic Structure Measurements and Fundamental Symmetry Tests in a Thallium Atomic Beam

    NASA Astrophysics Data System (ADS)

    Majumder, P. K.; Doret, S. C.

    2002-05-01

    Using a recently constructed thallium atomic beam apparatus, we have begun a series of laser spectroscopy measurements with the goal of providing precise, independent cross-checks on the accuracy of new calculations of parity nonconservation in thallium(M. Kozlov et al.), Phys Rev. A64, 053107 (2001). We are currently completing a measurement of the Stark shift within the 378 nm 6P_1/2-7S_1/2 transition. For this experiment, we use a frequency-stabilized external cavity diode laser system at 755 nm, an acousto-optic modulator, and external resonant frequency-doubling cavity to obtain a small amount of tunable UV light. The laser beam intersects the collimated atomic beam at right angles, and we can apply a precisely-calibrated electric field of up to 30 kV/cm in the interaction region. We observe a factor of ten Doppler narrowing and roughly 30% absorption on resonance of the strongest hyperfine line within this transition. We will present precise Stark shift results based on several very different experimental methods. We plan next to introduce 1283 nm light into the atomic beam to study the 6P_1/2-6P_3/2 `forbidden' M1 transition. Using a double FM modulation/detection scheme to improve our signal-to-noise ratio, we will measure both the Stark shift and the Stark-induced amplitudes here. In the longer term, we are developing an atomic beam experiment using the 1283 nm laser to search for a long-range T-odd, but P-even interaction in thallium.

  13. Structure and atomic vibrations in bimetallic Ni13 - n Al n clusters

    NASA Astrophysics Data System (ADS)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2015-04-01

    The binding energy, equilibrium geometry, and vibration frequencies in bimetallic clusters Ni13 - n Al n ( n = 0-13) have been calculated using the embedded atom method potentials. It has been shown that the icosahedral structure is the most stable in monoatomic and bimetallic clusters. A tendency of Al atoms to segregate on the cluster surface has been revealed in agreement with the experimental data. The calculations of the atomic vibrations have shown the nonmonotonic dependence of the minimum and maximum vibration frequencies of cluster atoms on its composition and the coupling of their extreme values with the most stable atomic configuration. The increase in the number of Al atoms leads to the shift of the frequency spectrum and the substantial redistribution of the localization of vibrations on the cluster atoms.

  14. Gunshot residue testing in suicides: Part II: Analysis by inductive coupled plasma-atomic emission spectrometry.

    PubMed

    Molina, D Kimberley; Castorena, Joe L; Martinez, Michael; Garcia, James; DiMaio, Vincent J M

    2007-09-01

    Several different methods can be employed to test for gunshot residue (GSR) on a decedent's hands, including scanning electron microscopy with energy dispersive x-ray (SEM/EDX) and inductive coupled plasma-atomic emission spectrometry (ICP-AES). In part I of this 2-part series, GSR results performed by SEM/EDX in undisputed cases of suicidal handgun wounds were studied. In part II, the same population was studied, deceased persons with undisputed suicidal handgun wounds, but GSR testing was performed using ICP-AES. A total of 102 cases were studied and analyzed for caliber of weapon, proximity of wound, and the results of the GSR testing. This study found that 50% of cases where the deceased was known to have fired a handgun immediately prior to death had positive GSR results by ICP/AES, which did not differ from the results of GSR testing by SEM/EDX. Since only 50% of cases where the person is known to have fired a weapon were positive for GSR by either method, this test should not be relied upon to determine whether someone has discharged a firearm and is not useful as a determining factor of whether or not a wound is self-inflicted or non-self-inflicted. While a positive GSR result may be of use, a negative result is not helpful in the medical examiner setting as a negative result indicates that either a person fired a weapon prior to death or a person did not fire a weapon prior to death.

  15. Sterically directed nitronate complexes of 2,6-di-tert-butyl-4-nitrophenoxide with Cu(ii) and Zn(ii) and their H-atom transfer reactivity.

    PubMed

    Porter, Thomas R; Hayes, Ellen C; Kaminsky, Werner; Mayer, James M

    2017-02-21

    The bulky 2,6-di-tert-butyl-4-nitrophenolate ligand forms complexes with [Tp(tBu)Cu(II)](+) and [Tp(tBu)Zn(II)](+) binding via the nitro group in an unusual nitronato-quinone resonance form (Tp(tBu) = hydro-tris(3-tert-butyl-pyrazol-1-yl)borate). The Cu complex in the solid state has a five-coordinate κ(2)-nitronate structure, while the Zn analogue has a four-coordinate κ(1)-nitronate ligand. 4-Nitrophenol, without the 2,6-di-tert-butyl substituents, instead binds to [Tp(tBu)Cu(II)](+) through the phenolate oxygen. This difference in binding is very likely due to the steric difficulty in binding a 2,6-di-tert-butyl-phenolate ligand to the [Tp(tBu)M(II)](+) unit. Tp(tBu)Cu(II)(κ(2)-O2N(t)Bu2C6H2O) reacts with the hydroxylamine TEMPO-H (2,2,6,6-tetramethylpiperidin-1-ol) by abstracting a hydrogen atom. This system thus shows an unusual sterically enforced transition metal-ligand binding motif and a copper-phenolate interaction that differs from what is typically observed in biological and chemical catalysis.

  16. Molecular orbital calculations on atomic structures of Si-based covalent amorphous ceramics

    SciTech Connect

    Matsunaga, K.; Matsubara, H.

    1999-07-01

    The authors have performed ab-initio Hartree-Fock molecular orbital calculations of local atomic structures and chemical bonding states in Si-N covalent amorphous ceramics. Solute elements such as boron, carbon and oxygen were considered in the Si-N network, and the bonding characteristics around the solute elements were analyzed. When a nitrogen atom is substituted by a carbon atom, it was found that Si-C bonds reinforce the Si-N network due to strong covalency.

  17. Oxidation of Structural Fe(II) in Biotite by Lithotrophic Fe(II)-oxidizing microorganisms

    NASA Astrophysics Data System (ADS)

    Shelobolina, E.; Blöthe, M.; Xu, H.; Konishi, H.; Roden, E.

    2008-12-01

    The potential for microbial involvement in the oxidation of Fe(II)-bearing phyllosilicates is an understudied aspect of soil/sediment Fe biogeochemistry. An important property of structural Fe in Fe-bearing smectites is their ability to undergo multiple redox cycles without being mobilized. An obvious choice of mineral substrate for enumeration/isolation of Fe(II)-oxidizing microorganisms would be reduced smectite. But reduced smectite is readily oxidized by air. That is why biotite was chosen as a substrate for this study. In contrast to smectite, biotite is more stable in the presence of air, but incapable of redox cycling. Once Fe(II) is oxidized, biotite is weathered to expendable 2:1 phyllosilicates or kaolinite. First, we evaluated the ability of a neutral-pH lithoautotrophic nitrate-reducing enrichment culture (MPI culture), recovered by Straub et al (Appl. Environ. Microbiol., 1996, 62:1458-1460) from a freshwater ditch, to oxidize two different specimens of biotite. The culture was capable of multiple transfers in anaerobic nitrate-containing biotite suspensions. The growth of MPI culture resulted in decrease of 0.5 N HCl-extractable Fe(II) content and simultaneous nitrate reduction. Cell yields were comparable to those observed for other neutral-pH lithoautotrophic Fe(II)-oxidizing bacteria. High resolution TEM examination revealed structural and chemical changes at the edges of oxidized biotite and formation of reddish amorphous precipitates dominated by Si and Fe. To further evaluate efficiency of biotite for recovery of oxygen- and nitrate-dependent Fe(II) oxidizing cultures microbial enumeration study was performed using subsoil from a site near Madison, WI. The soil is rich in Fe-bearing smectite and shows evidence of redoximorphic features. The enumeration of Fe(II) oxidizing organisms from this sediment showed 10-fold higher efficiency of biotite over soluble Fe(II) for recovery of Fe(II)-oxidizers. Isolation and identification of both aerobic and

  18. Synthesis, Structure, and Magnetic Electrochemical Properties of a Family of Tungstoarsenates Containing Just Co(II) Centers or Both Co(II) and Fe(III) Centers.

    PubMed

    Ayingone Mezui, Charyle S; de Oliveira, Pedro; Teillout, Anne-Lucie; Marrot, Jérôme; Berthet, Patrick; Lebrini, Mounim; Mbomekallé, Israël M

    2017-02-20

    The three polyoxotungstates [(NaOH2)2Co(II)2(As2W15O56)2](18-) (1), [(NaOH2)(Co(II)OH2)Co(II)2(As2W15O56)2](17-) (2), and [(Co(II)OH2)2Co(II)2(As2W15O56)2](16-) (3) have been prepared in aqueous solution upon mixing cobalt(II) salts with the ligand [As2W15O56](12-). The reaction of 1 or 2 with the Fe(3+) ion leads invariably to the same species [(Fe(III)OH2)(Co(II)OH2)Co(II)2(As2W15O56)2](15-) (4) possessing three cobalt atoms and a single iron atom. However, if the Fe-containing homologue of compound 1, that is, the polyoxotungstate [(NaOH2)2Fe(III)2(As2W15O56)2](16-) (5), is employed instead to react with the Co(2+) ion, the species [(Co(II)OH2)2Fe(III)2(As2W15O56)2](14-) (6) is obtained, having two cobalt atoms and two iron atoms. The compounds 1, 2, 3, 4, and 6 are described for the first time and have been characterized by several physicochemical methods such as FTIR, UV-visible, ATG, and elemental analysis. Structural analysis by single-crystal X-ray diffraction has been carried out with compounds 2 (monoclinic space group P21/c, a = 17.0622(5) Å, b = 15.0828(4) Å, c = 32.0872(8) Å, β = 91.170(1)°, and Z = 2) and 3 (triclinic space group P1̅, a = 13.6137(7) Å, b = 13.8836(8) Å, c = 22.9276(6) Å, α = 89.906(3)°, β = 78.356(2)°, γ = 61.451(2)°, and Z = 1). Electrochemical studies undertaken with all the above-mentioned compounds and some of their homologues shed light on the influence of the chemical composition on their electrocatalytic properties toward substrates such as the nitrite ion and dioxygen. Magnetic measurements evidence anisotropic ferromagnetic interactions between Co(2+) ions and antiferromagnetic interactions between Fe(3+) ions. The nature and the strength of the Co(2+)-Fe(3+) interactions depend on the relative orientations of their 3d orbitals. The effective magnetic moment of the Co(2+) ions varies with the temperature and with the distortion of the octahedral sites in which they are located.

  19. Crystal structures of three lead(II) acetate-bridged di-amino-benzene coordination polymers.

    PubMed

    Geiger, David K; Parsons, Dylan E; Zick, Patricia L

    2014-12-01

    Poly[tris-(acetato-κ(2) O,O')(μ2-acetato-κ(3) O,O':O)tetra-kis-(μ3-acetato-κ(4) O,O':O:O')bis-(benzene-1,2-di-amine-κN)tetra-lead(II)], [Pb4(CH3COO)8(C6H8N2)2] n , (I), poly[(acetato-κ(2) O,O')(μ3-acetato-κ(4) O,O':O:O')(4-chloro-benzene-1,2-diamine-κN)lead(II)], [Pb(CH3COO)2(C6H7ClN2)] n , (II), and poly[(κ(2) O,O')(μ3-acetato-κ(4) O,O':O:O')(3,4-di-amino-benzo-nitrile-κN)lead(II)], [Pb(CH3COO)2(C7H7N3)] n , (III), have polymeric structures in which monomeric units are joined by bridging acetate ligands. All of the Pb(II) ions exhibit hemidirected coordination. The repeating unit in (I) is composed of four Pb(II) ions having O6, O6N, O7 and O6N coordination spheres, respectively, where N represents a monodentate benzene-1,2-di-amine ligand and O acetate O atoms. Chains along [010] are joined by bridging acetate ligands to form planes parallel to (10-1). (II) and (III) are isotypic and have one Pb(II) ion in the asymmetric unit that has an O6N coordination sphere. Pb2O2 units result from a symmetry-imposed inversion center. Polymeric chains parallel to [100] exhibit hydrogen bonding between the amine and acetate ligands. In (III), additional hydrogen bonds between cyano groups and non-coordinating amines join the chains by forming R 2 (2)(14) rings.

  20. The atom in a molecule: Implications for molecular structure and properties

    NASA Astrophysics Data System (ADS)

    Langhoff, Peter; Mills, Jeffrey; Boatz, Jerry

    2016-05-01

    The apparent impossibility of meaningful assignments of indistinguishable electrons to particular atomic nuclei in a molecule seemingly precludes quantum-mechanical definition of fragment atomic Hamiltonian operators. Structural symmetry, conformations, and isomers, as well as the electronic energies and properties of constituent atoms are accordingly perceived as ill defined. Here we provide assignments of electrons to atoms in molecules and define their energies and properties. A separable Hilbert space in the form of orthonormal (Eisenschitz-London) outer-products of atomic eigenstates facilitates assignments of electrons to particular atomic nuclei and also provides support for totally antisymmetric solutions of the Schrödinger equation. Self-adjoint atomic operators within a molecule are shown to have Hermitian matrix representatives and physically significant expectation values in molecular eigenstates. Nuanced descriptions of molecular structures and properties emerge naturally from this representation in the absence of additional subjective conditions, including the interplay between atomic promotion and interaction energies, atomic hybridization and charge apportionment, and atomic-state entanglements upon dissociation, attributes revealed by illustrative calculations. Work support in part by Grants from AFRL, NRC, ASEE, NSF.

  1. Synthesis and structure of a new copper(II) complex with 3,4'-bi-1,2,4-triazolate.

    PubMed

    Idouli, Y; Guédira, F; Rghioui, L; El Ammari, L; El Hajjaji, S; Zaydoun, S

    2011-01-01

    The salt diaquo-diammine-bis(3,4'-bi-1,2,4-triazolate) copper(II) of the formula [Cu(bTA-)2(NH3)2(H2O)2] has been synthesized and structurally characterized by X-ray single crystal diffraction analysis. This complex adopts a monomeric structure. This monomer crystallizes in the triclinic system, space group P1 with a=5.9657 Å; b=6.8975 Å; c=9.9892 Å; α=106.181°; β=97.868°; γ=90.800° and Z=1. The Cu atom is coordinated by two nitrogen atoms of two monodentate bitriazolate ligands, two nitrogen atoms of NH3 and two water molecules in a distorted octahedral geometry. The complex has been also characterized by elemental analysis and studied by electronic and vibrational spectroscopy. The obtained results are in good agreement with the structure determined by X-ray diffraction analysis.

  2. Structure of the Interacting Starburst Galaxy II Zw 23

    NASA Astrophysics Data System (ADS)

    Cigan, P. J.; Gallagher, J. S.; Rudie, G.; Wehner, E. H.

    2005-09-01

    II Zw 23 (UGC 3179) is a luminous (MB -21) nearby compact narrow emission line starburst galaxy with blue optical colors and strong emission lines. We present a photometric and morphological study of II Zw 23 and its interacting companion, PC016099, using data obtained with the WIYN 3.5-m telescope in combination with a WFPC2 image from the HST archives. II Zw 23 has a highly disturbed outer structure with long trails of debris that may be feeding tidal dwarfs. Its central regions appear disk-like, a structure that is consistent with the overall rotation pattern observed in the Hα emission line velocity field measured from Densepak observations obtained with WIYN. We discuss these results in terms of the different evolutionary paths followed by stars and gas during strong interactions and the possibility of rapid secondary galactic disk formation in such events.

  3. Characteristics of Spontaneous Emission of Polarized Atoms in Metal Dielectric Multiple Layer Structures

    NASA Astrophysics Data System (ADS)

    Zhao, Li-Ming; Gu, Ben-Yuan; Zhou, Yun-Song

    2007-11-01

    The spontaneous emission (SE) progress of polarized atoms in a stratified structure of air-dielectric(D0)-metal(M)-dielectric(D1)-air can be controlled effectively by changing the thickness of the D1 layer and rotating the polarized direction of atoms. It is found that the normalized SE rate of atoms located inside the D0 layer crucially depends on the atomic position and the thickness of the D1 layer. When the atom is located near the D0-M interface, the normalized atomic SE rate as a function of the atomic position is abruptly onset for the thin D1 layer. However, with the increasing thickness of the D1 layer, the corresponding curve profile exhibits plateau and stays nearly unchanged. The substantial change of the SE rate stems from the excitation of the surface plasmon polaritons in metal-dielectric interface, and the feature crucially depends on the thickness of D1 layer. If atoms are positioned near the D0-air interface, the substantial variation of the normalized SE rate appears when rotating the polarized direction of atoms. These findings manifest that the atomic SE processes can be flexibly controlled by altering the thickness of the dielectric layer D1 or rotating the orientation of the polarization of atoms.

  4. Atomic data from the Iron project. XIII. Electron excitation rates and emissivity ratios for forbidden transitions in NI II and Fe II.

    NASA Astrophysics Data System (ADS)

    Bautista, M. A.; Pradhan, A. K.

    1996-02-01

    Electron impact excitation rates and emissivity line ratios are reported for Optical and IR transitions in Ni II and Fe II arising from low-lying even parity levels. A total of 7 LS terms were included for Ni II, which result in 17 fine structure levels and 136 transitions. Coupling effects and resonance structures considered in the present calculations result in significant differences with the earlier distorted wave calculations by Nussbaumer & Storey (1982), although a reasonable agreement is found for the line diagnostics of some strong transitions in Ni II. Whereas an extensive set of collisional data has been presented earlier by Zhang & Pradhan for Fe II in the Iron Project series, in this paper we report collision strengths for some transitions missing from their dataset using an improved eigenfunction expansion for Fe II which includes the lowest 18 LS terms giving 52 fine structure levels and 1326 transitions. The present dataset provides a useful check on several forbidden transitions in Fe II and essentially confirms the diagnostics derived from the earlier work. The present calculations were carried out on the massively parallel processor Cray T3D with a parallelized version of the Iron Project R-matrix codes; to our knowledge these are the first such calculations.

  5. Method for large-scale fabrication of atomic-scale structures on material surfaces using surface vacancies

    DOEpatents

    Lim, Chong Wee; Ohmori, Kenji; Petrov, Ivan Georgiev; Greene, Joseph E.

    2004-07-13

    A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

  6. Cis-Diammine(Pyridine)Chloroplatinum(II), a Monofunctional Platinum(II) Antitumor Agent: Uptake, Structure, Function, And Prospects

    SciTech Connect

    Lovejoy, K.S.; Todd, R.C.; Zhang, S.; McCormick, M.S.; D'Aquino, J.A.; Reardon, J.T.; Sancar, A.; Giacomini, K.M.; Lippard, S.J.

    2009-05-19

    We have identified unique chemical and biological properties of a cationic monofunctional platinum(II) complex, cis-diammine(pyridine)chloroplatinum(II), cis-[Pt(NH{sub 3}){sub 2}(py)Cl]{sup +} or cDPCP, a coordination compound previously identified to have significant anticancer activity in a mouse tumor model. This compound is an excellent substrate for organic cation transporters 1 and 2, also designated SLC22A1 and SLC22A2, respectively. These transporters are abundantly expressed in human colorectal cancers, where they mediate uptake of oxaliplatin, cis-[Pt(DACH)(oxalate)] (DACH = trans-R,R-1,2-diaminocyclohexane), an FDA-approved first-line therapy for colorectal cancer. Unlike oxaliplatin, however, cDPCP binds DNA monofunctionally, as revealed by an x-ray crystal structure of cis-{l_brace}Pt(NH{sub 3}){sub 2}(py){r_brace}{sup 2+} bound to the N7 atom of a single guanosine residue in a DNA dodecamer duplex. Although the quaternary structure resembles that of B-form DNA, there is a base-pair step to the 5{prime} side of the Pt adduct with abnormally large shift and slide values, features characteristic of cisplatin intrastrand cross-links. cDPCP effectively blocks transcription from DNA templates carrying adducts of the complex, unlike DNA lesions of other monofunctional platinum(II) compounds like {l_brace}Pt(dien){r_brace}{sup 2+}. cDPCP-DNA adducts are removed by the nucleotide excision repair apparatus, albeit much less efficiently than bifunctional platinum-DNA intrastrand cross-links. These exceptional characteristics indicate that cDPCP and related complexes merit consideration as therapeutic options for treating colorectal and other cancers bearing appropriate cation transporters.

  7. Correlation between atomic structure evolution and strength in a bulk metallic glass at cryogenic temperature.

    PubMed

    Tan, J; Wang, G; Liu, Z Y; Bednarčík, J; Gao, Y L; Zhai, Q J; Mattern, N; Eckert, J

    2014-01-28

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs.

  8. Phase-space structures - II. Hierarchical Structure Finder

    NASA Astrophysics Data System (ADS)

    Maciejewski, M.; Colombi, S.; Springel, V.; Alard, C.; Bouchet, F. R.

    2009-07-01

    A new multidimensional Hierarchical Structure Finder (HSF) to study the phase-space structure of dark matter in N-body cosmological simulations is presented. The algorithm depends mainly on two parameters, which control the level of connectivity of the detected structures and their significance compared to Poisson noise. By working in six-dimensional phase space, where contrasts are much more pronounced than in three-dimensional (3D) position space, our HSF algorithm is capable of detecting subhaloes including their tidal tails, and can recognize other phase-space structures such as pure streams and candidate caustics. If an additional unbinding criterion is added, the algorithm can be used as a self-consistent halo and subhalo finder. As a test, we apply it to a large halo of the Millennium Simulation, where 19 per cent of the halo mass is found to belong to bound substructures, which is more than what is detected with conventional 3D substructure finders, and an additional 23-36 per cent of the total mass belongs to unbound HSF structures. The distribution of identified phase-space density peaks is clearly bimodal: high peaks are dominated by the bound structures and show a small spread in their height distribution; low peaks belong mostly to tidal streams, as expected. However, the projected (3D) density distribution of the structures shows that some of the streams can have comparable density to the bound structures in position space. In order to better understand what HSF provides, we examine the time evolution of structures, based on the merger tree history. Given the resolution limit of the Millennium Simulation, bound structures typically make only up to six orbits inside the main halo. The number of orbits scales approximately linearly with the redshift corresponding to the moment of merging of the structures with the halo. At fixed redshift, the larger the initial mass of the structure which enters the main halo, the faster it loses mass. The difference in

  9. Structured Forms Reference Set of Binary Images II (SFRS2)

    National Institute of Standards and Technology Data Gateway

    NIST Structured Forms Reference Set of Binary Images II (SFRS2) (PC database for purchase)   The second NIST database of structured forms (Special Database 6) consists of 5,595 pages of binary, black-and-white images of synthesized documents containing hand-print. The documents in this database are 12 different tax forms with the IRS 1040 Package X for the year 1988.

  10. Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations

    PubMed Central

    Resta, Andrea; Leoni, Thomas; Barth, Clemens; Ranguis, Alain; Becker, Conrad; Bruhn, Thomas; Vogt, Patrick; Le Lay, Guy

    2013-01-01

    Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer. PMID:23928998

  11. Atomic structures of silicene layers grown on Ag(111): scanning tunneling microscopy and noncontact atomic force microscopy observations.

    PubMed

    Resta, Andrea; Leoni, Thomas; Barth, Clemens; Ranguis, Alain; Becker, Conrad; Bruhn, Thomas; Vogt, Patrick; Le Lay, Guy

    2013-01-01

    Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer.

  12. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

    PubMed Central

    Liebschner, Dorothee; Dauter, Miroslawa; Brzuszkiewicz, Anna; Dauter, Zbigniew

    2013-01-01

    Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The Cα and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies

  13. Spectroscopic and DFT studies of zinc(II) complexes of diamines and thiocyanate; crystal structure of (cis-1,2-diaminocyclohexane)bis(thiocyanato-κN)zinc(II)

    NASA Astrophysics Data System (ADS)

    Akhtar, Muhammad; Alotaibi, Mshari A.; Alharthi, Abdulrahman I.; Zierkiewicz, Wiktor; Tahir, Muhammad Nawaz; Mazhar, Muhammad; Isab, Anvarhusein A.; Monim-ul-Mehboob, Muhammad; Ahmad, Saeed

    2017-01-01

    Zinc(II) complexes of diamines, cis-1,2-diaminocyclohexane (Dach) and N,N,N,N-tetramethylethylenediamine (Tmen), [Zn(Dach)(NCS)2] (1) and [Zn(Tmen)(NCS)2] (2) have been prepared and characterized by elemental analysis, IR, 1H &13C NMR spectroscopy. The crystal structure of [Zn(Dach)(NCS)2] (1) was determined by X-ray crystallography. In 1, the Zn(II) atom is bound to one 1,2-diaminocyclohexane molecule and to two terminal thiocyanate ions via the nitrogen atoms adopting a slightly distorted tetrahedral geometry. In the crystal structure, molecules are linked through intermolecular Nsbnd H⋯S hydrogen bonds, forming chains running along the a axis. The structures of 1 and 2 as well as of [Zn(En)(NCS)2] (3) (En = 1,2-diaminoethane) were predicted using theoretical (DFT) method. The interaction energies (ΔE) for NCS anions obtained by B3LYP-D3 method are about -140 kcal mol-1, while the calculated ΔE values for neutral organic ligands are about twice smaller. The atomic charges and second-order interaction energies between orbitals were calculated with natural bond orbital (NBO) analysis.

  14. Realizing high magnetic moments in fcc Fe nanoparticles through atomic structure stretch.

    PubMed

    Baker, S H; Roy, M; Thornton, S C; Binns, C

    2012-05-02

    We describe the realization of a high moment state in fcc Fe nanoparticles through a controlled change in their atomic structure. Embedding Fe nanoparticles in a Cu(1-x)Au(x) matrix causes their atomic structure to switch from bcc to fcc. Extended x-ray absorption fine structure (EXAFS) measurements show that the structure in both the matrix and the Fe nanoparticles expands as the amount of Au in the matrix is increased, with the data indicating a tetragonal stretch in the Fe nanoparticles. The samples were prepared directly from the gas phase by co-deposition, using a gas aggregation source and MBE-type sources respectively for the nanoparticle and matrix materials. The structure change in the Fe nanoparticles is accompanied by a sharp increase in atomic magnetic moment, ultimately to values of ~2.5 ± 0.3 μ(B)/atom .

  15. Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite.

    PubMed

    Chin, Yiing; Panduwinata, Dwi; Sintic, Maxine; Sum, Tze Jing; Hush, Noel S; Crossley, Maxwell J; Reimers, Jeffrey R

    2011-01-20

    The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.

  16. Electron correlation and relativistic effects in atomic structure calculations of the thorium atom.

    PubMed

    Roy, S K; Prasad, Rajendra; Chandra, P

    2011-06-21

    Relativistic two-component ab initio calculations have been performed for the Th atom. The spin free low lying states have been calculated at state-averaged complete active space self-consistent field (SA-CASSCF) and multi-state complete active space second-order perturbation (MS-CASPT2) level of theories using different sets of active orbitals. The spin-orbit states have been computed using Douglas-Kroll type of atomic mean-field integral approach. The effects of dynamic electron correlation have been studied at the MS-CASPT2 level. The energy levels of spin-orbit states below 30,000 cm(-1) obtained by the inclusion of dynamic electron correlation are in very good agreement with the experimental values. The radiative properties such as weighted transition probabilities (gA) and oscillator strengths (gf) among several spin-orbit states have been calculated at the SA-CASSCF and MS-CASPT2 levels and are expected to be very helpful for future experiments.

  17. Structural Hamiltonian chaos in the coherent parametric atom-field interaction

    NASA Astrophysics Data System (ADS)

    Ioussoupov, V. I.; Kon'kov, L. E.; Prants, S. V.

    2001-07-01

    We consider one of the simplest semiclassical models in laser and atomic physics, a collection of two-level atoms interacting coherently with an electromagnetic standing wave in an ideal single-mode cavity within the rotating-wave approximation (RWA). In the strong-coupling limit, atoms and a cavity field constitute a strongly coupled atom-field dynamical system whose atomic and field variables oscillate in a self-consistent way with the Rabi frequency. It is proven analytically by the Melnikov method and numerically by computing maximal Lyapunov exponents and Poincaré sections that the parametric Rabi oscillations in a vibrating cavity may be chaotic in a sense of exponential sensitivity to initial conditions. Wavelet spectra computed with typical signals of the oscillations demonstrate clearly that Hamiltonian chaos in the coherent atom-field interaction with modulated coupling is structural. Structural chaos is characterized by positive values of the maximal Lyapunov exponents and regular structures which coexist in the same signal. Duration of a train of regular oscillations is defined by the period of modulation, but oscillations between successive trains are chaotic. Results of numerical experiments and estimation of the control parameters and approximations involved show that a Rydberg atom maser operating with a collection of two-level atoms inside a high-quality superconducting microwave cavity is a promising device for observing manifestations of structural Hamiltonian chaos in real experiments.

  18. Arguments, Contradictions, Resistances, and Conceptual Change in Students' Understanding of Atomic Structure.

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo

    2002-01-01

    Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…

  19. Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

    Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…

  20. Structural and functional dynamics of plant photosystem II.

    PubMed Central

    Anderson, Jan M; Chow, W S

    2002-01-01

    Given the unique problem of the extremely high potential of the oxidant P(+)(680) that is required to oxidize water to oxygen, the photoinactivation of photosystem II in vivo is inevitable, despite many photoprotective strategies. There is, however, a robustness of photosystem II, which depends partly on the highly dynamic compositional and structural heterogeneity of the cycle between functional and non-functional photosystem II complexes in response to light level. This coordinated regulation involves photon usage (energy utilization in photochemistry) and excess energy dissipation as heat, photoprotection by many molecular strategies, photoinactivation followed by photon damage and ultimately the D1 protein dynamics involved in the photosystem II repair cycle. Compelling, though indirect evidence suggests that the radical pair P(+)(680)Pheo(-) in functional PSII should be protected from oxygen. By analogy to the tentative oxygen channel of cytochrome c oxidase, oxygen may be liberated from the two water molecules bound to the catalytic site of the Mn cluster, via a specific pathway to the membrane surface. The function of the proposed oxygen pathway is to prevent O(2) from having direct access to P(+)(680)Pheo(-) and prevent the generation of singlet oxygen via the triplet-P(680) state in functional photosytem IIs. Only when the, as yet unidentified, potential trigger with a fateful first oxidative step destroys oxygen evolution, will the ensuing cascade of structural perturbations of photosystem II destroy the proposed oxygen, water and proton pathways. Then oxygen has direct access to P(+)(680)Pheo(-), singlet oxygen will be produced and may successively oxidize specific amino acids of the phosphorylated D1 protein of photosystem II dimers that are confined to appressed granal domains, thereby targeting D1 protein for eventual degradation and replacement in non-appressed thylakoid domains. PMID:12437881

  1. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    DOE PAGES

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; ...

    2014-01-01

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) hasmore » relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

  2. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    SciTech Connect

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; Mullins, David R.; Carroll, Kyler J.; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M.

    2014-01-01

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.

  3. Crystal structure of lead(II) tartrate: a redetermination.

    PubMed

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.

  4. Crystal structure of lead(II) tartrate: a redetermination

    PubMed Central

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ6 O 1,O 3:O 1′:O 2,O 4:O 4′-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▸). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions. PMID:25705458

  5. Functional implications on the mechanism of the function of photosystem II including water oxidation based on the structure of photosystem II.

    PubMed Central

    Fromme, Petra; Kern, Jan; Loll, Bernhard; Biesiadka, Jaceck; Saenger, Wolfram; Witt, Horst T; Krauss, Norbert; Zouni, Athina

    2002-01-01

    The structure of photosystem I at 3.8 A resolution illustrated the main structural elements of the water-oxidizing photosystem II complex, including the constituents of the electron transport chain. The location of the Mn cluster within the complex has been identified for the first time to our knowledge. At this resolution, no individual atoms are visible, however, the electron density of the Mn cluster can be used to discuss both the present models of the Mn cluster as revealed from various spectroscopic methods and the implications for the mechanisms of water oxidation. Twenty-six chlorophylls from the antenna system of photosystem II have been identified. They are arranged in two layers, one close to the stromal side and one close to the lumenal side. Comparing the structure of the antenna system of photosystem II with the chlorophyll arrangement in photosystem I, which was recently determined at 2.5 A resolution shows that photosystem II lacks the central domain of the photosystem I antenna, which is discussed in respect of the repair cycle of photosystem II due to photoinhibition. PMID:12437872

  6. Syntheses, characterizations and crystal structures of two new lead(II) amino and carboxylate-sulfonates with a layered and a pillared layered structure

    NASA Astrophysics Data System (ADS)

    Yuan, Yan-Ping; Mao, Jiang-Gao; Song, Jun-Ling

    2004-03-01

    Reactions of lead(II) acetate with m-aminobenzenesulfonic acid (H L1) and 5-sulfoisophthalic acid (H 3L2) afforded two new lead(II) sulfonates, Pb( L1) 21 and Pb 2( L2)( μ3-OH)(H 2O) 2. In compound 1, the lead(II) ion is eight-coordinated by two sulfonate groups bidentately, two sulfonate groups unidentately and two amino groups from six ligands. Each L1 ligand is tetradentate and bridges with three Pb(II) ions. The interconnection of the Pb(II) ions via bridging sulfonate ligands resulted in <100> and <200> layers. In compound 2, one Pb(II) ion is six-coordinated by a carboxylate group bidentately, by two carboxylate groups unidentately, by a sulfonate oxygen atom and by an OH anion, whereas the other one is six-coordinated by a bidentate chelating carboxylate group, two μ3-OH anions, a sulfonate oxygen atom and an aqua ligand. The interconnection of irregular PbO 6 polyhedra via carboxylate-sulfonate ligands resulted in the formation of a pillared layered structure with the 2D layer being formed; the lead(II) ions, hydroxyl groups, carboxylate and sulfonate groups and the benzene ring as the pillar agent.

  7. On the way to unveiling the atomic structure of superheavy elements

    NASA Astrophysics Data System (ADS)

    Laatiaoui, Mustapha

    2016-12-01

    Optical spectroscopy of the transfermium elements (atomic number Z > 100) is nowadays one of the most fascinating and simultaneously challenging tasks in atomic physics. On the one hand, key atomic and even nuclear ground-state properties may be obtained by studying the spectral lines of these heaviest elements. On the other hand, these elements have to be produced "online" by heavy-ion induced fusion-evaporation reactions yielding rates on the order of a few atoms per second at most, which renders their optical spectroscopy extremely difficult. Only recently, a first foray of laser spectroscopy into this heaviest element region was reported. Several atomic transitions in the element nobelium (Z = 102) were observed and characterized, using an ultra-sensitive and highly efficient resonance ionization technique. The findings confirm the predictions and additionally provide a benchmark for theoretical modelling. The work represents an important stepping stone towards experimental studies of the atomic structure of superheavy elements.

  8. Relevance of the photosynthetic reaction center from purple bacteria to the structure of photosystem II

    SciTech Connect

    Michel, H.; Deisenhofer, J.

    1988-01-12

    Photosynthetic organisms are able to oxidize organic or inorganic compounds upon the absorption of light, and they use the extracted electron for the fixation of carbon dioxide. The most important oxidation product is oxygen due to the splitting of water. In eukaryotes these processes occur in photosystem II of chloroplasts. Among prokaryotes photosynthetic oxygen evolution is restricted to cyanobacteria and prochloron-type organisms. How water is split in the oxygen-evolving complex of photosystem II belongs to the most important question to be answered. The primary charge separation occurs in the reaction center of photosystem II. This reaction center is a complex consisting of peripheral and integral membrane proteins, several chlorophyll A molecules, two pheophytin A molecules, two and three plastoquinone molecules, and one non-heme iron atom. The location of the photosystem II reaction center is still a matter of debate. Nakatani et al. (l984) concluded from fluorescence measurements that a protein of apparent molecular weight 47,000 (CP47) is the apoprotein of the photosystem II reaction center. A different view emerged from work with the photosynthetic reaction centers from the purple bacteria. The amino acid sequence of the M subunit of the reaction center from Phodopseudomonas (Rps.) sphaeroides has sequence homologies with the D1 protein from spinach. A substantial amount of structural information can be obtained with the reaction center from Rhodopseudomonas viridis, which can be crystallized. Here the authors discuss the structure of the photosynthetic reaction center from the purple bacterium Rps. viridis and describe the role of those amino acids that are conserved between the bacterial and photosystem II reaction center.

  9. Obtaining of images of ordered and disordered nanocrystal structures by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Parfenov, P. S.; Litvin, A. P.; Ushakova, E. V.; Fedorov, A. V.; Baranov, A. V.

    2017-01-01

    The morphology of films, superlattices, and other structures of colloidal nanocrystals has been investigated by atomic force microscopy (AFM). The capabilities of ultrasharp and conventional probes for AFM are compared. The problems of detection of nanocrystal close packing are discussed.

  10. X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations.

    PubMed

    Jayatilaka, Dylan; Dittrich, Birger

    2008-05-01

    An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

  11. Structural and functional characteristics of plant proteinase inhibitor-II (PI-II) family.

    PubMed

    Rehman, Shazia; Aziz, Ejaz; Akhtar, Wasim; Ilyas, Muhammad; Mahmood, Tariq

    2017-02-09

    Plant proteinase inhibitor-II (PI-II) proteins are one of the promising defensive proteins that helped the plants to resist against different kinds of unfavorable conditions. Different roles for PI-II have been suggested such as regulation of endogenous proteases, modulation of plant growth and developmental processes and mediating stress responses. The basic knowledge on genetic and molecular diversity of these proteins has provided significant insight into their gene structure and evolutionary relationships in various members of this family. Phylogenetic comparisons of these family genes in different plants suggested that the high rate of retention of gene duplication and inhibitory domain multiplication may have resulted in the expansion and functional diversification of these proteins. Currently, a large number of transgenic plants expressing PI-II genes are being developed for enhancing the defensive capabilities against insects, bacteria and pathogenic fungi. Much emphasis is yet to be given to exploit this ever expanding repertoire of genes for improving abiotic stress resistance in transgenic crops. This review presents an overview about the current knowledge on PI-II family genes, their multifunctional role in plant defense and physiology with their potential applications in biotechnology.

  12. Semiempirical Studies of Atomic Structure. Final Report for July 1, 2000 - June 30, 2003

    SciTech Connect

    Curtis, L. J.

    2004-05-01

    This project has developed a comprehensive and reliable base of accurate atomic structure data for complex many-electron systems. This has been achieved through the use of sensitive data-based parametric systematizations, precise experimental measurements, and supporting theoretical computations. The atomic properties studies involved primary data (wavelengths, frequency intervals, lifetimes, relative intensities, production rates, etc.) and derived structural parameters (energy levels, ionization potentials, line strengths, electric polarizabilities, branching fractions, excitation functions, etc).

  13. Atomic structure of a symmetric 27{degrees}[001] tilt grain boundary in MgO

    SciTech Connect

    Yan, Yanfa; Chisholm, M.F.; Pennycook, S.J.

    1997-04-01

    The atomic structure of a symmetric 27 degree[001] tilt grain boundary in magnesium oxide has been determined by high-resolution Z-contrast imaging using a 300kV VG HB603U scanning transmission electron microscope with a 1.3 A probe. The atomic configuration in the grain boundary core is found to be considerably less open than the structures proposed for similar materials.

  14. Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation.

    PubMed

    Lauria, Antonino; Bonsignore, Riccardo; Terenzi, Alessio; Spinello, Angelo; Giannici, Francesco; Longo, Alessandro; Almerico, Anna Maria; Barone, Giampaolo

    2014-04-28

    We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 1 > 2 > 3, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in

  15. Atom and Amine Adsorption on Flat and Stepped Gold Surfaces & Structure, Stability and Spin Ordering in Manganese Sulfide Clusters

    NASA Astrophysics Data System (ADS)

    Lewoczko, April D.

    In part I, we investigate gold catalysis in the chemistry of organonitrogen compounds. We examine the adsorption of oxygen, nitrogen and sulfur atoms on the gold (111), (100) and (211) surfaces using density functional theory (DFT). Sulfur atoms bind most strongly, followed by oxygen and nitrogen atoms with stronger adsorption for greater coordination to the surface. We see a trend of stronger adsorption to undercoordinated gold, but find it is non-universal with the adsorption strength trend: (111) > (211) > (100). We consider the diffusion of oxygen, nitrogen and sulfur adatoms and find facile long-range diffusion of oxygen atoms on the (100) surface. Lastly, we compare the adsorption of methylamine on gold to that of a selection of alkylamines, methanol and methanethiol. In each case, the ontop site is preferred with stronger adsorption at low coordinated gold. At oxygen atom coverages of 0.125 -- 0.25 ML on Au (111), we find cooperative adsorption of methylamine and oxygen atoms. Energetic costs for adsorbate tilt from the surface normal and rotation about the gold-nitrogen bond are calculated. While methylamine rotation is barrierless on the (111) and (211) surfaces, it has a low energetic barrier for the 0.125 ML and 0.25 ML O atom pre-covered Au (111) surfaces. In part II, we interpret the experimental mass spectrum of small gas phase manganese sulfide clusters using DFT and elucidate the role of ionicity and spin ordering in sizes with special stability, i.e. magic clusters. We first consider nine low lying minima (MnS)6 structures and reveal antiferromagnetic (AFM) spin ordering with a ˜0.1 eV/pair AFM energy benefit and a ˜0.1 A shrinkage of average Mn-Mn distances over clusters with ferromagnetic (FM) spin ordering. We calculate energetic barriers for interconversion between the two lowest lying (MnS)6 isomers and predict an elevated cluster melting temperature due to increased configurational entropy in a pre-melted state. Second, we demonstrate the

  16. New metastable hybrid phase, Zn 2(OH) 2(C 8H 4O 4), exhibiting unique oxo-penta-coordinated Zn(II) atoms

    NASA Astrophysics Data System (ADS)

    Carton, Anne; Mesbah, Adel; Aranda, Lionel; Rabu, Pierre; François, Michel

    2009-04-01

    The metastable phase ( phase 1) Zn(OH) 2(tp) 2 (tp = C 8H 4O 42-) was found to be an intermediate forming during the hydrothermal synthesis of Zn 3(OH) 4tp ( phase 2). Its structure has been determined ab initio from synchrotron powder diffraction data and refined with the Rietveld method: space group P2 1/ c, a = 3.48856(2) Å, b = 5.84645(2) Å, c = 22.1331(1) Å, β = 103.46(1)°, Dx = 2.488 g/cm 3, Rp = 0.10, RB = 0.095 (402 independent reflections). The structures of the two analogues were compared. Whereas a mixed coordination of the zinc atoms was found in phase 2, phase 1 exhibits only penta-coordinated Zn(II). Moreover, different optical properties were observed, Zn 2(OH) 2(tp) showing photoluminescence at 378 nm under λex = 316 nm.

  17. Progress towards a precision measurement of the n=2 triplet P fine structure of atomic helium

    NASA Astrophysics Data System (ADS)

    Kato, K.; Fitzakerley, D. W.; George, M. C.; Vutha, A. C.; Storry, C. H.; Hessels, E. A.

    2016-05-01

    We report progress on the measurement of the J = 1 to J = 2 23 P fine-structure interval of atomic helium. The measurement uses a liquid-nitrogen-cooled DC discharge source of metastable helium and the atomic beam is laser cooled in the transverse directions. The atoms are excited to 23 P by a 1083-nm diode laser, and the fine-structure transition is driven by microwaves using the frequency-offset separated oscillatory fields technique. The transition is detected by further laser excitation to a Rydberg state, followed by Stark ionization. This work is supported by NSERC, CRC.

  18. Research as a guide for curriculum development: An example from introductory spectroscopy. II. Addressing student difficulties with atomic emission spectra

    NASA Astrophysics Data System (ADS)

    Ivanjek, L.; Shaffer, P. S.; McDermott, L. C.; Planinic, M.; Veza, D.

    2015-02-01

    This is the second of two closely related articles (Paper I and Paper II) that together illustrate how research in physics education has helped guide the design of instruction that has proved effective in improving student understanding of atomic spectroscopy. Most of the more than 1000 students who participated in this four-year investigation were science majors enrolled in the introductory calculus-based physics course at the University of Washington (UW) in Seattle, WA, USA. The others included graduate and undergraduate teaching assistants at UW and physics majors in introductory and advanced physics courses at the University of Zagreb, Zagreb, Croatia. About half of the latter group were preservice high school physics teachers. Paper I describes how several conceptual and reasoning difficulties were identified among university students as they tried to relate a discrete line spectrum to the energy levels of atoms in a light source. This second article (Paper II) illustrates how findings from this research informed the development of a tutorial that led to improvement in student understanding of atomic emission spectra.

  19. Structure determination in 55-atom Li-Na and Na-K nanoalloys.

    PubMed

    Aguado, Andrés; López, José M

    2010-09-07

    The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

  20. Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.

    PubMed

    Athanasiadis, A; Vlassi, M; Kotsifaki, D; Tucker, P A; Wilson, K S; Kokkinidis, M

    1994-07-01

    The crystal structure of the dimeric PvuII restriction endonuclease (R.PvuII) has been determined at a resolution of 2.4A. The protein has a mixed alpha/beta architecture and consists of two subdomains. Despite a lack of sequence homology, extensive structural similarities exist between one R.PvuII subdomain and the DNA-binding subdomain of EcoRV endonuclease (R.EcoRV); the dimerization subdomains are unrelated. Within the similar domains, flexible segments of R.PvuII are topologically equivalent to the DNA-binding turns of R.EcoRV; potential catalytic residues can be deduced from the structural similarities to R.EcoRV. Conformational flexibility is important for the interaction with DNA. A possible classification of endonuclease structures on the basis of the positions of the scissile phosphates is discussed.

  1. Synthesis, structure, magnetic properties and biological activity of supramolecular copper(II) and nickel(II) complexes with a Schiff base ligand derived from vitamin B6.

    PubMed

    Mukherjee, Tirtha; Costa Pessoa, João; Kumar, Amit; Sarkar, Asit R

    2013-02-21

    Three new complexes of Cu(II) and Ni(II), [Cu(II)(H(2)pydmedpt)](2+)·2Cl(-) (1), [Ni(II)(H(2)pydmedpt)](2+)·2Cl(-) (2) and [Ni(II)(pydmedpt)(OH)](-)·K(+) (3) of the Schiff base ligand [H(2)pydmedpt](2+)·2Cl(-) were synthesized by the in situ reaction of pyridoxal (pyd), a vitamer of vitamin B(6), N,N-bis[3-aminopropyl]methylamine (medpt) and copper(II) acetate or nickel(II) acetate, respectively. The molecular structures of 1 and 2 were determined by single crystal X-ray diffraction studies. The structure of 3 in the solid state was inferred by elemental analysis, diffuse reflectance spectrum, variable temperature magnetic moment studies and DFT calculations. The binding of the Schiff base ligand to the metal centers involves two phenolato oxygens, two imine nitrogens and one amine nitrogen. The coordination geometry around Cu in 1 is distorted square pyramidal and that around the Ni atom in 2 is intermediate between square-pyramidal and trigonal-bipyramidal. In the crystals the compounds form supramolecular one dimensional chain structures stabilized by hydrogen bonding and π-π stacking interactions. Variable temperature magnetic moment data of 2 indicate the presence of a momomeric high spin Ni(II) centre in the complex. The solid state diffuse reflectance spectrum, conductance and elemental analysis suggest that 3 is a Ni(II) complex with a tetragonally distorted octahedral field, the sixth position being occupied by the oxygen atom of a hydroxyl group. The variable temperature magnetic moment of 3 indicates the presence of a ferromagnetic dinuclear species (29.2%) along with the major monomeric species, the intra-dimer exchange term J value being 14.3 cm(-1). The competitive binding of 1 and 2 with DNA was studied in the concentration range 40 to 400 μM, the apparent binding constants being K = 2.9 × 10(3) and 6.7 × 10(3) M(-1), respectively. Human Serum Albumin (HSA) binding studies were carried out at concentrations of 800-1000 μM and 400-500

  2. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water

    PubMed Central

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P.; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  3. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water

    NASA Astrophysics Data System (ADS)

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P.; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-08-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.

  4. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    PubMed

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-08-19

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.

  5. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

    SciTech Connect

    Liebschner, Dorothee; Dauter, Miroslawa; Brzuszkiewicz, Anna; Dauter, Zbigniew

    2013-08-01

    Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C{sup α} and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained

  6. Structural studies on some dithiophosphonato complexes of Ni(II), Cd(II), Hg(II) and theoretical studies on a dithiophosphonato Ni(II) complex using density functional theory

    NASA Astrophysics Data System (ADS)

    Sağlam, Ertuğrul Gazi; Ebinç, Ahmet; Zeyrek, Celal Tuğrul; Ünver, Hüseyin; Hökelek, Tuncer

    2015-11-01

    In this study, three dithiophosphonic acid complexes, namely, trans-bis-[O-3-methylbutyl (4-methoxyphenyl)dithiophosphonato]nickel(II), Ni(L)2; bis-{bis-[O-3-phenylpropyl (4-methoxyphenyl)dithiophosphonato]cadmium(II)}, [Cd(L)2]2 and bis-{bis-[O-3-methylbutyl (4-methoxyphenyl)dithiophosphonato]mercury(II)}, [Hg(L)2]2 were prepared. The compounds were characterized by elemental analysis; MS; FTIR and Raman spectroscopies and were also investigated by 1H-, 13C- and 31P- NMR. The Ni(L)2 complex was elucidated by X-ray crystallography, molecular characterization and density functional modelling studies. The molecular structure obtained from X-ray single-crystal analysis of the Ni(L)2 complex in the ground state has been compared using density functional theory (DFT), B3LYP functional with 6-311G(d,p) basis set. In addition to the optimized geometrical structures, atomic charges and nonlinear optical (NLO) effects have been investigated by using DFT. The experimental (spectroscopic) and calculated vibrational frequencies (using DFT) of the Ni(L)2 have been compared. There exists a good correlation between experimental and theoretical data for the Ni(L)2 complex.

  7. Prediction of structural and mechanical properties of atom-decorated porous graphene via density functional calculations

    NASA Astrophysics Data System (ADS)

    Ansari, Reza; Ajori, Shahram; Malakpour, Sina

    2016-04-01

    The considerable demand for novel materials with specific properties has motivated the researchers to synthesize supramolecular nanostructures through different methods. Porous graphene is the first two-dimensional hydrocarbon synthesized quite recently. This investigation is aimed at studying the mechanical properties of atom-decorated (functionalized) porous graphene by employing density functional theory (DFT) calculation within both local density approximations (LDA) and generalized gradient approximations (GGA). The atoms are selected from period 3 of periodic table as well as Li and O atom from period 2. The results reveal that metallic atoms and noble gases are adsorbed physically on porous graphene and nonmetallic ones form chemical bonds with carbon atom in porous graphene structure. Also, it is shown that, in general, atom decoration reduces the values of mechanical properties such as Young's, bulk and shear moduli as well as Poisson's ratio, and this reduction is more considerable in the case of nonmetallic atoms (chemical adsorption), especially oxygen atoms, as compared to metallic atoms and noble gases (physical adsorption).

  8. Synthesis, structural features, and methyl methacrylate polymerisation of binuclear zinc(II) complexes with tetradentate pyrazolyl ligands

    NASA Astrophysics Data System (ADS)

    Kim, Sunghoon; Kim, Dongil; Lee, Ha-Jin; Lee, Hyosun

    2014-04-01

    The reaction of ZnCl2 with ancillary ligands, including 1,4-bis-(N,N-di-(1H-pyrazolyl-1-methyl)amine)benzene (L1) and 4,4‧-bis-(N,N-di(1H-pyrazolyl-1-methyl)phenyl)methane (L2), in ethanol yields Zn(II) chloride complexes, i.e., 1,4-bis-(N,N-di-(1H-pyrazolyl-1-methyl)amine)benzene(dichloro)Zn(II) [L1Zn2Cl4] and 4,4‧-bis-(N,N-di-(1H-pyrazolyl-1-methyl)phenyl)methane(dichloro)Zn(II) [L2Zn2Cl4]. The X-ray crystal structures of Zn(II) complexes revealed that they are binuclear, and each zinc atom has a distorted tetrahedral geometry which involves a nitrogen atom from two pyrazole groups and two chloro ligands. The catalytic activity of [L1Zn2Cl4] and [L2Zn2Cl4] for the polymerisation of methyl methacrylate (MMA) in the presence of modified methylaluminoxane (MMAO) increased by twofold compared to the corresponding monomeric Zn(II) complex, N,N-bis(1H-pyrazolyl-1-methyl)aniline(dichloro)Zn(II) [LZnCl2], at 60 °C.

  9. Atomic structure and properties of grain boundaries in ceramics through Z-contrast electron microscopy

    SciTech Connect

    Pennycook, S.J.; Nellist, P.D.; Browning, N.D.

    1996-08-01

    The bulk properties of a large range of materials are controlled by the atomic structure and chemistry of grain boundaries, but how this occurs, at the fundamental atomic level, remains poorly understood. This is due largely to the many degrees of freedom associated with grain boundaries - five geometrical degrees of freedom along with a myriad of possibilities involving impurity segregation. Based on Z- contrast electron microscopy, a method have been developed for determining grain boundary atomic structure and chemistry directly from experimental data. The method utilizes the incoherent nature of the Z-contrast image; as there is no phase problem associated with an incoherent image, it represents a compositionally sensitive structure image which may be directly inverted to give atomic column positions. This method extracts the column locations to an accuracy of {+-}0.2 {Angstrom}, while preserving the intensity information. The procedure has been applied to SrTiO{sub 3} and YBCO.

  10. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    PubMed Central

    Feng, Bin; Sugiyama, Issei; Hojo, Hajime; Ohta, Hiromichi; Shibata, Naoya; Ikuhara, Yuichi

    2016-01-01

    Material performance is significantly governed by grain boundaries (GBs), a typical crystal defects inside, which often exhibit unique properties due to the structural and chemical inhomogeneity. Here, it is reported direct atomic scale evidence that oxygen vacancies formed in the GBs can modify the local surface oxygen dynamics in CeO2, a key material for fuel cells. The atomic structures and oxygen vacancy concentrations in individual GBs are obtained by electron microscopy and theoretical calculations at atomic scale. Meanwhile, local GB oxygen reduction reactivity is measured by electrochemical strain microscopy. By combining these techniques, it is demonstrated that the GB electrochemical activities are affected by the oxygen vacancy concentrations, which is, on the other hand, determined by the local structural distortions at the GB core region. These results provide critical understanding of GB properties down to atomic scale, and new perspectives on the development strategies of high performance electrochemical devices for solid oxide fuel cells. PMID:26838958

  11. Adhesion and Atomic Structures of Gold on Ceria Nanostructures: The Role of Surface Structure and Oxidation State of Ceria Supports.

    PubMed

    Lin, Yuyuan; Wu, Zili; Wen, Jianguo; Ding, Kunlun; Yang, Xiaoyun; Poeppelmeier, Kenneth R; Marks, Laurence D

    2015-08-12

    We report an aberration-corrected electron microscopy analysis of the adhesion and atomic structures of gold nanoparticle catalysts supported on ceria nanocubes and nanorods. Under oxidative conditions, the as-prepared gold nanoparticles on the ceria nanocubes have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod supports. Under the reducing conditions of water-gas shift reaction, the extended gold atom layers and rafts vanish. In addition, the gold particles on the nanocubes change in morphology and increase in size while those on the nanorods are almost unchanged. The size, morphology, and atomic interface structures of gold strongly depend on the surface structures of ceria supports ((100) surface versus (111) surface) and the reaction environment (reductive versus oxidative). These findings provide insights into the deactivation mechanisms and the shape-dependent catalysis of oxide supported metal catalysts.

  12. Two isomeric lead(II) carboxylate-phosphonates: syntheses, crystal structures and characterizations

    NASA Astrophysics Data System (ADS)

    Lei, Chong; Mao, Jiang-Gao; Sun, Yan-Qiong

    2004-07-01

    Two isomeric layered lead(II) carboxylate-phosphonates of N-(phosphonomethyl)- N-methyl glycine ([MeN(CH 2CO 2H)(CH 2PO 3H 2)]=H 3L), namely, monoclinic Pb 3L 2·H 2O 1 and triclinic Pb 3L 2·H 2O 2, have been synthesized and structurally determined. Compound 1 synthesized by hydrothermal reaction at 150°C is monoclinic, space group C2/ c with a=19.9872(6), b=11.9333(1) and c=15.8399(4) Å, β=110.432(3)°, V=3540.3(1) Å 3, and Z=8. The structure of compound 1 features a <400> layer in which the lead(II) ions are bridged by both phosphonate and carboxylate groups. The lattice water molecules are located between the layers, forming hydrogen bonds with the non-coordinated carboxylate oxygen atoms. Compound 2 with a same empirical formula as compound 1 was synthesized by hydrothermal reaction at 170°C. It has a different layer structure from that of compound 1 due to the adoption of a different coordination mode for the ligand. It crystallizes in the triclinic system, space group P 1¯ with cell parameters of a=7.1370(6), b=11.522(1), c=11.950(1) Å, α=110.280(2), β=91.625(2), γ=95.614(2)°, V=915.3(1) Å 3 and Z=2. The structure of compound 2 features a <020> metal carboxylate-phosphonate double layer built from 1D lead(II) carboxylate chains interconnected with 1D lead(II) phosphonate double chains. XRD powder patterns of compounds 1 and 2 indicate that each compound exists as a single phase.

  13. Understanding atom transfer radical polymerization: effect of ligand and initiator structures on the equilibrium constants.

    PubMed

    Tang, Wei; Kwak, Yungwan; Braunecker, Wade; Tsarevsky, Nicolay V; Coote, Michelle L; Matyjaszewski, Krzysztof

    2008-08-13

    Equilibrium constants in Cu-based atom transfer radical polymerization (ATRP) were determined for a wide range of ligands and initiators in acetonitrile at 22 degrees C. The ATRP equilibrium constants obtained vary over 7 orders of magnitude and strongly depend on the ligand and initiator structures. The activities of the Cu(I)/ligand complexes are highest for tetradentate ligands, lower for tridentate ligands, and lowest for bidentate ligands. Complexes with tripodal and bridged ligands (Me6TREN and bridged cyclam) tend to be more active than those with the corresponding linear ligands. The equilibrium constants are largest for tertiary alkyl halides and smallest for primary alkyl halides. The activities of alkyl bromides are several times larger than those of the analogous alkyl chlorides. The equilibrium constants are largest for the nitrile derivatives, followed by those for the benzyl derivatives and the corresponding esters. Other equilibrium constants that are not readily measurable were extrapolated from the values for the reference ligands and initiators. Excellent correlations of the equilibrium constants with the Cu(II/I) redox potentials and the carbon-halogen bond dissociation energies were observed.

  14. Effect of quenching temperature and size on atom movement and local structural change for small copper clusters containing 51-54 atoms during quenching processes

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Fan, Q. N.

    2016-01-01

    Structural changes are sensitive to the atom number for the small size clusters. However, it is hardly predicted for the effects of quenching temperature and contained atom number on the atom movements of these clusters with the modification of a removing or adding atom. In this paper, we demonstrate the formation of many topologically non-equivalent Cu clusters containing 51-54 atoms during quenching processes by means of atomistic simulations. By modifying annealing temperature, different pathways are observed. The simulation results show that the quenching temperature has large effect on the atom movements and the scenario of the formation and growth of local structures in the clusters is greatly different for the four clusters only with one atom difference. When the quenching temperature is high, most atoms in the clusters move individually. In the meantime, changes in the atom packing can be observed in these clusters. Low quenching temperature is helpful to slow down the atom movements and form the structures on icosahedral geometry.

  15. Atomic structure relaxation in nanocrystalline NiO studied by EXAFS spectroscopy: Role of nickel vacancies

    NASA Astrophysics Data System (ADS)

    Anspoks, A.; Kalinko, A.; Kalendarev, R.; Kuzmin, A.

    2012-11-01

    Nanocrystalline NiO samples have been studied using the Ni K-edge extended x-ray absorption fine structure (EXAFS) spectroscopy and recently developed modeling technique, combining classical molecular dynamics with ab initio multiple-scattering EXAFS calculations (MD-EXAFS). Conventional analysis of the EXAFS signals from the first two coordination shells of nickel revealed that (i) the second shell average distance R(Ni-Ni2) expands in nanocrystalline NiO compared to microcrystalline NiO, in agreement with overall unit cell volume expansion observed by x-ray diffraction; (ii) on the contrary, the first shell average distance R(Ni-O1) in nanocrystalline NiO shrinks compared to microcrystalline NiO; (iii) the thermal contribution into the mean-square relative displacement σ2 is close in both microcrystalline and nanocrystalline NiO and can be described by the Debye model; (iv) the static disorder is additionally present in nanocrystalline NiO in both the first Ni-O1 and second Ni-Ni2 shells due to nanocrystal structure relaxation. Within the MD-EXAFS method, the force-field potential models have been developed for nanosized NiO using as a criterion the agreement between the experimental and theoretical EXAFS spectra. The best solutions have been obtained for the 3D cubic-shaped nanoparticle models with nonzero Ni vacancy concentration Cvac: Cvac≈0.4-1.2% for NiO nanoparticles having the cube size of L≈3.6-4.2 nm and Cvac≈1.6-2.0% for NiO thin film composed of cubic nanograins with a size of L≈1.3-2.1 nm. Thus our results show that the Ni vacancies in nanosized NiO play important role in its atomic structure relaxation along with the size reduction effect.

  16. Tetrabromidocuprates(II)—Synthesis, Structure and EPR

    PubMed Central

    Zabel, André; Winter, Alette; Kelling, Alexandra; Schilde, Uwe; Strauch, Peter

    2016-01-01

    Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g‖ and g⊥) of the tensors could be determined and information on the structural changes in the [CuBr4]2− anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids. PMID:27104522

  17. Structural features of atomized white cast iron powder

    NASA Astrophysics Data System (ADS)

    Gulyaev, A. P.; Astakhov, S. I.

    1991-01-01

    White cast iron powder rapidly quenched from the liquid condition with presence of the same phases and structural components differs markedly in structure from normally cast white iron. With an increase in cooling rate vcool during solidification the amount of eutectic decreases. However, with an increase in carbon content this tendency is weakened and with 3.9% the structure of powder cast iron is almost entirely of eutectic.

  18. Atomic-Structural Synergy for Catalytic CO Oxidation over Palladium-Nickel Nanoalloys

    SciTech Connect

    Shan, Shiyao; Petkov, Valeri; Yang, Lefu; Luo, Jin; Joseph, Pharrah; Mayzel, Dina; Prasai, Binay; Wang, Lingyan; Engelhard, Mark; Zhong, Chuan-Jian

    2014-05-05

    Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium–nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

  19. Atomic-Structural Synergy for Catalytic CO Oxidation over Palladium-Nickel Nanoalloys

    SciTech Connect

    Shan, Shiyao; Petkov, Valeri; Yang, Lefu; Luo, Jin; Joseph, Pharrah; Mayzel, Dina; Prasai, Binay; Wang, Lingyan; Engelhard, Mark H.; Zhong, Chuan-Jian

    2014-05-05

    Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly-active and stable catalysts. However the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable a maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

  20. Atomic-structural synergy for catalytic CO oxidation over palladium-nickel nanoalloys.

    PubMed

    Shan, Shiyao; Petkov, Valeri; Yang, Lefu; Luo, Jin; Joseph, Pharrah; Mayzel, Dina; Prasai, Binay; Wang, Lingyan; Engelhard, Mark; Zhong, Chuan-Jian

    2014-05-14

    Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

  1. Structural characterization of a metal-based perfusion tracer: copper(II) pyruvaldehyde bis(N4-methylthiosemicarbazone).

    PubMed

    John, E; Fanwick, P E; McKenzie, A T; Stowell, J G; Green, M A

    1989-01-01

    Copper(II) pyruvaldehyde bis(N4-methylthiosemicarbazone), Cu(PTSM), has been obtained as a dark red crystalline solid from EtOH-DMSO solvent mixture and structurally characterized by x-ray crystallography. The molecule possesses the expected pseudo-square planar N2S2 metal coordination sphere; however, the copper center also interacts through its axial coordination site with the sulfur atom of an adjacent Cu(PTSM) molecule in the crystal lattice. The structure of this compound is compared with the structures of other metal complexes that have been proposed in the nuclear medicine literature as perfusion tracers.

  2. Neutral (bis-beta-diketonato) iron(III), cobalt(II), nickel(II), copper(II) and zinc(II) metallocycles: structural, electrochemical and solvent extraction studies.

    PubMed

    Clegg, Jack K; Bray, David J; Gloe, Kerstin; Gloe, Karsten; Hayter, Michael J; Jolliffe, Katrina A; Lawrance, Geoffrey A; Meehan, George V; McMurtrie, John C; Lindoy, Leonard F; Wenzel, Marco

    2007-05-07

    Neutral dimeric metallocyclic complexes of type [M(2)(L(1))(2)B(n)] (where M = cobalt(II), nickel(II) and zinc(II), L(1) is the doubly deprotonated form of a 1,3-aryl linked bis-beta-diketone ligand of type 1,3-bis(RC(O)CH(2)C(O))C(6)H(4) (R=Me, n-Pr, t-Bu) and B is pyridine (Py) or 4-ethylpyridine (EtPy)) have been synthesised, adding to similar complexes already reported for copper(II). New lipophilic ligand derivatives with R = octyl or nonyl were also prepared for use in solvent extraction experiments. Structural, electrochemical and solvent extraction investigations of selected metal complex systems from the above series are reported, with the X-ray structures of [Co(2)(L(1))(2)(Py)(4)] x 2.25CHCl(3) x 0.5H(2)O (R=Pr), [Co(2)(L(1))(2)(EtPy)(4)] (R=t-Bu), [Ni(2)(L(1))(2)(EtPy)(4)] (R=t-Bu), [Zn(2)(L(1))(2)(EtPy)(2)] (R=Me) and [Zn(2)(L(1))(2)(EtPy)(4)] (R=t-Bu) being presented. The electrochemistry of H(2)L(1) (R=t-Bu) and of [Fe(2)(L(1))(3)], [Co(2)(L(1))(2)(Py)(4)], [Ni(2)(L(1))(2)(Py)(4)], [Cu(2)(L(1))(2)] and [Zn(2)(L(1))(2)(Py)(2)] has been examined. Oxidative processes for the complexes are dominantly irreversible, but several examples of quasireversible behaviour were observed and support the assignment of an anodic process, seen between +1.0 and +1.6 V, as a metal-centred oxidation. The reduction processes for the respective metal complexes are not simple, and irreversible in most cases. Solvent extraction studies (water/chloroform) involving variable concentrations of metal, bis-beta-diketone and heterocyclic base have been performed for cobalt(II) and zinc(II) using a radiotracer technique to probe the stoichiometries of the extracted species in each case. Synergism was observed when 4-ethylpyridine was added to the bis-beta-diketone ligand in the chloroform phase. Competitive extraction studies show a clear uptake preference for copper(II) over cobalt(II), nickel(II), zinc(II) and cadmium(II).

  3. Atomic Models of Strong Solids Interfaces Viewed as Composite Structures

    NASA Astrophysics Data System (ADS)

    Staffell, I.; Shang, J. L.; Kendall, K.

    2014-02-01

    This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.

  4. Copper(II) complexes with pyrazole derivatives - Synthesis, crystal structure, DFT calculations and cytotoxic activity

    NASA Astrophysics Data System (ADS)

    Kupcewicz, Bogumiła; Ciolkowski, Michal; Karwowski, Boleslaw T.; Rozalski, Marek; Krajewska, Urszula; Lorenz, Ingo-Peter; Mayer, Peter; Budzisz, Elzbieta

    2013-11-01

    The series of pyrazole derivatives (1a-4a) were used as bidentate N,N' ligands to obtain neutral Cu(II) complexes of ML2Cl2 type (1b-4b). The molecular structures of ligand 1a and Cu(II) complex 4b were determined by X-ray crystallography and theoretical DFT calculations. In this study, three functionals B3LYP, BP86 and mPW1PW91 with different basis sets and two effective core potentials Los Alamos and Stuttgart/Dresden were performed. The DFT study disclosed the usefulness of BP86 functional with SDD-ECP for Cu(II) ion and dedicated D95 basis set for other non-transition metal atoms, with the exclusion of Cl for which 6-31++G(2df,2pd) were used. The structural analysis shows that the presence of phenyl substituent in a pyrazole ring contributed to Cu-N bond elongation, which can result in different reactivity of complexes 1b and 3b. The cytotoxicity of the obtained compounds was evaluated on three cancer cells lines: HL-60, NALM-6 and WM-115. The complexes have exhibited similar moderate antiproliferative activity. All the complexes, except for 1b, were found to be more active against three cancer cell lines than uncomplexed pyrazoles. The lipophilicity and electrochemical properties of ligands and complexes was also studied. For complexes with ligand 1a and 3a only one reduction process at the metal centre occurs (Cu(II) → Cu(I)) with oxidization of Cu(I)-Cu(II) in the backward step.

  5. Communication: Single crystal x-ray diffraction observation of hydrogen bonding between 1-propanol and water in a structure II clathrate hydrate.

    PubMed

    Udachin, Konstantin; Alavi, Saman; Ripmeester, John A

    2011-03-28

    Single crystal x-ray crystallography is used to detect guest-host hydrogen bonding in structure II (sII) binary clathrate hydrate of 1-propanol and methane. X-ray structural analysis shows that the 1-propanol oxygen atom is at a distance of 2.749 and 2.788 Å from the closest clathrate hydrate water oxygen atoms from a hexagonal face of the large sII cage. The 1-propanol hydroxyl hydrogen atom is disordered and at distances of 1.956 and 2.035 Å from the closest cage water oxygen atoms. These distances are compatible with guest-water hydrogen bonding. The C-C-C-O torsional angle in 1-propanol in the cage is 91.47° which corresponds to a staggered conformation for the guest. Molecular dynamics studies of this system demonstrated guest-water hydrogen bonding in this hydrate. The molecular dynamics simulations predict most probable distances for the 1-propanol-water oxygen atoms to be 2.725 Å, and the average C-C-C-O torsional angle to be ~59° consistent with a gauche conformation. The individual cage distortions resulting from guest-host hydrogen bonding from the simulations are rather large, but due to the random nature of the hydrogen bonding of the guest with the 24 water molecules making up the hexagonal faces of the large sII cages, these distortions are not observed in the x-ray structure.

  6. Atomic layer deposition of Cu(i) oxide films using Cu(ii) bis(dimethylamino-2-propoxide) and water.

    PubMed

    Avila, J R; Peters, A W; Li, Zhanyong; Ortuño, M A; Martinson, A B F; Cramer, C J; Hupp, J T; Farha, O K

    2017-04-13

    To grow films of Cu2O, bis-(dimethylamino-2-propoxide)Cu(ii), or Cu(dmap), is used as an atomic layer deposition precursor using only water vapor as a co-reactant. Between 110 and 175 °C, a growth rate of 0.12 ± 0.02 Å per cycle was measured using an in situ quartz crystal microbalance (QCM). X-ray photoelectron spectroscopy (XPS) confirms the growth of metal-oxide films featuring Cu(i).

  7. Magnetic-field effects in transitions of X Li molecules (X: even isotopes of group II atoms)

    SciTech Connect

    Gopakumar, Geetha; Abe, Minori; Hada, Masahiko; Kajita, Masatoshi

    2011-10-15

    We analyze the Zeeman shift in the (v,N)=(0,0){yields}(1,0) transition frequency of X Li molecules (X: even isotopes of group II atoms), which is of interest in metrology. The Zeeman shift in the transition frequency between stretching states is found to be less than 1 mHz with a magnetic field of 1 G. X {sup 6}Li molecules are more advantageous than X {sup 7}Li molecules for measuring the transition frequency without the Zeeman shift because of the smaller g factor of the Li nuclear spin.

  8. Visualization of the atomic structure of solid solutions with the NaCl structure

    NASA Astrophysics Data System (ADS)

    Babanov, Yu. A.; Ponomarev, D. A.; Ustinov, V. V.

    2015-04-01

    It has been shown how an atomic cluster for a solid solution with a rock salt structure can be constructed using the Pauling model. Simulation has been performed for 343000 ions of Ni x Zn1 - x O3 ( x = 0, 0.3, 0.5, 0.7, 1.0) oxide substitutional solid solutions. Coordinates of all cluster ions are obtained and distribution functions of ion pairs (Ni-O, Ni-Ni, Ni-Zn, Zn-Zn, Zn-O, O-O) are constructed as functions of distance. The shape of the normal distribution indicates the existence of bounded chaos in the system of oxide solid solutions. The width of the Gaussian distribution function is determined by the difference of metal ionic radii. The results are in agreement with both X-ray diffraction and EXAFS spectroscopy data.

  9. Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction

    NASA Astrophysics Data System (ADS)

    Song, Chenchen; Martínez, Todd J.

    2017-01-01

    In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N2.5) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

  10. Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction.

    PubMed

    Song, Chenchen; Martínez, Todd J

    2017-01-21

    In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N(2.5)) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

  11. Structure and oxidation state of hemitite surfaces reacted with aqueous Fe(II) at acidic and neutral pH.

    SciTech Connect

    Catalano, J. G.; Fenter, P.; Park, C.; Zhang, Z.; Rosso, K. M.; Washington Univ.; PNNL

    2010-01-01

    Structural changes and surface oxidation state were examined following the reaction of hematite (0 0 1), (0 1 2), and (1 1 0) with aqueous Fe(II). X-ray reflectivity measurements indicated that Fe(II) induces changes in the structure of all three surfaces under both acidic (pH 3) and neutral (pH 7) conditions. The structural changes were generally independent of pH although the extent of surface transformation varied slightly between acidic and neutral conditions; no systematic trends with pH were observed. Induced changes on the (1 1 0) and (0 1 2) surfaces include the addition or removal of partial surface layers consistent with either growth or dissolution. In contrast, a <1 nm thick, discontinuous film formed on the (0 0 1) surface that appears to be epitaxial yet is not a perfect extension of the underlying hematite lattice, being either structurally defective, compositionally distinct, or nanoscale in size and highly relaxed. Resonant anomalous X-ray reflectivity measurements determined that the surface concentration of Fe(II) present after reaction at pH 7 was below the detection limit of approximately 0.5-1 {micro}mol/m{sup 2} on all surfaces. These observations are consistent with Fe(II) oxidative adsorption, whereby adsorbed Fe(II) is oxidized by structural Fe(III) in the hematite lattice, with the extent of this reaction controlled by surface structure at the atomic scale. The observed surface transformations at pH 3 show that Fe(II) oxidatively adsorbs on hematite surfaces at pH values where little net adsorption occurs, based on historical macroscopic Fe(II) adsorption behavior on fine-grained hematite powders. This suggests that Fe(II) plays a catalytic role, in which an electron from an adsorbed Fe(II) migrates to and reduces a lattice Fe(III) cation elsewhere, which subsequently desorbs in a scenario with zero net reduction and zero net adsorption. Given the general pH-independence and substantial mass transfer involved, this electron and atom

  12. Structure and oxidation state of hematite surfaces reacted with aqueous Fe(II) at acidic and neutral pH

    SciTech Connect

    Catalano, Jeffrey G.; Fenter, Paul; Park, Changyong; Zhang, Zhan; Rosso, Kevin M.

    2010-03-01

    Structural changes and surface oxidation state were examined following the reaction of hematite (0 0 1), (0 1 2), and (1 1 0) with aqueous Fe(II). X-ray reflectivity measurements indicated that Fe(II) induces changes in the structure of all three surfaces under both acidic (pH 3) and neutral (pH 7) conditions. The structural changes were generally independent of pH although the extent of surface transformation varied slightly between acidic and neutral conditions; no systematic trends with pH were observed. Induced changes on the (1 1 0) and (0 1 2) surfaces include the addition or removal of partial surface layers consistent with either growth or dissolution. In contrast, a <1 nm thick, discontinuous film formed on the (0 0 1) surface that appears to be epitaxial yet is not a perfect extension of the underlying hematite lattice, being either structurally defective, compositionally distinct, or nanoscale in size and highly relaxed. Resonant anomalous X-ray reflectivity measurements determined that the surface concentration of Fe(II) present after reaction at pH 7 was below the detection limit of approximately 0.5–1 μmol/m2 on all surfaces. These observations are consistent with Fe(II) oxidative adsorption, whereby adsorbed Fe(II) is oxidized by structural Fe(III) in the hematite lattice, with the extent of this reaction controlled by surface structure at the atomic scale. The observed surface transformations at pH 3 show that Fe(II) oxidatively adsorbs on hematite surfaces at pH values where little net adsorption occurs, based on historical macroscopic Fe(II) adsorption behavior on fine-grained hematite powders. This suggests that Fe(II) plays a catalytic role, in which an electron from an adsorbed Fe(II) migrates to and reduces a lattice Fe(III) cation elsewhere, which subsequently desorbs in a scenario with zero net reduction and zero net adsorption. Finally, given the general pH-independence and substantial mass transfer involved, this electron and

  13. Sequestration of chelated copper by structural Fe(II): Reductive decomplexation and transformation of Cu(II)-EDTA.

    PubMed

    He, Hongping; Wu, Deli; Zhao, Linghui; Luo, Cong; Dai, Chaomeng; Zhang, Yalei

    2016-05-15

    Chelated coppers, such as Cu(II)-EDTA, are characteristically refractory and difficult to break down because of their high stability and solubility. Cu(II)-EDTA sequestration by structural Fe(II) (Fe(II)) was investigated intensively in this study. Up to 101.21mgCu(II)/gFe(II) was obtained by Fe(II) in chelated copper sequestration under near neutral pH condition (pH 7.70). The mechanism of Cu(II)-EDTA sequestration by Fe(II) was concluded as follows: 3Cu(II)-EDTA+7Fe(II)+9H2O → Cu(0)↓+ Cu2O↓(the major product)+2Fe2O3·H2O↓+3Fe(II)-EDTA +14H(+) Novel results strongly indicate that Cu(II) reductive transformation induced by surface Fe(II) was mainly responsible for chelated copper sequestration. Cu(0) generation was initially facilitated, and subsequent reduction of Cu(II) into Cu(I) was closely combined with the gradual increase of ORP (Oxidation-Reduction Potential). Cu-containing products were inherently stable, but Cu2O would be reoxidized to Cu(II) with extra-aeration, resulting in the release of copper, which was beneficial to Cu reclamation. Concentration diminution of Cu(II)-EDTA within the electric double layer and competitive adsorption were responsible for the negative effects of Ca(2+), Mg(2+). By generating vivianite, PO4(3-) was found to decrease surface Fe(II) content. This study is among the first ones to identify the indispensible role of reductive decomplexation in chelated copper sequestration. Given the high feasibility and reactivity, Fe(II) may provide a potential alternative in chelated metals pollution controlling.

  14. Quantitative structure-activity relationship study using refractotopological state atom index on some neonicotinoid insecticides.

    PubMed

    Debnath, Bikash; Gayen, Shovanlal; Basu, Anindya; Ghosh, Balaram; Srikanth, Kolluru; Jha, Tarun

    2004-12-01

    Importance of atom-level topological descriptors like electrotopological state atom (E-state) index in QSAR study is increasing. These descriptors help to relate structure and activity at atomic/fragmental level. In view of the earlier success of E-state index on some azidopyridinyl neonicotinoid insecticides, a relatively new atom-level topological descriptor; refractotopological state atom (R-state) index was used in this work. This was used to identify the important atoms/fragments related to dispersive/van der Waals interactions of neonicotinoids with the nicotinic acetylcholine receptor (nAChR). This study showed the structural requirements for the mammal alpha(4)beta(2) and Drosophila nAChR agonistic activity. It also revealed that substituted imine, nitromethylene at X-position were selective to the insecticidal activity. Azido substitution at pyridine ring of neonicotinoids disfavored the binding with the receptors. This study confirmed the validity of the R-state index as a new tool for quantitative structure-activity relationships. It has the ability to find out the required structural features as well as to predict the activity of the neonicotinoids.

  15. Synthesis, crystal structure and luminescent properties of one coordination polymer of cadmium(II) with mixed thiocyanate and hexamethylenetetramine ligands.

    PubMed

    Bai, Yan; Shang, Wei-Li; Dang, Dong-Bin; Sun, Ji-De; Gao, Hui

    2009-03-01

    A novel Cd(II) coordination polymer [Cd(SCN)(2)(hmt)(1/2)(H(2)O)](2).H(2)O (hmt=hexamethylenetetramine) has been synthesized and characterized by IR, elemental analysis, TG technique and X-ray crystallography. Cd(II) atom has an distorted octahedral environment with an N(3)S(2)O donor set. Every six Cd(II) centers are linked by hmt and thiocyanato bridges to form a planar 2D coordination polymer containing hexagonal metallocyclic rings [Cd(6)(SCN)(8)(hmt)(2)]. A 2D layer structure is held together with its neighboring ones via a set of hydrogen-bonding interactions to form a 3D supramolecular structure. The luminescent properties of the title complex in the solid state were investigated.

  16. Structure Learning and Statistical Estimation in Distribution Networks - Part II

    SciTech Connect

    Deka, Deepjyoti; Backhaus, Scott N.; Chertkov, Michael

    2015-02-13

    Limited placement of real-time monitoring devices in the distribution grid, recent trends notwithstanding, has prevented the easy implementation of demand-response and other smart grid applications. Part I of this paper discusses the problem of learning the operational structure of the grid from nodal voltage measurements. In this work (Part II), the learning of the operational radial structure is coupled with the problem of estimating nodal consumption statistics and inferring the line parameters in the grid. Based on a Linear-Coupled(LC) approximation of AC power flows equations, polynomial time algorithms are designed to identify the structure and estimate nodal load characteristics and/or line parameters in the grid using the available nodal voltage measurements. Then the structure learning algorithm is extended to cases with missing data, where available observations are limited to a fraction of the grid nodes. The efficacy of the presented algorithms are demonstrated through simulations on several distribution test cases.

  17. Kaonic atoms and in-medium K-N amplitudes II: Interplay between theory and phenomenology

    NASA Astrophysics Data System (ADS)

    Friedman, E.; Gal, A.

    2013-02-01

    A microscopic kaonic-atom optical potential VK-(1) is constructed, using the Ikeda-Hyodo-Weise NLO chiral K-N subthreshold scattering amplitudes constrained by the kaonic hydrogen SIDDHARTA measurement, and incorporating Pauli correlations within the Waas-Rho-Weise generalization of the Ericson-Ericson multiple-scattering approach. Good fits to kaonic atom data over the entire periodic table require additionally sizable K-NN-motivated absorptive and dispersive phenomenological terms, in agreement with our former analysis based on a post-SIDDHARTA in-medium chirally-inspired NLO separable model by Cieplý and Smejkal. Such terms are included by introducing a phenomenological potential VK-(2) and coupling it self-consistently to VK-(1). Properties of resulting kaonic atom potentials are discussed with special attention paid to the role of K--nuclear absorption and to the extraction of density-dependent amplitudes representing K- multi-nucleon processes.

  18. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  19. Molecular structure identification and position of a dopant ion in diaqua(2,2‧-bipyridine)malonatozinc(II) by spectroscopic studies - II: VO(II)

    NASA Astrophysics Data System (ADS)

    Parthipan, Krishnan; Ramesh, Hema; Sambasiva Rao, P.

    2011-04-01

    Single crystal EPR, optical, FT-IR and powder XRD studies of VO(II) ion doped diaqua(2,2'-bipyridine) malonato zinc complex were carried out at room temperature to ascertain the structural properties. In EPR, the angular variation of vanadium hyperfine lines indicated a single site, with spin Hamiltonian parameters as: g xx = 1.968, g yy = 1.964, g zz = 1.928, A xx = 7.54 mT, A yy = 6.36 mT and A zz = 18.81 mT. In addition, the dopant had entered the lattice in an interstitial position and the position had been identified with the help of atom positions of the host lattice. The EPR and optical data was corroborated to obtain various bonding parameters, from which the nature of the bonding in the complex was discussed. FT-IR and powder XRD studies were used to observe the effect of dopant on structural parameters of the host lattice.

  20. Atomic structure and chemistry of human serum albumin

    NASA Technical Reports Server (NTRS)

    He, Xiao M.; Carter, Daniel C.

    1992-01-01

    The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

  1. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    PubMed

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  2. Atomic structure of the Y complex of the nuclear pore.

    PubMed

    Kelley, Kotaro; Knockenhauer, Kevin E; Kabachinski, Greg; Schwartz, Thomas U

    2015-05-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.

  3. Synthesis, crystal structure and luminescence properties of acenaphthene benzohydrazide based ligand and its zinc(II) complex

    NASA Astrophysics Data System (ADS)

    Kumar, Mukesh; Roy, Soumyabrata; Faizi, Md. Serajul Haque; Kumar, Santosh; Singh, Mantu Kumar; Kishor, Shyam; Peter, Sebastian C.; John, Rohith P.

    2017-01-01

    The complex compound of zinc(II) supported by (Z)-2-hydroxy-N‧-(1-oxoacenaphthylen-2(1H) ylidene)benzohydrazide ligand (H2L1) has been reported and discussed. The reaction of zinc acetate with H2L1 ligand leads to the formation of a mononuclear zinc(ii) complex, [Zn(HL1)2H2O]. The ligand, H2L1 has been characterized by elemental analysis, 1H, 13C and 1Hsbnd COSY -NMR, IR and ESI-MS, while the complex was characterized by elemental analysis, IR, and ESI-MS. The crystal structures of the free ligand H2L1 and the complex have also been determined by single crystal X-ray diffraction. The ligand chelates with metal centre with a nitrogen atom of imino moiety and an oxygen atom of enolic group. The complex shows distorted trigonal bipyramidal geometry around the metal centre with oxygen atoms lying in the equatorial plane and imino nitrogen atoms along the axial direction. The DFT/TD-DFT calculations were performed on both the ligand and its zinc complex to get insight into the structural, electronic and optical properties. The photoluminescence, fluorescence properties of the complex have been investigated.

  4. The structure of filled skutterudites and the local vibration behavior of the filling atom

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaojuan; Zong, Peng-an; Chen, Xihong; Tao, Juzhou; Lin, He

    2017-02-01

    Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites YbxCo4Sb12 (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb LⅢ-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.

  5. TEMPERATURE STRUCTURE AND METALLICITY IN H II REGIONS

    SciTech Connect

    Rodriguez, Monica; GarcIa-Rojas, Jorge E-mail: jogarcia@iac.e

    2010-01-10

    The metallicities implied by collisionally excited lines (CELs) of heavy elements in H II regions are systematically lower than those implied by recombination lines (RLs) by factors of approx2, introducing uncertainties of the same order in the metallicities inferred for the interstellar medium of any star-forming galaxy. Most explanations of this discrepancy are based on the different sensitivities of CELs and RLs to electron temperature, and invoke either some extra heating mechanism producing temperature fluctuations in the ionized region or the addition of cold gas in metal-rich inclusions or ionized by cosmic rays or X-rays. These explanations will change the temperature structure of the ionized gas from the one predicted by simple photoionization models, and depending on which one is correct, will imply different metallicities for the emitting gas. We select nine H II regions with observed spectra of high quality and show that simple models with metallicities close to the ones implied by oxygen CELs reproduce easily their temperature structure, measured with T{sub e}([N II])/T{sub e}([O III]), and their oxygen CELs emission. We discuss the strong constraints that this agreement places on the possible explanations of the discrepancy and suggest that the simplest explanation, namely errors in the line recombination coefficients by factors approx2, might be the correct one. In such case, CELs will provide the best estimates of metallicity.

  6. Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution

    PubMed Central

    Nayak, Maheswar; Pradhan, P. C.; Lodha, G. S.

    2015-01-01

    We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field. PMID:25726866

  7. Structure of photosystem II and substrate binding at room temperature.

    PubMed

    Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin D; Koroidov, Sergey; Brewster, Aaron S; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G; Stan, Claudiu A; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Vo Pham, Long; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T; Andi, Babak; Orville, Allen M; Glownia, James M; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S; Lane, Thomas J; Aquila, Andy; Koglin, Jason E; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Moriarty, Nigel W; Liebschner, Dorothee; Afonine, Pavel V; Waterman, David G; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I; Brunger, Axel T; Zwart, Petrus H; Adams, Paul D; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K; Kern, Jan; Yachandra, Vittal K; Yano, Junko

    2016-12-15

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

  8. Structure of photosystem II and substrate binding at room temperature

    PubMed Central

    Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

    2016-01-01

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment-protein complex, couples the one-electron photochemistry at the reaction center with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC) (Fig. 1a, Extended Data Fig. 1). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, where S1 is the dark stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution2,3. A detailed understanding of the O-O bond formation mechanism remains a challenge, and elucidating the structures of the OEC in the different S-states, as well as the binding of the two substrate waters to the catalytic site4-6, is a prerequisite for this purpose. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage free, room temperature (RT) structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å structure of PS II7 at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, RT measurements are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analog, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10-13. Thus, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms. PMID:27871088

  9. Regularities and symmetries in atomic structure and spectra

    NASA Astrophysics Data System (ADS)

    Pain, Jean-Christophe

    2013-09-01

    The use of statistical methods for the description of complex quantum systems was primarily motivated by the failure of a line-by-line interpretation of atomic spectra. Such methods reveal regularities and trends in the distributions of levels and lines. In the past, much attention was paid to the distribution of energy levels (Wigner surmise, random-matrix model…). However, information about the distribution of the lines (energy and strength) is lacking. Thirty years ago, Learner found empirically an unexpected law: the logarithm of the number of lines whose intensities lie between 2kI0 and 2k+1I0, I0 being a reference intensity and k an integer, is a decreasing linear function of k. In the present work, the fractal nature of such an intriguing regularity is outlined and a calculation of its fractal dimension is proposed. Other peculiarities are also presented, such as the fact that the distribution of line strengths follows Benford's law of anomalous numbers, the existence of additional selection rules (PH coupling), the symmetry with respect to a quarter of the subshell in the spin-adapted space (LL coupling) and the odd-even staggering in the distribution of quantum numbers, pointed out by Bauche and Cossé.

  10. One-dimensional Co(II)/Ni(II) complexes of 2-hydroxyisophthalate: Structures and magnetic properties

    SciTech Connect

    Wang, Kai; Zou, Hua-Hong; Chen, Zi-Lu; Zhang, Zhong; Sun, Wei-Yin; Liang, Fu-Pei

    2015-03-15

    The solvothermal reactions of 2-hydroxyisophthalic acid (H{sub 3}ipO) with M(NO{sub 3}){sub 2}∙6H{sub 2}O (M=Co, Ni) afforded two complexes [Co{sub 2}(HipO){sub 2}(Py){sub 2}(H{sub 2}O){sub 2}] (1) and [Ni(HipO)(Py)H{sub 2}O] (2) (Py=pyridine). They exhibit similar zig-zag chain structures with the adjacent two metal centers connected by a anti-syn bridging carboxylate group from the HipO{sup 2−} ligand. The magnetic measurements reveal the dominant antiferromagnetic interactions and spin-canting in 1 while ferromagnetic interactions in 2. Both of them exhibit magnetocaloric effect (MCE) with the resulting entropy changes (−ΔS{sub m}) of 12.51 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 1 and 11.01 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 2, representing the rare examples of one-dimensional complexes with MCE. - Graphical abstract: Synopsis: Two Co(II)/Ni(II) complexes with zig-zag chain structures have been reported. 1-Co shows cant-antiferromagnetism while 2-Ni shows ferromagnetism. Magnetocaloric effect is also found in both of them. - Highlights: • Two one-dimensional Co(II)/Ni(II) complexes were solvothermally synthesized. • The Co-complex exhibits canted antiferromagnetism. • The Ni-complex exhibits ferromagnetism. • Both of the complexes display magnetocaloric effect.

  11. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

    PubMed

    Das, Rhiju; Qian, Bin; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael D; Bhat, Divya; Chivian, Dylan; Kim, David E; Sheffler, William H; Malmström, Lars; Wollacott, Andrew M; Wang, Chu; Andre, Ingemar; Baker, David

    2007-01-01

    We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions.

  12. Knee structure in double ionization of noble atoms in circularly polarized laser fields

    NASA Astrophysics Data System (ADS)

    Chen, Xiang; Wu, Yan; Zhang, Jingtao

    2017-01-01

    Nonsequential double ionization is characterized by a knee structure in the plot of double-ionization probability versus laser intensity. In circularly polarized (CP) laser fields, this structure has only been observed for Mg atoms. By choosing laser fields according to a scaling law, we exhibit the knee structure in CP laser fields for Ar and He atoms. The collision of the ionized electron with the core enhances the ionization of the second electron and forms the knee structure. The electron recollision is universal in CP laser fields, but the ionization probability in the knee region decreases as the wavelength of the driven field increases. For experimental observations, it is beneficial to use target atoms with small ionization potentials and laser fields with short wavelengths.

  13. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  14. Correlation, relativistic, and quantum electrodynamics effects on the atomic structure of eka-thorium

    SciTech Connect

    Gaigalas, Gediminas; Gaidamauskas, Erikas; Rudzikas, Zenonas; Magnani, Nicola; Caciuffo, Roberto

    2010-02-15

    Large-scale multiconfiguration Dirac-Fock calculations have been performed for the superheavy element eka-thorium, Z=122. The resulting atomic structure is compared with that obtained by various computational approaches involving different degrees of approximation in order to elucidate the role that correlation, relativistic, Breit, and quantum electrodynamics corrections play in determining the low-energy atomic spectrum. The accuracy of the calculations is assessed by comparing theoretical results obtained for thorium with available experimental data.

  15. Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy

    NASA Technical Reports Server (NTRS)

    Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.

    1991-01-01

    Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.

  16. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.

    PubMed

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-03-11

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

  17. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    SciTech Connect

    Schaefer, Michael E-mail: schlaf@mail.usf.edu; Schlaf, Rudy E-mail: schlaf@mail.usf.edu

    2015-08-14

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru{sup 0}) and its oxide (RuO{sub 2}) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru{sup 0} and RuO{sub 2} films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO{sub 2} and 0.04 Å/cycle for Ru.{sup 0} An interface dipole of up to −0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO{sub 2}/OH compound whose surface is saturated with hydroxyl groups.

  18. Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

    ERIC Educational Resources Information Center

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

    2015-01-01

    A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

  19. Ultrathin film of nickel on the Cu (100) surface: Atomic structure and phonons

    SciTech Connect

    Borisova, Svetlana D. E-mail: rusina@ispms.tsc.ru Rusina, Galina G. E-mail: rusina@ispms.tsc.ru

    2014-11-14

    We investigated the structural and vibrational properties of the Cu (100) surface covered with ultrathin (1-5 ML) Ni films using interaction potential from the embedded atom method. The surface relaxation, dispersion relation and polarization of vibrational modes are discussed. Our calculated structural parameters are in good agreement with experimental results. The obtained vibrational frequencies compare well with the available experimental data.

  20. Getting CAD in shape: the atomic structure of human dihydroorotase domain.

    PubMed

    Hermoso, Juan A

    2014-02-04

    CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD.

  1. Structure and stability of a silicon cluster on sequential doping with carbon atoms

    NASA Astrophysics Data System (ADS)

    AzeezullaNazrulla, Mohammed; Joshi, Krati; Israel, S.; Krishnamurty, Sailaja

    2016-02-01

    SiC is a highly stable material in bulk. On the other hand, alloys of silicon and carbon at nanoscale length are interesting from both technological as well fundamental view point and are being currently synthesized by various experimental groups (Truong et. al., 2015 [26]). In the present work, we identify a well-known silicon cluster viz., Si10 and dope it sequentially with carbon atoms. The evolution of electronic structure (spin state and the structural properties) on doping, the charge redistribution and structural properties are analyzed. It is interesting to note that the ground state SiC clusters prefer to be in the lowest spin state. Further, it is seen that carbon atoms are the electron rich centres while silicon atoms are electron deficient in every SiC alloy cluster. The carbon-carbon bond lengths in alloy clusters are equivalent to those seen in fullerene molecules. Interestingly, the carbon atoms tend to aggregate together with silicon atoms surrounding them by donating the charge. As a consequence, very few Si-Si bonds are noted with increasing concentrations of C atoms in a SiC alloy. Physical and chemical stability of doped clusters is studied by carrying out finite temperature behaviour and adsorbing O2 molecule on Si9C and Si8C2 clusters, respectively.

  2. Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms.

    PubMed

    Sobolev, V; Edelman, M

    1995-03-01

    Functional identity and significant similarities in cofactors and sequence exist between the L and M reaction center proteins of the photosynthetic bacteria and the D1 and D2 photosystem-II reaction center proteins of cyanobacteria, algae, and plants. A model of the quinone (QB) binding site of the D1 protein is presented based upon the resolved structure of the QB binding pocket of the L subunit, and introducing novel quantitative notions of complementarity and contact surface between atoms. This model, built without using traditional methods of molecular mechanics and restricted to residues in direct contact with QB, accounts for the experimentally derived functional state of mutants of the D1 protein in the region of QB. It predicts the binding of both the classical and phenol-type PSII herbicides and rationalizes the relative levels of tolerance of mutant phenotypes.

  3. Comparison of two methods for blood lead analysis in cattle: graphite-furnace atomic absorption spectrometry and LeadCare(R) II system.

    PubMed

    Bischoff, Karyn; Gaskill, Cynthia; Erb, Hollis N; Ebel, Joseph G; Hillebrandt, Joseph

    2010-09-01

    The current study compared the LeadCare(R) II test kit system with graphite-furnace atomic absorption spectrometry for blood lead (Pb) analysis in 56 cattle accidentally exposed to Pb in the field. Blood Pb concentrations were determined by LeadCare II within 4 hr of collection and after 72 hr of refrigeration. Blood Pb concentrations were determined by atomic absorption spectrometry, and samples that were coagulated (n = 12) were homogenized before analysis. There was strong rank correlation (R(2) = 0.96) between atomic absorption and LeadCare II (within 4 hr of collection), and a conversion formula was determined for values within the observed range (3-91 mcg/dl, although few had values >40 mcg/dl). Median and mean blood pb concentrations for atomic absorption were 7.7 and 15.9 mcg/dl, respectively; for LeadCare II, medians were 5.2 mcg/dl at 4 hr and 4.9 mcg/dl at 72 hr, and means were 12.4 and 11.7, respectively. LeadCare II results at 4 hr strongly correlated with 72 hr results (R(2) = 0.96), but results at 72 hr were lower (P < 0.01). There was no significant difference between coagulated and uncoagulated samples run by atomic absorption. Although there have been several articles that compared LeadCare with other analytical techniques, all were for the original system, not LeadCare II. The present study indicated that LeadCare II results correlated well with atomic absorption over a wide range of blood Pb concentrations and that refrigerating samples for up to 72 hr before LeadCare II analysis was acceptable for clinical purposes.

  4. Structural Fluctuations and Thermophysical Properties of Molten II-VI Compounds

    NASA Technical Reports Server (NTRS)

    Su, Ching-Hua; Zhu, Shen; Li, Chao; Scripa, R.; Lehoczky, Sandra L.; Kim, Y. W.; Baird, J. K.; Lin, B.; Ban, Heng; Benmore, Chris

    2003-01-01

    The objectives of the project are to conduct ground-based experimental and theoretical research on the structural fluctuations and thermophysical properties of molten II-VI compounds to enhance the basic understanding of the existing flight experiments in microgravity materials science programs as well as to study the fundamental heterophase fluctuation phenomena in these melts by: 1) conducting neutron scattering analysis and measuring quantitatively the relevant thermophysical properties of the II-VI melts (such as viscosity, electrical conductivity, thermal diffusivity and density) as well as the relaxation characteristics of these properties to advance the understanding of the structural properties and the relaxation phenomena in these melts and 2) performing theoretical analyses on the melt systems to interpret the experimental results. All the facilities required for the experimental measurements have been procured, installed and tested. It has long been recognized that liquid Te presents a unique case having properties between those of metals and semiconductors. The electrical conductivity for Te melt increases rapidly at melting point, indicating a semiconductor-metal transition. Te melts comprise two features, which are usually considered to be incompatible with each other: covalently bound atoms and metallic-like behavior. Why do Te liquids show metallic behavior? is one of the long-standing issues in liquid metal physics. Since thermophysical properties are very sensitive to the structural variations of a melt, we have conducted extensive thermophysical measurements on Te melt.

  5. Student perception and conceptual development as represented by student mental models of atomic structure

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

    The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced

  6. Atomic Structure and Phase Transformations in Pu Alloys

    SciTech Connect

    Schwartz, A J; Cynn, H; Blobaum, K M; Wall, M A; Moore, K T; Evans, W J; Farber, D L; Jeffries, J R; Massalski, T B

    2008-04-28

    Plutonium and plutonium-based alloys containing Al or Ga exhibit numerous phases with crystal structures ranging from simple monoclinic to face-centered cubic. Only recently, however, has there been increased convergence in the actinides community on the details of the equilibrium form of the phase diagrams. Practically speaking, while the phase diagrams that represent the stability of the fcc {delta}-phase field at room temperature are generally applicable, it is also recognized that Pu and its alloys are never truly in thermodynamic equilibrium because of self-irradiation effects, primarily from the alpha decay of Pu isotopes. This article covers past and current research on several properties of Pu and Pu-(Al or Ga) alloys and their connections to the crystal structure and the microstructure. We review the consequences of radioactive decay, the recent advances in understanding the electronic structure, the current research on phase transformations and their relations to phase diagrams and phase stability, the nature of the isothermal martensitic {delta} {yields} {alpha}{prime} transformation, and the pressure-induced transformations in the {delta}-phase alloys. New data are also presented on the structures and phase transformations observed in these materials following the application of pressure, including the formation of transition phases.

  7. H-atom abstraction reaction for organic substrates via mononuclear copper(II)-superoxo species as a model for DbetaM and PHM.

    PubMed

    Fujii, Tatsuya; Yamaguchi, Syuhei; Hirota, Shun; Masuda, Hideki

    2008-01-07

    Hydrogen atom abstraction reactions have been implicated in oxygenation reactions catalyzed by copper monooxygenases such as peptidylglycine alpha-hydroxylating monooxygenase (PHM) and dopamine beta-monooxygenase (DbetaM). We have investigated mononuclear copper(I) and copper(II) complexes with bis[(6-neopentylamino-2-pyridyl)methyl][(2-pyridyl)methyl]amine (BNPA) as functional models for these enzymes. The reaction of [Cu(II)(bnpa)]2+ with H2O2, affords a quasi-stable mononuclear copper(II)-hydroperoxo complex, [Cu(II)(bnpa)(OOH)]+ (4) which is stabilized by hydrophobic interactions and hydrogen bonds in the vicinity of the copper(II) ion. On the other hand, the reaction of [Cu(I)(bnpa)]+ (1) with O2 generates a trans-mu-1,2-peroxo dicopper(II) complex [Cu(II)2(bnpa)2(O2(2-]2+ (2). Interestingly, the same reactions carried out in the presence of exogenous substrates such as TEMPO-H, produce a mononuclear copper(II)-hydroperoxo complex 4. Under these conditions, the H-atom abstraction reaction proceeds via the mononuclear copper(II)-superoxo intermediate [Cu(II)(bnpa)(O2-)]+ (3), as confirmed from indirect observations using a spin trap reagent. Reactions with several substrates having different bond dissociation energies (BDE) indicate that, under our experimental conditions the H-atom abstraction reaction proceeds for substrates with a weak X-H bond (BDE < 72.6 kcal mol(-1)). These investigations indicate that the copper(II)-hydroperoxo complex is a useful tool for elucidation of H-atom abstraction reaction mechanisms for exogenous substrates. The useful functionality of the complex has been achieved via careful control of experimental conditions and the choice of appropriate ligands for the complex.

  8. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)

    SciTech Connect

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2009-01-12

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  9. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)*

    PubMed Central

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6Å resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12Å deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates. PMID:18667417

  10. Characterization of asphaltene structure using atomic force microscopy.

    PubMed

    Sabbaghi, S; Shariaty-Niassar, M; Ayatollahi, Sh; Jahanmiri, A

    2008-09-01

    In this study, at the first stage, asphaltene was extracted. The roughness of asphaltene coating at different rpm was studied using an image analysis confocal microscopy. The basics of quantum mechanics and statistical thermodynamics are used to predict the potential energy and the intermolecular forces of asphaltene molecules. The functional forms for the potential energy and intermolecular forces are evaluated. Our final goal is to be able to observe and determine the surface structures of asphaltene micelles with scanning probe microscopes. So, the focus of the work on these unusual molecules is to characterize their structure, dynamics and thermodynamics and to establish the relationship between these properties and petroleum fluid behaviour. The existence of various nanostructures of asphaltene in petroleum has been extensively discussed. A set of fitted data is used to check the validity of the calculated results. The good agreement between the proposed models and the data is promising.

  11. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    DOE PAGES

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

  12. Atomic structure of biodegradable Mg-based bulk metallic glass.

    PubMed

    Christie, J K

    2015-05-21

    We have used highly accurate first-principles molecular dynamics simulations to elucidate the structure of Mg60Zn35Ca5 and Mg72Zn23Ca5 bulk metallic glasses, which are candidate materials for biomedical implants; these two compositions exhibit different behaviours when implanted. The environments of each species are different, and average coordination numbers are ∼13 for Mg, ∼11 for Zn and ∼18-19 for Ca. A wide range of local environments were found and icosahedral motifs, often seen in bulk metallic glasses, were among the most common for both Mg and Zn. Through the computation of a chemical short-range order parameter, a moderate avoidance of Zn-Zn bonding over Zn-Mg or Zn-Ca was observed. No statistically significant difference in structure was observed between the two compositions.

  13. Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.

    PubMed

    Zhang, Zhe; Chen, Jue

    2016-12-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.

  14. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

    PubMed

    Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H

    1988-11-01

    The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  15. Photoassociation of a cold-atom-molecule pair. II. Second-order perturbation approach

    SciTech Connect

    Lepers, M.; Vexiau, R.; Bouloufa, N.; Dulieu, O.; Kokoouline, V.

    2011-04-15

    The electrostatic interaction between an excited atom and a diatomic ground-state molecule in an arbitrary rovibrational level at large mutual separations is investigated with a general second-order perturbation theory, in the perspective of modeling the photoassociation between cold atoms and molecules. We find that the combination of quadrupole-quadrupole and van der Waals interactions competes with the rotational energy of the dimer, limiting the range of validity of the perturbative approach to distances larger than 100 Bohr radii. Numerical results are given for the long-range interaction between Cs and Cs{sub 2}, showing that the photoassociation is probably efficient for any Cs{sub 2} rotational energy.

  16. The Ame2016 atomic mass evaluation * (II). Tables, graphs and references

    SciTech Connect

    Wang, Meng; Audi, G.; Kondev, F. G.; Huang, W. J.; Naimi, S.; Xu, Xing

    2017-01-01

    This paper is the second part of the new evaluation of atomic masses, Ame2016. Using least-squares adjustments to all evaluated and accepted experimental data, described in Part I, we derive tables with numerical values and graphs to replace those given in Ame2012. The first table lists the recommended atomic mass values and their uncertainties. It is followed by a table of the influences of data on primary nuclides, a table of various reaction and decay energies, and finally, a series of graphs of separation and decay energies. The last section of this paper lists all references of the input data used in the Ame2016 and the Nubase2016 evaluations (first paper in this issue). Amdc: http://amdc.impcas.ac.cn/

  17. Structural/Functional Role of Chloride in Photosystem II

    PubMed Central

    Rivalta, Ivan; Amin, Muhamed; Luber, Sandra; Vassiliev, Serguei; Pokhrel, Ravi; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Bruce, Doug; Brudvig, Gary W.; Gunner, M. R.; Batista, Victor S.

    2011-01-01

    Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt-bridge between D2-K317 and D1-D61 that could suppress proton transfer to the lumen. PMID:21678923

  18. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    PubMed Central

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  19. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    NASA Astrophysics Data System (ADS)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  20. Synthesis, characterization and crystal structure of copper(II) complex of succinate and 2,2‧-bipyridyl

    NASA Astrophysics Data System (ADS)

    Thebo, Khalid H.; Shad, Hazoor A.; Malik, Mohammad A.; Helliwell, Madeleine

    2010-04-01

    The mixed ligand copper(II) complex of succinate and 2,2'-bipyridyl was synthesized from disodium succinate, 2,2'-bipyridine and copper nitrate. The structure of the synthesized complex was determined by micro-analysis, IR, thermogravimetric analysis and X-ray crystallography. The thermal decomposition of the complex under an inert atmosphere has been studied. The crystal structure is monoclinic space group P2 1/ n with parameters a = 15.080(9) Å, b = 22.406(13) Å, c = 15.138(9) Å, β = 91.539°, V = 5113(5) Å 3, Z = 4, 1.534 Mg/m 3, R = 0.0911 and Mr = 1181.08. The geometry around copper atom is distorted octahedral. The complex consists of a dimer in which each Cu atom is linked through two carboxylate-oxygen atoms from a tetradentate succinate ligand and four nitrogen atoms from two chelating 2,2'-bipyridyl groups. The succinate ligand bridges between the two Cu atoms.

  1. Atomic Structure of Au329(SR)84 Faradaurate Plasmonic Nanomolecules

    SciTech Connect

    Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; Cullen, David; Dass, Amala

    2015-04-03

    To design novel nanomaterials, it is important to precisely control the composition, determine the atomic structure, and manipulate the structure to tune the materials property. Here we present a comprehensive characterization of the material whose composition is Au329(SR)84 precisely, therefore referred to as a nanomolecule. The size homogeneity was shown by electron microscopy, solution X-ray scattering, and mass spectrometry. We proposed its atomic structure to contain the Au260 core using experiments and modeling of a total-scattering-based atomic-pair distribution functional analysis. HAADF-STEM images shows fcc-like 2.0 ± 0.1 nm diameter nanomolecules.

  2. Atomic resolution structure of serine protease proteinase K at ambient temperature

    PubMed Central

    Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro

    2017-01-01

    Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. PMID:28361898

  3. Atomic resolution structure of serine protease proteinase K at ambient temperature.

    PubMed

    Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro

    2017-03-31

    Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.

  4. Determination of atomic structure at surfaces and interfaces by high-resolution stem

    SciTech Connect

    Pennycook, S.J.; Chisholm, M.F.; Nellist, P.D.; Browning, N.D.; Wallis, D.J.; Dickey, E.C.

    1996-12-31

    It is over 100 y since Lord Rayleigh first showed the differences between coherent and incoherent imaging in the light microscope, pointing out the advantages of the latter for resolution and image interpretation. The annular detector in the high-resolution STEM provides the same advantages for electrons, allowing incoherent imaging at atomic resolution, with image contrast strongly dependent on atomic number (Z). Since incoherent imaging has no phase problem, these Z-contrast images may be directly inverted to given the (projected) atomic positions. A maximum entropy method avoids false detail associated with direct deconvolution, and gives atomic coordinates to an accuracy of {+-}0.1{Angstrom}. Electron energy loss spectroscopy can provide valuable complementary information on light element bonding and the presence of impurities in specific atomic planes selected from the image. Together, these techniques have revealed some surprisingly complex interfacial structures. For surface studies, the 1.3{Angstrom} probe of the VG Microscopes HB603U STEM provides sufficient penetration and contrast to image single Pt and Rh atoms on {gamma}-alumina supports. Such images reveal preferred atomic configurations and allow possible surface adsorption sites to be deduced.

  5. A solid phase extraction procedure for the determination of Cd(II) and Pb(II) ions in food and water samples by flame atomic absorption spectrometry.

    PubMed

    Daşbaşı, Teslima; Saçmacı, Şerife; Ülgen, Ahmet; Kartal, Şenol

    2015-05-01

    A relatively rapid, accurate and precise solid phase extraction method is presented for the determination of cadmium(II) and lead(II) in various food and water samples. Quantitation is carried out by flame atomic absorption spectrometry (FAAS). The method is based on the retention of the trace metal ions on Dowex Marathon C, a strong acid cation exchange resin. Some important parameters affecting the analytical performance of the method such as pH, flow rate and volume of the sample solution; type, concentration, volume, flow rate of the eluent; and matrix effects on the retention of the metal ions were investigated. Common coexisting ions did not interfere on the separation and determination of the analytes. The detection limits (3 σb) for Cd(II) and Pb(II) were found as 0.13 and 0.18 μg L(-1), respectively, while the limit of quantification values (10 σb) were computed as 0.43 and 0.60 μg L(-1) for the same sequence of the analytes. The precision (as relative standard deviation was lower than 4% at 5 μg L(-1) Cd(II) and 10 μg L(-1) Pb(II) levels, and the preconcentration factor was found to be 250. The accuracy of the proposed procedure was verified by analysing the certified reference materials, SPS-WW2 Batch 108 wastewater level 2 and INCT-TL-1 tea leaves, with the satisfactory results. In addition, for the accuracy of the method the recovery studies (⩾ 95%) were carried out. The method was applied to the determination of the analytes in the various natural waters (lake water, tap water, waste water with boric acid, waste water with H2SO4) and food samples (pomegranate flower, organic pear, radish leaf, lamb meat, etc.), and good results were obtained. While the food samples almost do not contain cadmium, they have included lead at low levels of 0.13-1.12 μg g(-1).

  6. Atomic intermixing and segregation at the interface of InAs/GaSb type II superlattices

    NASA Astrophysics Data System (ADS)

    Li, Xiaochao; Zhang, Yong; Jiang, Dongwei; Guo, Fengyun; Wang, Dongbo; Zhao, Liancheng

    2017-04-01

    To determine the interfacial atomic intermixing of the InAs/GaSb T2SL, an innovative and straightforward method based on TEM techniques is proposed to analysize and investigate the interface stoichiometry of the InAs/GaSb T2SL. Using this method, the chemical components of the interfaces in InAs/GaSb T2SL can be quantitatively determined by fitting with the sigmoidal function and Muraki's segregation model. It is found that the intermixing at the cationic and anionic sublattice is different, and the interface GaSb-on-InAs is slightly sharper than the InAs-on-GaSb interface. Furthermore, we identified segregation of Sb and In atoms and quantitatively measured their incorporation in the lattice. It is also found that the In and Sb segregations mainly occur at the GaSb-on-InAs and InAs-on-GaSb interfaces, respectively and the Sb segregation is larger than the In segregation in the as-grown InAs/GaSb superlattice because of the different atomic exchanges energy.

  7. Ni(II) and Fe(II) complexes based on bis(imino)aryl pincer ligands: synthesis, structural characterization and catalytic activities.

    PubMed

    Zhang, Jingshun; Gao, Wei; Lang, Xiaomei; Wu, Qiaolin; Zhang, Lei; Mu, Ying

    2012-08-28

    Bis(imino)aryl NCN pincer Ni(II) complexes 2,6-(ArN=CH)(2)C(6)H(3)NiBr (1: Ar = 2,6-Me(2)C(6)H(3); 2: Ar = 2,6-Et(2)C(6)H(3); 3: Ar = 2,6-(i)Pr(2)C(6)H(3)) were prepared via the oxidative-addition of Ni(0)(Ph(3)P)(4) with bis(N-aryl)-2-bromoisophthalaldimine. These nickel complexes were characterized by NMR and elemental analyses. Their solid molecular structures were established by X-ray diffraction analyses. The nickel metal centers adopt distorted square planar geometries with the bromine atoms acting as one coordinate ligands. The NCN pincer Fe(II) complexes 2,6-(ArN=CH)(2)C(6)H(3)Fe(μ-Cl)(2)Li(THF)(2) (4: Ar = 2,6-Me(2)C(6)H(3); 5: Ar = 2,6-Et(2)C(6)H(3); 6: Ar = 2,6-(i)Pr(2)C(6)H(3)) were synthesized by lithium salt metathesis reactions of the ligand lithium salts with FeCl(2). X-ray structure analyses of 4 and 5 revealed that the Fe(II) complexes are hetero-dinuclear with the iron atoms in trigonal bipyramidal environments. When activated with MAO, the nickel complexes are active for norbornene vinyl polymerization but are inert for butadiene polymerization. The Fe(II) complexes show moderate activities in butadiene polymerization when activated with alkylaluminium, affording the cis-1,4 enriched polymer.

  8. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up.

    PubMed

    Hoelz, André; Glavy, Joseph S; Beck, Martin

    2016-07-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  9. Towards the atomic structure of the Nuclear Pore Complex: When top down meets bottom up

    PubMed Central

    Hoelz, André; Glavy, Joseph S.; Beck, Martin

    2016-01-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, due to sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom up approaches rely on biochemical interaction studies and crystal structure determination of NPC components, top down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, bridging the resolution gap from higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function. PMID:27273515

  10. Synthesis of Calcium(II) Amidinate Precursors for Atomic Layer Deposition through a Redox Reaction between Calcium and Amidines.

    PubMed

    Kim, Sang Bok; Yang, Chuanxi; Powers, Tamara; Davis, Luke M; Lou, Xiabing; Gordon, Roy G

    2016-08-22

    We have prepared two new Ca(II) amidinates, which comprise a new class of ALD precursors. The syntheses proceed by a direct reaction between Ca metal and the amidine ligands in the presence of ammonia. Bis(N,N'-diisopropylformamidinato)calcium(II) (1) and bis(N,N'-diisopropylacetamidinato)calcium(II) (2) adopt dimeric structures in solution and in the solid state. X-ray crystallography revealed asymmetry in one of the bridging ligands to afford the structure [(η(2) -L)Ca(μ-η(2) :η(2) -L)(μ-η(2) :η(1) -L)Ca(η(2) -L)]. These amidinate complexes showed unprecedentedly high volatility as compared to the widely employed and commercially available Ca(II) precursor, [Ca3 (tmhd)6 ]. In CaS ALD with 1 and H2 S, the ALD window was approximately two times wider and lower in temperature by about 150 °C than previously reported with [Ca3 (tmhd)6 ] and H2 S. Complexes 1 and 2, with their excellent volatility and thermal stability (up to at least 350 °C), are the first homoleptic Ca(II) amidinates suitable for use as ALD precursors.

  11. Synthesis of Calcium(II) Amidinate Precursors for Atomic Layer Deposition through a Redox Reaction between Calcium and Amidines

    PubMed Central

    Kim, Sang Bok; Yang, Chuanxi; Powers, Tamara; Davis, Luke M.; Lou, Xiabing

    2016-01-01

    Abstract We have prepared two new CaII amidinates, which comprise a new class of ALD precursors. The syntheses proceed by a direct reaction between Ca metal and the amidine ligands in the presence of ammonia. Bis(N,N′‐diisopropylformamidinato)calcium(II) (1) and bis(N,N′‐diisopropylacetamidinato)calcium(II) (2) adopt dimeric structures in solution and in the solid state. X‐ray crystallography revealed asymmetry in one of the bridging ligands to afford the structure [(η2‐L)Ca(μ‐η2:η2‐L)(μ‐η2:η1‐L)Ca(η2‐L)]. These amidinate complexes showed unprecedentedly high volatility as compared to the widely employed and commercially available CaII precursor, [Ca3(tmhd)6]. In CaS ALD with 1 and H2S, the ALD window was approximately two times wider and lower in temperature by about 150 °C than previously reported with [Ca3(tmhd)6] and H2S. Complexes 1 and 2, with their excellent volatility and thermal stability (up to at least 350 °C), are the first homoleptic CaII amidinates suitable for use as ALD precursors. PMID:27351794

  12. Structure of adsorbed organometallic rhodium: model single atom catalysts.

    PubMed

    Bennett, R A; McCavish, N D; Basham, M; Dhanak, V R; Newton, M A

    2007-02-02

    We have determined the structure of a complex rhodium carbonyl chloride [Rh(CO)2Cl] molecule adsorbed on the TiO2(110) surface by the normal incidence x-ray standing wave technique. The data show that the technique is applicable to reducible oxide systems and that the dominant adsorbed species is undissociated with Rh binding atop bridging oxygen and to the Cl found close to the fivefold coordinated Ti ions in the surface. A minority geminal dicarbonyl species, where Rh-Cl bond scission has occurred, is found bridging the bridging oxygen ions forming a high-symmetry site.

  13. Atomic calligraphy: the direct writing of nanoscale structures using a microelectromechanical system.

    PubMed

    Imboden, Matthias; Han, Han; Chang, Jackson; Pardo, Flavio; Bolle, Cristian A; Lowell, Evan; Bishop, David J

    2013-07-10

    We present a microelectromechanical system (MEMS) based method for the resist-free patterning of nanostructures. Using a focused ion beam to customize larger MEMS machines, we fabricate apertures with features less than 50 nm in diameter on plates that can be moved with nanometer precision over an area greater than 20 × 20 μm(2). Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter positioned micrometers above the aperture enables high speed control of not only where but also when atoms are deposited. With this shutter, different-sized apertures can be opened and closed selectively for nanostructure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms.

  14. The Three-Dimensional Structural Basis of Type II Hyperprolinemia

    SciTech Connect

    Srivastava, Dhiraj; Singh, Ranjan K.; Moxley, Michael A.; Henzl, Michael T.; Becker, Donald F.; Tanner, John J.

    2012-08-31

    Type II hyperprolinemia is an autosomal recessive disorder caused by a deficiency in {Delta}{sup 1}-pyrroline-5-carboxylate dehydrogenase (P5CDH; also known as ALDH4A1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. Here, we report the first structure of human P5CDH (HsP5CDH) and investigate the impact of the hyperprolinemia-associated mutation of Ser352 to Leu on the structure and catalytic properties of the enzyme. The 2. 5-{angstrom}-resolution crystal structure of HsP5CDH was determined using experimental phasing. Structures of the mutant enzymes S352A (2.4 {angstrom}) and S352L (2.85 {angstrom}) were determined to elucidate the structural consequences of altering Ser352. Structures of the 93% identical mouse P5CDH complexed with sulfate ion (1.3 {angstrom} resolution), glutamate (1.5 {angstrom}), and NAD{sup +} (1.5 {angstrom}) were determined to obtain high-resolution views of the active site. Together, the structures show that Ser352 occupies a hydrophilic pocket and is connected via water-mediated hydrogen bonds to catalytic Cys348. Mutation of Ser352 to Leu is shown to abolish catalytic activity and eliminate NAD{sup +} binding. Analysis of the S352A mutant shows that these functional defects are caused by the introduction of the nonpolar Leu352 side chain rather than the removal of the Ser352 hydroxyl. The S352L structure shows that the mutation induces a dramatic 8-{angstrom} rearrangement of the catalytic loop. Because of this conformational change, Ser349 is not positioned to interact with the aldehyde substrate, conserved Glu447 is no longer poised to bind NAD{sup +}, and Cys348 faces the wrong direction for nucleophilic attack. These structural alterations render the enzyme inactive.

  15. The three-dimensional structural basis of type II hyperprolinemia.

    PubMed

    Srivastava, Dhiraj; Singh, Ranjan K; Moxley, Michael A; Henzl, Michael T; Becker, Donald F; Tanner, John J

    2012-07-13

    Type II hyperprolinemia is an autosomal recessive disorder caused by a deficiency in Δ(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH; also known as ALDH4A1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. Here, we report the first structure of human P5CDH (HsP5CDH) and investigate the impact of the hyperprolinemia-associated mutation of Ser352 to Leu on the structure and catalytic properties of the enzyme. The 2. 5-Å-resolution crystal structure of HsP5CDH was determined using experimental phasing. Structures of the mutant enzymes S352A (2.4 Å) and S352L (2.85 Å) were determined to elucidate the structural consequences of altering Ser352. Structures of the 93% identical mouse P5CDH complexed with sulfate ion (1.3 Å resolution), glutamate (1.5 Å), and NAD(+) (1.5 Å) were determined to obtain high-resolution views of the active site. Together, the structures show that Ser352 occupies a hydrophilic pocket and is connected via water-mediated hydrogen bonds to catalytic Cys348. Mutation of Ser352 to Leu is shown to abolish catalytic activity and eliminate NAD(+) binding. Analysis of the S352A mutant shows that these functional defects are caused by the introduction of the nonpolar Leu352 side chain rather than the removal of the Ser352 hydroxyl. The S352L structure shows that the mutation induces a dramatic 8-Å rearrangement of the catalytic loop. Because of this conformational change, Ser349 is not positioned to interact with the aldehyde substrate, conserved Glu447 is no longer poised to bind NAD(+), and Cys348 faces the wrong direction for nucleophilic attack. These structural alterations render the enzyme inactive.

  16. Atomic structure, alloying behavior, and magnetism in small Fe-Pt clusters

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Kumar, Vijay

    2015-09-01

    We report results of the atomic structure, alloying behavior, and magnetism in F emP tn(m +n =2 -10 ) clusters using projector augmented wave (PAW) pseudopotential method and spin-polarized generalized gradient approximation (GGA) for the exchange-correlation energy. These results are compared with those obtained by using HCTH exchange-correlation functional and LANL2DZ basis set in the Gaussian program and the overall trends are found to be similar. As in bulk Fe-Pt alloys, clusters with equal composition of Fe and Pt have the largest binding energy and the largest heat of nanoalloy formation for a given number of atoms in the cluster. There are some deviations due to the different symmetries in clusters and in cases where the total number of atoms is odd. The lowest energy isomers tend to maximize bonds between unlike atoms with Fe (Pt) atoms occupying high (low) coordination sites in the core (surface) of the cluster. The binding energy, heat of formation, and the second order difference of the total energy show F e2P t2 , F e4P t4 , and F e4P t6 clusters to be the most stable ones among the different clusters we have studied. The magnetic moments on Fe atoms are high in Pt-rich clusters as well as in small Fe-rich clusters and decrease as the aggregation of Fe atoms and the cluster size increases. The maximum value of the magnetic moments on Fe atoms is ˜3.8 μB , whereas for Pt atoms it is 1 μB. These are quite high compared with the values for bulk Fe as well as bulk FePt and F e3Pt phases while bulk Pt is nonmagnetic. There is significant charge transfer from those Fe atoms that interact directly with Pt atoms. We discuss the hybridization between the electronic states of Pt and Fe atoms as well as the variation in the magnetic moments on Fe and Pt atoms. Our results provide insight into the understanding of the nanoalloy behavior of Fe-Pt and we hope that this would help to design Fe based nanoalloys and their assemblies with high magnetic moments for

  17. Using Machine Learning to Accelerate Complex Atomic Structure Elucidation

    NASA Astrophysics Data System (ADS)

    Brouwer, William; Calderin, Lazaro; Sofo, Jorge

    2012-02-01

    Workers in various scientific disciplines seek to develop chemical models for extended and molecular systems. The modeling process revolves around the gradual refinement of model assumptions, through comparison of experimental and computational results. Solid state Nuclear Magnetic Resonance (NMR) is one such experimental technique, providing great insight into chemical order over Angstrom length scales. However, interpretation of spectra for complex materials is difficult, often requiring intensive simulations. Similarly, working forward from the model in order to produce experimental quantities via ab initio is computationally demanding. The work involved in these two significant steps, compounded by the need to iterate back and forth, drastically slows the discovery process for new materials. There is thus great motivation for the derivation of structural models directly from complex experimental data, the subject of this work. Using solid state NMR experimental datasets, in conjunction with ab initio calculations of measurable NMR parameters, a network of machine learning kernels are trained to rapidly yield structural details, on the basis of input NMR spectra. Results for an environmentally relevant material will be presented, and directions for future work.

  18. Crystal structure of bis-(1-ethyl-pyridinium) dioxonium hexa-cyanidoferrate(II).

    PubMed

    Tanaka, Rikako; Matsushita, Nobuyuki

    2017-02-01

    The title compound, (C7H10N)2(H3O)2[Fe(CN)6] or (Etpy)2(H3O)2[Fe(CN)6] (Etpy(+) is 1-ethyl-pyridinium), crystallizes in the space group Pnnm. The Fe(II) atom of the [Fe(CN)6](4-) anion lies on a site with site symmetry ..2/m, and has an octa-hedral coordination sphere defined by six cyanido ligands. Both the Etpy(+) and the oxonium cations are located on a mirror plane. In the crystal, electron-donor anions of [Fe(CN)6](4-) and electron-acceptor cations of Etpy(+) are each stacked parallel to the b axis, resulting in a columnar structure with segregated moieties. The crystal packing is stabilized by a three-dimensional O-H⋯N hydrogen-bonding network between the oxonium ions and the cyanide ligands of [Fe(CN)6](4-).

  19. Dye-sensitized solar cells: Atomic scale investigation of interface structure and dynamics

    NASA Astrophysics Data System (ADS)

    Ma, Wei; Zhang, Fan; Meng, Sheng

    2014-08-01

    Recent progress in dye-sensitized solar cells (DSC) research is reviewed, focusing on atomic-scale investigations of the interface electronic structures and dynamical processes, including the structure of dye adsorption onto TiO2, ultrafast electron injection, hot-electron injection, multiple-exciton generation, and electron—hole recombination. Advanced experimental techniques and theoretical approaches are briefly summarized, and then progressive achievements in photovoltaic device optimization based on insights from atomic scale investigations are introduced. Finally, some challenges and opportunities for further improvement of dye solar cells are presented.

  20. The influence of the atomic structure of basal planes on interplanar distance in pyrolytic carbon materials

    NASA Astrophysics Data System (ADS)

    Borgardt, N. I.; Prihodko, A. S.; Seibt, M.

    2016-12-01

    The atomic structure of carbon materials is studied using the example of pyrocarbon and boronrich pyrocarbon by means of the method of reconstruction of the wave function in transmission electron microscopy. It is shown that the digital processing of the phase distributions of these functions allows us to find the average distance between the basal planes. Using the method of molecular dynamics for the formation of the test structures and obtaining for them the calculated phase distributions, the effect of depletion of the basal planes of the carbon atoms on the interplanar distance in the pyrocarbon materials is quantified.

  1. FASTRAN II - FATIGUE CRACK GROWTH STRUCTURAL ANALYSIS (UNIX VERSION)

    NASA Technical Reports Server (NTRS)

    Newman, J. C.

    1994-01-01

    Predictions of fatigue crack growth behavior can be made with the Fatigue Crack Growth Structural Analysis (FASTRAN II) computer program. As cyclic loads are applied to a selected crack configuration with an initial crack size, FASTRAN II predicts crack growth as a function of cyclic load history until either a desired crack size is reached or failure occurs. FASTRAN II is based on plasticity-induced crack-closure behavior of cracks in metallic materials and accounts for load-interaction effects, such as retardation and acceleration, under variable-amplitude loading. The closure model is based on the Dugdale model with modifications to allow plastically deformed material to be left along the crack surfaces as the crack grows. Plane stress and plane strain conditions, as well as conditions between these two, can be simulated in FASTRAN II by using a constraint factor on tensile yielding at the crack front to approximately account for three-dimensional stress states. FASTRAN II contains seventeen predefined crack configurations (standard laboratory fatigue crack growth rate specimens and many common crack configurations found in structures); and the user can define one additional crack configuration. The baseline crack growth rate properties (effective stress-intensity factor against crack growth rate) may be given in either equation or tabular form. For three-dimensional crack configurations, such as surface cracks or corner cracks at holes or notches, the fatigue crack growth rate properties may be different in the crack depth and crack length directions. Final failure of the cracked structure can be modelled with fracture toughness properties using either linear-elastic fracture mechanics (brittle materials), a two-parameter fracture criterion (brittle to ductile materials), or plastic collapse (extremely ductile materials). The crack configurations in FASTRAN II can be subjected to either constant-amplitude, variable-amplitude or spectrum loading. The applied

  2. FASTRAN II - FATIGUE CRACK GROWTH STRUCTURAL ANALYSIS (IBM PC VERSION)

    NASA Technical Reports Server (NTRS)

    Newman, J. C.

    1994-01-01

    Predictions of fatigue crack growth behavior can be made with the Fatigue Crack Growth Structural Analysis (FASTRAN II) computer program. As cyclic loads are applied to a selected crack configuration with an initial crack size, FASTRAN II predicts crack growth as a function of cyclic load history until either a desired crack size is reached or failure occurs. FASTRAN II is based on plasticity-induced crack-closure behavior of cracks in metallic materials and accounts for load-interaction effects, such as retardation and acceleration, under variable-amplitude loading. The closure model is based on the Dugdale model with modifications to allow plastically deformed material to be left along the crack surfaces as the crack grows. Plane stress and plane strain conditions, as well as conditions between these two, can be simulated in FASTRAN II by using a constraint factor on tensile yielding at the crack front to approximately account for three-dimensional stress states. FASTRAN II contains seventeen predefined crack configurations (standard laboratory fatigue crack growth rate specimens and many common crack configurations found in structures); and the user can define one additional crack configuration. The baseline crack growth rate properties (effective stress-intensity factor against crack growth rate) may be given in either equation or tabular form. For three-dimensional crack configurations, such as surface cracks or corner cracks at holes or notches, the fatigue crack growth rate properties may be different in the crack depth and crack length directions. Final failure of the cracked structure can be modelled with fracture toughness properties using either linear-elastic fracture mechanics (brittle materials), a two-parameter fracture criterion (brittle to ductile materials), or plastic collapse (extremely ductile materials). The crack configurations in FASTRAN II can be subjected to either constant-amplitude, variable-amplitude or spectrum loading. The applied

  3. Synthesis, X-ray crystal structure and spectroscopy of a Werner-type host Co(II) complex, trans-bisisothiocyanatotetrakis( trans-4-styrylpyridine)cobalt(II)

    NASA Astrophysics Data System (ADS)

    Karunakaran, C.; Thomas, K. R. J.; Shunmugasundaram, A.; Murugesan, R.

    2000-05-01

    Single crystals of the title Co(II) complex, [Co(stpy) 4(NCS) 2] [stpy= trans-4-styrylpyridine] are prepared and characterized by elemental analysis, IR, and UV-visible spectroscopy and X-ray crystal structure determination. The complex crystallizes in the orthorhombic space group Pna2 1 with unit-cell parameters, a=32.058(3), b=15.362(5), c=9.818(5) Å, and Z=4. The structure consists of discrete monomeric units of [Co(stpy) 4(NCS) 2]. The equatorial positions of the Co(II) polyhedron are occupied by nitrogen atoms of the four stpy ligands and the axial positions are occupied by the nitrogen atoms of the two thiocyanate ions. The unit cell packing reveals interpenetration of styryl groups owing to conformational flexibility of phenyl and pyridyl rings in stpy ligands. Thus, it leads to efficient packing of the crystal lattice leaving no space available for guest inclusion. IR spectra reveal nitrogen coordination from stpy and terminal -NCS coordination of the thiocyanate group. The optical reflectance bands 475, 540 (shoulder) and 1022 nm suggest octahedral geometry in accordance with the X-ray data. However, the optical spectrum of acetonitrile solution shows an intense band at 615 nm and a weak shoulder at 570 nm suggesting participation of the solvent molecules in the coordination sphere. These bands indicate the presence of both tetrahedral and octahedral species in solution.

  4. Extended x-ray absorption fine structure studies of the atomic structure of nanoparticles in different metallic matrices.

    PubMed

    Baker, S H; Roy, M; Gurman, S J; Binns, C

    2009-05-06

    It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.

  5. Crystal structure and magnetic properties of NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl

    SciTech Connect

    Jin Tengteng; Liu Wei; Chen Shuang; Prots, Yurii; Schnelle, Walter; Zhao Jingtai; Kniep, Ruediger; Hoffmann, Stefan

    2012-08-15

    A new copper(II) oxide phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], has been synthesized by flux synthesis. Single-crystal X-ray diffraction data show that the title compound crystallizes in the monoclinic system, space group P2{sub 1}/c (No. 14), with lattice parameters a=8.392(2) A, b=6.3960(10) A, c=16.670(2) A, {beta}=109.470(10) Degree-Sign , V=843.6(3) A{sup 3}, Z=4. The crystal structure is characterized by a complex chain of copper-centered polyhedra running along [0 1 0] which are connected by phosphate tetrahedra. The resulting three-dimensional polyhedra framework exhibits channels filled by additional copper and sodium atoms. Field and temperature dependent measurements of the specific heat and the magnetic susceptibility reveal low-dimensional magnetic behavior. The compound starts to decompose at 700 K under release of oxygen and evaporation of Cu{sup I}Cl as shown by simultaneous thermogravimetry and mass spectrometry. - Graphical abstract: The crystal structure of the new copper(II) phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], exhibits linear chains of copper tetrahedra which show low-dimensional magnetic behavior proven by specific heat and magnetic susceptibility measurements. Highlights: Black-Right-Pointing-Pointer A new copper(II) oxide phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], has been synthesized by flux synthesis. Black-Right-Pointing-Pointer The crystal structure comprises chains of Cu{sub 4}O tetrahedra. Black-Right-Pointing-Pointer Low-dimensional behavior has been proven by magnetic and specific heat measurements. Black-Right-Pointing-Pointer On heating, Cu{sup I}Cl and oxygen are released shown by simultaneous thermogravimetry and mass spectrometry.

  6. ssDNA binding reveals the atomic structure of graphene.

    PubMed

    Husale, By Sudhir; Sahoo, Sangeeta; Radenovic, Aleksandra; Traversi, Floriano; Annibale, Paolo; Kis, Andras

    2010-12-07

    We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the π-π stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the π-π stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures.

  7. Materials by Design-A Perspective From Atoms to Structures.

    PubMed

    Buehler, Markus J

    2013-02-01

    Biological materials are effectively synthesized, controlled, and used for a variety of purposes-in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science.

  8. Synthesis, characterization and X-ray structural studies of four copper (II) complexes containing dinuclear paddle wheel structures

    PubMed Central

    2013-01-01

    Background Various dinuclear copper (II) complexes with octahedral geometry have been reported. The majority of these complexes contain N containing aromatic rings as axial ligands. There are also a few cases where the solvent used in the reaction occupies the axial position of the dinuclear copper (II) complex. This may occur by planned synthesis or some times by serendipity. Here we report some four copper (II) complexes containing solvent and or N containing heterocyclic ring as the axial ligand. Results Four compounds, each containing dinuclear Copper (II) units (with the most robust, frequently occurring paddle wheel structures) were synthesized and characterised by single crystal X-ray diffraction and by IR spectroscopy. The compounds 1 & 2 have the general formula Cu2(RCOO) 4(L)2 [(for (1) RCOO= 4-Chloro Benzoate, L= Isopropanol; for 2 RCOO= Benzoate, L= 2-Amino-4,6-dimethyl pyrimidine )] while 3 & 4 have the general formula, Cu2(RCOO) 4(S)2 Cu2(RCOO) 4(L)2 [RCOO=5-Chloro-thiophene-2-carboxylate L= 2-Amino-4,6-dimethyl pyrimidine, for 3 S= ethanol; for 4 S= methanol ]. A wide range of hydrogen bonds (of the O-H…O, N-H…O and N-H…N type) and π-π stacking interactions are present in the crystal structures. Conclusions All compounds contain the dinuclear units, in which two Cu (II) ions are bridged by four syn, syn-η1:η1:μ carboxylates, showing a paddle-wheel cage type with a distorted octahedral geometry. The compounds 1 &2 contain a single dimeric unit while 3 &4 contain two dimeric units. The structures 3 and 4 are very interesting co-crystals of two paddle wheel molecules. Also it is interesting to note that the compounds 3 &4 are isostructural with similar cell parameters. Both the compounds 3 &4 differ in the solvent molecule coordinated to copper in one of the dimeric units. In all the four compounds, each of the copper dimers has an inversion centre. Every copper has a distorted octahedral centre, formed by four oxygen atoms (from different

  9. Structure of the ESCRT-II endosomal trafficking complex.

    PubMed

    Hierro, Aitor; Sun, Ji; Rusnak, Alexander S; Kim, Jaewon; Prag, Gali; Emr, Scott D; Hurley, James H

    2004-09-09

    The multivesicular-body (MVB) pathway delivers transmembrane proteins and lipids to the lumen of the endosome. The multivesicular-body sorting pathway has crucial roles in growth-factor-receptor downregulation, developmental signalling, regulation of the immune response and the budding of certain enveloped viruses such as human immunodeficiency virus. Ubiquitination is a signal for sorting into the MVB pathway, which also requires the functions of three protein complexes, termed ESCRT-I, -II and -III (endosomal sorting complex required for transport). Here we report the crystal structure of the core of the yeast ESCRT-II complex, which contains one molecule of the Vps protein Vps22, the carboxy-terminal domain of Vps36 and two molecules of Vps25, and has the shape of a capital letter 'Y'. The amino-terminal coiled coil of Vps22 and the flexible linker leading to the ubiquitin-binding NZF domain of Vps36 both protrude from the tip of one branch of the 'Y'. Vps22 and Vps36 form nearly equivalent interactions with the two Vps25 molecules at the centre of the 'Y'. The structure suggests how ubiquitinated cargo could be passed between ESCRT components of the MVB pathway through the sequential transfer of ubiquitinated cargo from one complex to the next.

  10. Structural mechanisms of the Ih–II and II → Ic transitions between the crystalline phases of aqueous ice

    SciTech Connect

    Zheligovskaya, E. A.

    2015-09-15

    Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation of other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.

  11. Bridge over troubled water: resolving the competing photosystem II crystal structures.

    PubMed

    Petrie, Simon; Stranger, Rob; Gatt, Phillip; Pace, Ron J

    2007-01-01

    Density functional theory (DFT) calculations, at the Becke-Perdew/TZP level of theory, were used to investigate a set of CaMn(4)-containing clusters that model the active site of the water-oxidizing complex (WOC) of photosystem II (PSII). Metal-atom positions for three representative isomeric clusters of the formula [CaMn(4)C(9)N(2)O(16)H(10)](+)4 H(2)O are in good agreement with the disparate Mn(4) geometries of the three most recent X-ray crystal structures. Remarkably, interconversion between these three isomeric clusters is found to be facile, resulting from subtle changes in the coordination environment around the CaMn(4) centre. This result provides a clear rationalisation of the marked differences in reported crystal structures. Recent concerns have been raised regarding the opportunity for X-ray-damage-induced distortion of the metal-containing active centre during crystallographic analysis. Our calculations suggest that an even greater problem may be presented by the apparent fluxionality of the CaMn(4) skeleton within the active centre. Structural rearrangement may well precede crystallographic analysis, for example by the preferential "freezing-out" of one of several near-isoenergetic structures during the workup for crystallisation. This prospect, which our calculations cannot exclude, highlights the difficulties that will continue to be faced by experimentalists seeking unambiguous structural information on the WOC's active site.

  12. Structural changes of the oxygen-evolving complex in photosystem II during the catalytic cycle.

    PubMed

    Glöckner, Carina; Kern, Jan; Broser, Matthias; Zouni, Athina; Yachandra, Vittal; Yano, Junko

    2013-08-02

    The oxygen-evolving complex (OEC) in the membrane-bound protein complex photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn4CaO5 cluster in the OEC during the S state transitions using x-ray absorption spectroscopy (XAS). Overall structural changes of the Mn4CaO5 cluster, based on the manganese ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn4CaO5 cluster in the OEC obtained from a polarized XAS model and the 1.9-Å high resolution crystal structure. Additionally, we compared the S1 state XAS of the dimeric and monomeric form of PSII from Thermosynechococcus elongatus and spinach PSII. Although the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the manganese K-edge XAS between T. elongatus PSII and spinach PSII are found and may originate from differences in the second sphere ligand atom geometry.

  13. Crystal structure of bis­(azido-κN)bis­(quinolin-8-amine-κ2 N,N′)iron(II)

    PubMed Central

    Setifi, Fatima; Moon, Dohyun; Koen, Robeyns; Setifi, Zouaoui; Lamsayah, Morad; Touzani, Rachid

    2016-01-01

    The search for new mol­ecular materials with inter­esting magnetic properties using the pseudohalide azide ion and quinolin-8-amine (aqin, C9H8N2) as a chelating ligand, led to the synthesis and structure determination of the title complex, [Fe(N3)2(C9H8N2)2]. The complex shows an octa­hedral geometry, with the FeII atom surrounded by six N atoms; the two N3 − anions coordinate in a cis configuration, while the remaining N atoms originate from the two quinolin-8-amine ligands with the quinoline N atoms lying on opposite sides of the Fe atom. The crystal packing is dominated by layers of hydro­philic and aromatic regions parallel to the ac plane, stabilized by a two-dimensional hydrogen-bonded network and π–π stacking. PMID:27746947

  14. Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

    SciTech Connect

    Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena Safa; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

    2014-12-02

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

  15. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    PubMed Central

    Giordano, V. M.; Ruta, B

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization. PMID:26787443

  16. Adjoint design sensitivity analysis of reduced atomic systems using generalized Langevin equation for lattice structures

    SciTech Connect

    Kim, Min-Geun; Jang, Hong-Lae; Cho, Seonho

    2013-05-01

    An efficient adjoint design sensitivity analysis method is developed for reduced atomic systems. A reduced atomic system and the adjoint system are constructed in a locally confined region, utilizing generalized Langevin equation (GLE) for periodic lattice structures. Due to the translational symmetry of lattice structures, the size of time history kernel function that accounts for the boundary effects of the reduced atomic systems could be reduced to a single atom’s degrees of freedom. For the problems of highly nonlinear design variables, the finite difference method is impractical for its inefficiency and inaccuracy. However, the adjoint method is very efficient regardless of the number of design variables since one additional time integration is required for the adjoint GLE. Through numerical examples, the derived adjoint sensitivity turns out to be accurate and efficient through the comparison with finite difference sensitivity.

  17. Atomic Structure and Charge Density Waves of Blue Bronze by Variable Temperature Scanning Tunneling Microscopy

    SciTech Connect

    Nikiforov,M.; Isakovic, A.; Bonnell, D.

    2007-01-01

    Blue bronze (K{sub 0.3}MoO{sub 3}) has been the focus of a number of scattering, transport, scanning tunneling microscopy (STM), and theoretical studies that have provided insight into the relation between atomic structure and charge-density wave (CDW) formation. However, the full extent of a relation of the CDWs to the atomic lattice and the microscopic origin of CDW pinning are still not completely resolved. In this study STM is used to distinguish the atomic structure and CDWs at the (20{bar 1}) surface. Within the STM's spatial resolution, the CDWs are incommensurate with the lattice at midrange temperatures and approach commensurability at low temperatures. Incommensurate CDWs are present on the surface and the degree of the incommensurability between blue bronze lattice and CDW lattice agree well with those determined from bulk scattering techniques.

  18. The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold

    PubMed Central

    He, Xiang; Cheng, Feng; Chen, Zhao-Xu

    2016-01-01

    For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å2/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538

  19. An Analysis of Taiwanese Eighth Graders' Science Achievement, Scientific Epistemological Beliefs and Cognitive Structure Outcomes After Learning Basic Atomic Theory.

    ERIC Educational Resources Information Center

    Tsai, Chin-Chung

    1998-01-01

    Explores the interrelationships between students' general science achievement, scientific epistemological beliefs, and cognitive structure outcomes derived from instruction of basic atomic theory. Contains 19 references. (DDR)

  20. Spin crossover iron(II) coordination polymer chains: syntheses, structures, and magnetic characterizations of [Fe(aqin)2(μ2-M(CN)4)] (M = Ni(II), Pt(II), aqin = quinolin-8-amine).

    PubMed

    Setifi, Fatima; Milin, Eric; Charles, Catherine; Thétiot, Franck; Triki, Smail; Gómez-García, Carlos J

    2014-01-06

    New Fe(II) coordination polymeric neutral chains of formula [Fe(aqin)2(μ2-M(CN)4)] (M = Ni(II) (1) and Pt(II) (2)) (aqin = Quinolin-8-amine) have been synthesized and characterized by infrared spectroscopy, X-ray diffraction, and magnetic measurements. The crystal structure determinations of 1-2 reveal in both cases a one-dimensional structure in which the planar [M(CN)4](2-) (M = Ni(II) (1) and Pt(II) (2)) anion acts as a μ2-bridging ligand, and the two aqin molecules as chelating coligands. Examination of the intermolecular contacts in the two compounds reveals that the main contacts are ascribed to hydrogen bonding interactions involving the amine groups of the aqin chelating ligands and the nitrogen atoms of the two non bridging CN groups of the [M(CN)4](2-) (M = Ni(II) (1) and Pt(II) (2)) anion. The average values of the six Fe-N distances observed respectively at room temperature (293 K) and low temperature (120 K), that is, 2.142(3) and 2.035(2) Å for 1, and 2.178(3) and 1.990(2) Å for 2, and the thermal variation of the cell parameters (performed on 2) are indicative of the presence of an abrupt HS-LS spin crossover (SCO) transition in both compounds. The thermal dependence of the product of the molar magnetic susceptibility times the temperature (χmT), in cooling and warming modes, confirms the SCO behavior at about 145 and 133 K in 1 and 2, respectively, and reveals the presence of a small thermal hysteresis of about 2 K for each compound.

  1. Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

    PubMed

    Torres, A E; Fomine, S

    2015-04-28

    The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

  2. Crystal structure of lead(II) acetylacetonate and the structure of the acetylacetone solvated lead(II) ion in solution studied by large-angle X-ray scattering.

    PubMed

    Lyczko, Krzysztof; Narbutt, Jerzy; Paluchowska, Beata; Maurin, Jan K; Persson, Ingmar

    2006-09-07

    The crystal structure of bis(acetylacetonato)lead(II) and the structure of the acetylacetone solvated lead(II) ion in solution have been determined by single-crystal X-ray diffraction and large-angle X-ray scattering (LAXS), respectively. The acetylacetone is deprotonated and acts as a bidentate anionic ligand (acac-) in the solid Pb(acac)2 compound. The lead(II) ion binds four oxygen atoms strongly in a nearly flat pyramidal configuration with Pb-O bond lengths in the range 2.32-2.37 A, and additionally three oxygens from neighboring complexes at 3.01-3.26 A. Acetylacetone acts as a solvent (Hacac) at dissolution of lead(II) trifluoromethanesulfonate forming a pentasolvate with a mean Pb-O bond distance of 2.724(5) A. The 6s2 lone electron pair on the lead(II) ion becomes stereochemically active in the crystalline acetylacetonate complex, while it is inactive in the solvate in solution. The solution was also analysed using IR and 1H NMR spectroscopy.

  3. Solid phase extraction for evaluation of occupational exposure to Pb (II) using XAD-4 sorbent prior to atomic absorption spectroscopy.

    PubMed

    Shahtaheri, Seyed Jamaleddin; Khadem, Monireh; Golbabaei, Farideh; Rahimi-Froushan, Abbas; Ganjali, Mohammad Reza; Norouzi, Parviz

    2007-01-01

    Lead is an important constituent widely used in different industrial processes. For evaluation of workers' exposure to trace toxic metal of Pb (II), solid-phase extraction (SPE) was optimized. SPE using mini columns filled with XAD-4 resin was developed with regard to sample pH, ligand concentration, loading flow rate, elution solvent, sample volume, elution volume, the amount of resins, and sample matrix interferences. Lead ions were retained on a solid sorbent and then eluted, followed by a simple determination of analytes with flame atomic absorption spectrometery. The obtained recoveries of metal ions were greater than 92%. This method was validated with 3 different pools of spiked urine samples; it showed a good reproducibility over 6 consecutive days as well as 6 within-day experiments. This optimized method can be considered successful in simplifying sample preparation for a trace residue analysis of lead in different matrices when evaluating occupational and environmental exposures is required.

  4. Atomic layer deposited Al2O3 passivation of type II InAs/GaSb superlattice photodetectors

    NASA Astrophysics Data System (ADS)

    Salihoglu, Omer; Muti, Abdullah; Kutluer, Kutlu; Tansel, Tunay; Turan, Rasit; Kocabas, Coskun; Aydinli, Atilla

    2012-04-01

    Taking advantage of the favorable Gibbs free energies, atomic layer deposited (ALD) aluminum oxide (Al2O3) was used as a novel approach for passivation of type II InAs/GaSb superlattice (SL) midwave infrared (MWIR) single pixel photodetectors in a self cleaning process (λcut-off ˜ 5.1 μm). Al2O3 passivated and unpassivated diodes were compared for their electrical and optical performances. For passivated diodes, the dark current density was improved by an order of magnitude at 77 K. The zero bias responsivity and detectivity was 1.33 A/W and 1.9 × 1013 Jones, respectively at 4 μm and 77 K. Quantum efficiency (QE) was determined as %41 for these detectors. This conformal passivation technique is promising for focal plane array (FPA) applications.

  5. Structural analysis and physico-chemical characterization of mononuclear manganese(II) and polynuclear copper(II) complexes with pyridine-based alcohol

    NASA Astrophysics Data System (ADS)

    Zienkiewicz-Machnik, Małgorzata; Masternak, Joanna; Kazimierczuk, Katarzyna; Barszcz, Barbara

    2016-12-01

    Two novel manganese(II) and copper(II) complexes, mononuclear [Mn(H2O)2(2-(CH2)2OHpy)2](NO3)2 (1) and polynuclear [Cu(SO4)(2-(CH2)2OHpy)2]n (2), based on 2-(hydroxyethyl)pyridine (2-(CH2)2OHpy) were synthesised and fully characterised using X-ray structure analysis as well as spectroscopic, magnetic and thermal methods. Both central metal ions Mn(1) and Cu(1) are coordinated by two N,O-donor 2-(CH2)2OHpy ligands and possess an almost perfect octahedral geometry (a chromophore of {MN2O4} type). The coordination sphere of Mn(II) is completed by two molecules of water, whereas, in polynuclear complex 2, Cu(II) atoms are linked along the a crystallographic direction by bridging sulfate ligands in a μ2-κ2 binding mode to form chains. The intermolecular interactions in 1 and 2 have been interpreted in view of the 3D Hirshfeld surface analysis and associated 2D fingerprint plots. Furthermore, the complexes have been tested with ABTSrad + assay in order to assess their antioxidant activity. In addition, the IC50 values calculated for 1 and 2 revealed that the complexes show a higher antioxidant activity than corresponding ligand.

  6. Kangaroo IGF-II is structurally and functionally similar to the human [Ser29]-IGF-II variant.

    PubMed

    Yandell, C A; Francis, G L; Wheldrake, J F; Upton, Z

    1999-06-01

    Kangaroo IGF-II has been purified from western grey kangaroo (Macropus fuliginosus) serum and characterised in a number of in vitro assays. In addition, the complete cDNA sequence of mature IGF-II has been obtained by reverse-transcription polymerase chain reaction. Comparison of the kangaroo IGF-II cDNA sequence with known IGF-II sequences from other species revealed that it is very similar to the human variant, [Ser29]-hIGF-II. Both the variant and kangaroo IGF-II contain an insert of nine nucleotides that encode the amino acids Leu-Pro-Gly at the junction of the B and C domains of the mature protein. The deduced kangaroo IGF-II protein sequence also contains three other amino acid changes that are not observed in human IGF-II. These amino acid differences share similarities with the changes described in many of the IGF-IIs reported for non-mammalian species. Characterisation of human IGF-II, kangaroo IGF-II, chicken IGF-II and [Ser29]-hIGF-II in a number of in vitro assays revealed that all four proteins are functionally very similar. No significant differences were observed in the ability of the IGF-IIs to bind to the bovine IGF-II/cation-independent mannose 6-phosphate receptor or to stimulate protein synthesis in rat L6 myoblasts. However, differences were observed in their abilities to bind to IGF-binding proteins (IGFBPs) present in human serum. Kangaroo, chicken and [Ser29]-hIGF-II had lower apparent affinities for human IGFBPs than did human IGF-II. Thus, it appears that the major circulating form of IGF-II in the kangaroo and a minor form of IGF-II found in human serum are structurally and functionally very similar. This suggests that the splice site that generates both the variant and major form of human IGF-II must have evolved after the divergence of marsupials from placental mammals.

  7. Synthesis, characterization, crystal structure and antimicrobial studies of a novel Cu(II) complex based on itaconic acid and nicotinamide

    NASA Astrophysics Data System (ADS)

    Tella, Adedibu C.; Owalude, Samson O.; Ajibade, Peter A.; Simon, Nzikahyel; Olatunji, Sunday J.; Abdelbaky, Mohammed S. M.; Garcia-Granda, Santiago

    2016-12-01

    A novel complex was synthesized from Cu(II), nicotinamide and itaconic acid and is formulated as [Cu(C5H4O4)2(C6H6N2O)2(H2O)2·2(H2O)] (1). The compound was characterized by elemental analysis, FTIR spectroscopy, UV-Vis and single crystal X-ray diffraction. The complex crystallizes in the triclinic P-1 space group, with a = 7.5111(2) Å, b = 9.8529(3) Å, c = 10.5118(4) Å, α = 116.244(3)°, β = 90.291(3)°, γ = 103.335(3)°, V = 673.81(4) Å3, Z = 1.The octahedral geometry around the copper(II) ion is of the form CuN2O4 consisting of two molecules of nicotinamide acting as monodentate ligand through the nitrogen atoms, two molecules itaconate ligand and two coordinated water molecules each coordinating through the oxygen atoms. The structure of 1 showed infinite chains build up linking the molecules together via strong Osbnd H⋯O and Nsbnd H⋯O intermolecular hydrogen bonds generating a two dimensional network sheet along c axis. The antimicrobial study of the synthesized complex 1 was investigated and showed higher antibacterial activity against all the organisms comparing with Copper(II) nicotinamide 2 and Copper(II) itaconate 3.

  8. A new trinuclear zinc(II) complex and a heptacoordinated mononuclear cadmium(II) complex with a pyrimidine derived Schiff base ligand: Syntheses, crystal structures, photoluminescence and DFT calculations

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Jana, Atanu; Konar, Saugata; Chatterjee, Sudipta; Mondal, Tapan Kumar; Barik, Anil Kumar; Kar, Susanta Kumar

    2013-09-01

    The new N6 donor hexadentate Schiff base 2,4-bis [2-(pyridine-2-ylmethylidene) hydrazinyl] pyrimidine (L), its trinuclear Zn(II) complex, [Zn3(L)2Cl6] (1) and mononuclear heptacoordinate Cd(II) complex [Cd(L)(H2O)2](ClO4)2 (2) have been synthesised and characterised by crystallographically and spectroscopically. Complex 1 is featured by the triangular arrangement of three zinc atoms where the neighbouring Zn atoms are linked via half portion (N3 chromophore) of the same ligand molecule. In 1, the ligand molecules behave as hexadentate ones (employing both pyrimidine nitrogen atoms as active donor centres) to create the octahedral environment around Zn(II). The central and terminal Zn(II) atom has N6 and N3Cl3 chromophores respectively. In 2 the same ligand (L) behaves as pentadentate one (ignoring one pyrimidine nitrogen in the coordination process) to produce a pentagonal bipyramidal geometry with two apical water molecules. The geometries of both complexes were optimised in the singlet state by DFT method. The TDDFT calculations have been done on the optimised geometries to understand the electronic structure and spectral transition in the complexes. Complex 1 exhibits intraligand 1(π → π*) fluorescence in aqueous methanol solvent at room temperature.

  9. Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

    SciTech Connect

    Saito, M.; Suzuki, S. . E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

    2005-11-15

    Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The two rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.

  10. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    PubMed Central

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  11. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    PubMed Central

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-01-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112

  12. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

    PubMed

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J; Le Thi Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Muñiz Olite, Jorge L; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M

    2016-05-27

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel's Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

  13. Do General Physics Textbooks Discuss Scientists' Ideas about Atomic Structure? A Case in Korea

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Kwon, Sangwoon; Kim, Nahyun; Lee, Gyoungho

    2013-01-01

    Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general…

  14. Current State of Web Sites in Science Education--Focus on Atomic Structure.

    ERIC Educational Resources Information Center

    Tuvi, Inbal; Nachmias, Rafi

    2001-01-01

    Explores to what extent the web's advanced graphical tools and computational power are implemented in science education. Focuses on the pedagogical and technological characteristics of web sites attempting to teach the subject of atomic structure. (Contains 33 references.) (Author/YDS)

  15. Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

    ERIC Educational Resources Information Center

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

    The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

  16. Atomic structure and phason modes of the Sc-Zn icosahedral quasicrystal.

    PubMed

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-07-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = -0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye-Waller factor, which explains the vanishing of 'high-Q perp' reflections.

  17. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Ji, Chen; Hernandez, Oscar Javier; Nevo Dinur, Nir; Bacca, Sonia; Barnea, Nir

    2016-03-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

  18. Atomic and Molecular Structure in Chemical Education: A Critical Analysis from Various Perspectives of Science Education.

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

    Provides a critical analysis of the role that atomic theory plays in the science curriculum from elementary through secondary school. Examines structural concepts from the perspective of the theory of meaningful learning, information processing theory, and the alternative conceptions movement. Contains 54 references. (DDR)

  19. Heptacopper(II) and dicopper(II)-adenine complexes: synthesis, structural characterization, and magnetic properties

    DOE PAGES

    Leite Ferreira, B. J. M.; Brandão, Paula; Dos Santos, A. M.; ...

    2015-07-13

    The syntheses, crystal structures, and magnetic properties of two new copper(II) complexes with molecular formulas [Cu7(μ2-OH2)6(μ3-O)6(adenine)6(NO3)26H2O (1) and [Cu2(μ2-H2O)2(adenine)2(H2O)4](NO3)42H2O (2) are reported. We composed the heptanuclear compound of a central octahedral CuO6 core sharing edges with six adjacent copper octahedra. In 2, the copper octahedra shares one equatorial edge. In both compounds, these basic copper cluster units are further linked by water bridges and bridging adenine ligands through N3 and N9 donors. All copper(II) centers exhibit Jahn-Teller distorted octahedral coordination characteristic of a d9 center. Our study of the magnetic properties of the heptacopper complex revealed a dominant ferromagnetic intra-clustermore » interaction, while the dicopper complex exhibits antiferromagnetic intra-dimer interactions with weakly ferromagnetic inter-dimer interaction.« less

  20. Heptacopper(II) and dicopper(II)-adenine complexes: synthesis, structural characterization, and magnetic properties

    SciTech Connect

    Leite Ferreira, B. J. M.; Brandão, Paula; Dos Santos, A. M.; Gai, Z.; Cruz, C.; Reis, M. S.; Santos, T. M.; Félix, V.

    2015-07-13

    The syntheses, crystal structures, and magnetic properties of two new copper(II) complexes with molecular formulas [Cu72-OH2)63-O)6(adenine)6(NO3)26H2O (1) and [Cu22-H2O)2(adenine)2(H2O)4](NO3)42H2O (2) are reported. We composed the heptanuclear compound of a central octahedral CuO6 core sharing edges with six adjacent copper octahedra. In 2, the copper octahedra shares one equatorial edge. In both compounds, these basic copper cluster units are further linked by water bridges and bridging adenine ligands through N3 and N9 donors. All copper(II) centers exhibit Jahn-Teller distorted octahedral coordination characteristic of a d9 center. Our study of the magnetic properties of the heptacopper complex revealed a dominant ferromagnetic intra-cluster interaction, while the dicopper complex exhibits antiferromagnetic intra-dimer interactions with weakly ferromagnetic inter-dimer interaction.

  1. Molecular structure, UV/vis spectra, and cyclic voltammograms of Mn(II), Co(II), and Zn(II) 5,10,15,20-tetraphenyl-21-oxaporphyrins.

    PubMed

    Stute, Silvio; Götzke, Linda; Meyer, Dirk; Merroun, Mohamed L; Rapta, Peter; Kataeva, Olga; Seichter, Wilhelm; Gloe, Kerstin; Dunsch, Lothar; Gloe, Karsten

    2013-02-04

    The 5,10,15,20-tetraphenyl-21-oxaporphyrin complexes of Mn(II), Co(II), and Zn(II) have been crystallized and studied by X-ray diffraction, NMR and UV/vis spectroscopy, and mass spectrometry as well as cyclic voltammetry. The X-ray structure of the earlier described Cu(II) complex is also reported. All complex structures possess a five-coordinate, approximately square-pyramidal geometry with a slight deviation of the heteroaromatic moieties from planarity. The packing structures are characterized by parallel strands of complex molecules interacting by weak hydrogen bonds. In the case of Zn(II) an octahedral complex has also been isolated using a side-chain hydroxy functionalized oxaporphyrin ligand; the structure was verified by NMR and EXAFS spectroscopy. Cyclic voltammetry studies reveal that the reduction of the complex bound Mn(II), Co(II), and Zn(II) ions is a ligand-centered process whereas the first oxidation step depends on the metal ion present.

  2. 'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study.

    PubMed

    Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel

    2011-07-22

    A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

  3. Charge-state-dependent energy loss of slow ions. II. Statistical atom model

    NASA Astrophysics Data System (ADS)

    Wilhelm, Richard A.; Möller, Wolfhard

    2016-05-01

    A model for charge-dependent energy loss of slow ions is developed based on the Thomas-Fermi statistical model of atoms. Using a modified electrostatic potential which takes the ionic charge into account, nuclear and electronic energy transfers are calculated, the latter by an extension of the Firsov model. To evaluate the importance of multiple collisions even in nanometer-thick target materials we use the charge-state-dependent potentials in a Monte Carlo simulation in the binary collision approximation and compare the results to experiment. The Monte Carlo results reproduce the incident charge-state dependence of measured data well [see R. A. Wilhelm et al., Phys. Rev. A 93, 052708 (2016), 10.1103/PhysRevA.93.052708], even though the experimentally observed charge exchange dependence is not included in the model.

  4. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    SciTech Connect

    Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  5. Crystal structures of bis(cyanido)bis(N,N Prime -diethylthiourea-{kappa}S) mercury(II) and bis(cyanido)bis(N,N Prime -dipropylthiourea-{kappa}S) mercury(II)

    SciTech Connect

    Ahmad, Saeed Sadaf, Haseeba; Altaf, Muhammad; Stoeckli-Evans, Helen; Seerat-ur-Rehman; Bashir, Sarfaraz Ahmed

    2013-09-15

    Two mercury(II) complexes containing cyanide and, N,N Prime -diethylthiourea (detu) and N,N Prime -dipropylthiourea (dprtu) ligands, [(detu){sub 2}Hg(CN){sub 2}] (1) and [(dprtu){sub 2}Hg(CN){sub 2}] (2), respectively, have been prepared and characterized by X-ray crystallography. In the both complexes Hg atom lies on a 2-fold rotation axis, and is coordinated to the sulfur atoms of two thiourea ligands and to two cyanide carbon atoms. Both have a distorted tetrahedral environment with bond angles about the Hg atoms in the range of 93.41(4) Degree-Sign -146.75(19) Degree-Sign . In the crystal structures symmetry related molecules are linked via N-H-N hydrogen bonds resulting in the formation of a two-dimensional network in 1, while in 2 a double stranded one-dimensional chain is formed.

  6. Crystal structure of (perchlorato-κO)(1,4,7,10-tetra­aza­cyclo­dodecane-κ4 N)copper(II) perchlorate

    PubMed Central

    Gray, Jessica L.; Gerlach, Deidra L.; Papish, Elizabeth T.

    2017-01-01

    The crystal structure of the title salt, [Cu(ClO4)(C8H20N4)]ClO4, is reported. The CuII ion exhibits a square-pyramidal geometry and is coordinated by the four N atoms of the neutral 1,4,7,10-tetra­aza­cyclo­dodecane (cyclen) ligand and an O atom from one perchlorate anion, with the second perchlorate ion hydrogen-bonded to one of the amine N atoms of the cyclen ligand. Additional N—H⋯O hydrogen bonds between the amine H atoms and the coordinating and non-coordinating perchlorate groups create a three-dimensional network structure. Crystals were grown from a concentrated methanol solution at ambient temperature, resulting in no co-crystallization of solvent. PMID:28083129

  7. Crystal structure of (perchlorato-κO)(1,4,7,10-tetra-aza-cyclo-dodecane-κ(4)N)copper(II) perchlorate.

    PubMed

    Gray, Jessica L; Gerlach, Deidra L; Papish, Elizabeth T

    2017-01-01

    The crystal structure of the title salt, [Cu(ClO4)(C8H20N4)]ClO4, is reported. The Cu(II) ion exhibits a square-pyramidal geometry and is coordinated by the four N atoms of the neutral 1,4,7,10-tetra-aza-cyclo-dodecane (cyclen) ligand and an O atom from one perchlorate anion, with the second perchlorate ion hydrogen-bonded to one of the amine N atoms of the cyclen ligand. Additional N-H⋯O hydrogen bonds between the amine H atoms and the coordinating and non-coordinating perchlorate groups create a three-dimensional network structure. Crystals were grown from a concentrated methanol solution at ambient temperature, resulting in no co-crystallization of solvent.

  8. Structural characterization of copper(II) binding to alpha-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease.

    PubMed

    Rasia, Rodolfo M; Bertoncini, Carlos W; Marsh, Derek; Hoyer, Wolfgang; Cherny, Dmitry; Zweckstetter, Markus; Griesinger, Christian; Jovin, Thomas M; Fernández, Claudio O

    2005-03-22

    The aggregation of alpha-synuclein (AS) is characteristic of Parkinson's disease and other neurodegenerative synucleinopathies. We demonstrate here that Cu(II) ions are effective in accelerating AS aggregation at physiologically relevant concentrations without altering the resultant fibrillar structures. By using numerous spectroscopic techniques (absorption, CD, EPR, and NMR), we have located the primary binding for Cu(II) to a specific site in the N terminus, involving His-50 as the anchoring residue and other nitrogen/oxygen donor atoms in a square planar or distorted tetragonal geometry. The carboxylate-rich C terminus, originally thought to drive copper binding, is able to coordinate a second Cu(II) equivalent, albeit with a 300-fold reduced affinity. The NMR analysis of AS-Cu(II) complexes reveals the existence of conformational restrictions in the native state of the protein. The metallobiology of Cu(II) in Parkinson's disease is discussed by a comparative analysis with other Cu(II)-binding proteins involved in neurodegenerative disorders.

  9. Chromatin structure in bands and interbands of polytene chromosomes imaged by atomic force microscopy.

    PubMed

    de Grauw, C J; Avogadro, A; van den Heuvel, D J; vd Werf, K O; Otto, C; Kraan, Y; van Hulst, N F; Greve, J

    1998-01-01

    Polytene chromosomes from Drosophila melanogaster, observed from squash preparations, and chromosomes from Chironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed chromosomes and correspond to structures which are also observed in chromosomes of diploid cells. Unfixed chromosomes can be imaged in buffer and show less fiber-like details because of the inherent soft nature of the chromatin material.

  10. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

    PubMed

    Pyne, Alice; Thompson, Ruth; Leung, Carl; Roy, Debdulal; Hoogenboom, Bart W

    2014-08-27

    Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

  11. Theoretical study of the Pb(II)-catechol system in dilute aqueous solution: Complex structure and metal coordination sphere determination

    NASA Astrophysics Data System (ADS)

    Lapouge, Christine; Cornard, Jean-Paul

    2010-04-01

    We investigated the unknown interaction of Pb(II) with catechol ligand in diluted aqueous solution by electronic spectroscopies combined with quantum chemical calculations. The aim of this work is the determination of the complete structure of the complex formed and particularly the metal coordination sphere. Three successive steps have been necessary to reach this goal: (i) the comparison of the experimental electronic absorption spectrum with theoretical spectra calculated from various hypothetical structures, (ii) complexation reaction pathways calculations in vacuum and with taking into account the solvent effects and finally (iii) the fluorescence emission wavelength calculations. All these investigations led to identify a monodentate complex with the monodeprotonated ligand, in which the Pb atom presents a coordination number of five. The formula of the complex is [Pb(Hcat)(HO)4]mono+.

  12. An experimental and theoretical approach of spectroscopic and structural properties of a new chelidamate copper (II) complex.

    PubMed

    Vural, Hatice; Uçar, İbrahim; Soylu, M Serkan

    2014-03-25

    The crystal structure of new chelidamate complex of copper (II) ion, [Cu(chel)H2O(pym)]·H2O [chel: chelidamate or 4-hydroxypyridine-2,6-dicarboxylate; pym: 2-Pyridylmethanol] has been determined by single crystal X-ray crystallographic method. The complex was characterized by IR and UV-Vis spectroscopic techniques. The magnetic environment of copper (II) ion has been defined by electron paramagnetic technique (EPR). The central copper (II) ion is six-coordinate with a distorted octahedral geometry, which exhibits Jahn-Teller distortions along one of the O-Cu-O axes with tetragonality of 0.81. Chelidamate behaved as a tridentate ligand was bonded to Cu(II) ion through carboxyl oxygens with nitrogen. The crystal structure is stabilized by O-H⋯O hydrogen bond and π-π interactions. Theoretical calculations have been carried out by using the DFT method. The modeling of copper (II) complex was made by geometric optimization. The geometry optimization and EPR study were carried out using the following unrestricted hybrid density functionals: LSDA, BPV86, B3LYP, B3PW91, MPW1PW91 and HCTH. Frontier molecular orbital energies, absorption wavelengths and excitation energy were computed by time dependent DFT (TD-DFT) method with polarizable continuum model. IR spectra were discussed and compared to other relevant complexes together with theoretical results. The natural charges on the atoms and second-order interaction energies were derived from natural bond orbital analysis (NBO).

  13. Long range ordered magnetic and atomic structures of the quasicrystal approximant in the Tb-Au-Si system

    NASA Astrophysics Data System (ADS)

    Gebresenbut, Girma; Svante Andersson, Mikael; Beran, Přemysl; Manuel, Pascal; Nordblad, Per; Sahlberg, Martin; Pay Gomez, Cesar

    2014-08-01

    The atomic and magnetic structure of the 1/1 Tb(14)Au(70)Si(16) quasicrystal approximant has been solved by combining x-ray and neutron diffraction data. The atomic structure is classified as a Tsai-type 1/1 approximant with certain structural deviations from the prototype structures; there are additional atomic positions in the so-called cubic interstices as well as in the cluster centers. The magnetic property and neutron diffraction measurements indicate the magnetic structure to be ferrimagnetic-like below 9 K in contrast to the related Gd(14)Au(70)Si(16) structure that is reported to be purely ferromagnetic.

  14. Nanoscale structure and atomic disorder in the iron-based chalcogenides

    PubMed Central

    Saini, Naurang Lal

    2013-01-01

    The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S)1−xTex (11-type) and K0.8Fe1.6Se2 (122-type) systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S)1−xTex system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe–Se/S and Fe–Te distances in the ternary Fe(Se,S)1−xTex are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth) oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism. PMID:27877557

  15. Nanoscale structure and atomic disorder in the iron-based chalcogenides.

    PubMed

    Saini, Naurang Lal

    2013-02-01

    The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S)1-x Te x (11-type) and K0.8Fe1.6Se2 (122-type) systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S)1-x Te x system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe-Se/S and Fe-Te distances in the ternary Fe(Se,S)1-x Te x are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth) oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.

  16. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies

    NASA Astrophysics Data System (ADS)

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-01

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE

  17. A new nano-scale manganese (II) coordination polymer constructed from semicarbazone Schiff base and dicyanamide ligands: Synthesis, crystal structure and DFT calculations

    NASA Astrophysics Data System (ADS)

    Farhadi, Saeed; Mahmoudi, Farzaneh; Simpson, Jim

    2016-03-01

    A new nano-structured Mn(II) coordination polymer [Mn(HL)(dca)(Cl)]n(1), [HL= Pyridine-2-carbaldehyde semicarbazone, dca= dicyanamide] has been synthesized by a sonochemical method and has been characterized by scanning electron microscopy, X-ray powder diffraction elemental analysis and IR spectroscopy. Single crystals of compound 1 was synthesized by slow evaporation method and was structurally characterised by single crystal X-ray diffraction. The single crystal structure shows one dimensional zig-zag chains with end-to-end dicyanamide-bridged ligand. A distorted octahedral geometry around the Mn2+centers was achieved by NNO atoms from HL, two nitrogen atoms of dicyanamide and one chlorine atom. Also for more details, the structure of 1, has been optimized by density functional theory (DFT calculations).

  18. Atomic structure and handedness of the building block of a biological assembly.

    PubMed

    Loquet, Antoine; Habenstein, Birgit; Chevelkov, Veniamin; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Lange, Adam

    2013-12-26

    Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.

  19. Dual structure of saturated absorption resonance at an open atomic transition

    NASA Astrophysics Data System (ADS)

    Vasil'ev, V. V.; Velichanskii, V. L.; Zibrov, S. A.; Sivak, A. V.; Brazhnikov, D. V.; Taichenachev, A. V.; Yudin, V. I.

    2011-05-01

    Experiments on open transitions of the D 1 line of alkali metals (Cs and Rb isotopes) reveal the dual structure of saturated absorption resonance in the signal of a high-intensity optical wave in the presence of a low-intensity counterpropagating wave. Theoretical analysis shows that the observed shape of the resonance is associated with the openness of the atomic transition as well as with the Doppler effect for atoms in a gas. The results are of general physical significance for nonlinear spectroscopy and can also find application in metrology (frequency and time standards on open transitions).

  20. Dual structure of saturated absorption resonance at an open atomic transition

    SciTech Connect

    Vasil'ev, V. V. Velichanskii, V. L. Zibrov, S. A.; Sivak, A. V.; Brazhnikov, D. V. Taichenachev, A. V. Yudin, V. I.

    2011-05-15

    Experiments on open transitions of the D{sub 1} line of alkali metals (Cs and Rb isotopes) reveal the dual structure of saturated absorption resonance in the signal of a high-intensity optical wave in the presence of a low-intensity counterpropagating wave. Theoretical analysis shows that the observed shape of the resonance is associated with the openness of the atomic transition as well as with the Doppler effect for atoms in a gas. The results are of general physical significance for nonlinear spectroscopy and can also find application in metrology (frequency and time standards on open transitions).

  1. Structure and bonding at the atomic scale by scanning transmission electron microscopy.

    PubMed

    Muller, David A

    2009-04-01

    A new generation of electron microscopes is able to explore the microscopic properties of materials and devices as diverse as transistors, turbine blades and interfacial superconductors. All of these systems are made up of dissimilar materials that, where they join at the atomic scale, display very different behaviour from what might be expected of the bulk materials. Advances in electron optics have enabled the imaging and spectroscopy of these buried interface states and other nanostructures with atomic resolution. Here I review the capabilities, prospects and ultimate limits for the measurement of physical and electronic properties of nanoscale structures with these new microscopes.

  2. Studying the Atomic Nucleus - A New Era in Nuclear Structure Studies

    SciTech Connect

    Casten, R. F.

    2011-05-06

    The study of atomic nuclei is part of the fascinating quest to understand the fundamental nature and origins of matter. This field, nuclear structure, is undergoing a revolutionary transformation that is breaking cherished paradigms, opening new vistas of nuclear matter for study, and which has the promise of leading to a new comprehensive understanding. The advent of new facilities for the production and study of exotic nuclei provides access to an entirely new territory of nuclei, and advances in extreme computing are enabling similar advances in the theory of atomic nuclei.

  3. Efficient first-principles simulation of noncontact atomic force microscopy for structural analysis.

    PubMed

    Chan, T-L; Wang, C Z; Ho, K M; Chelikowsky, James R

    2009-05-01

    We propose an efficient scheme to simulate noncontact atomic force microscopy images by using first-principles self-consistent potential from the sample as input without explicit modeling of the atomic force microscopy tip. Our method is applied to various types of semiconductor surfaces including Si(111)-(7x7), TiO2(110)-(1x1), Ag/Si(111)-(sqrt[3]xsqrt[3])R30 degrees, and Ge/Si(105)-(1x2) surfaces. We obtain good agreement with experimental results and previous theoretical studies, and our method can aid in identifying different structural models for surface reconstruction.

  4. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOEpatents

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  5. Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubled a axis

    SciTech Connect

    Robbins, Arthur H.; Domsic, John F.; Agbandje-McKenna, Mavis; McKenna, Robert

    2010-05-01

    The crystal structure of human carbonic anhydrase II with a doubled a axis from that of the usually observed monoclinic cell has been determined and refined to 1.4 Å resolution. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ along a, but one of the molecules has two alternate orientations related by a rotation of approximately 2°. The crystal structure of human carbonic anhydrase II with a doubled a axis from that of the usually observed monoclinic unit cell has been determined and refined to 1.4 Å resolution. The diffraction data with h = 2n + 1 were systematically weaker than those with h = 2n. Consequently, the scaling of the data, structure solution and refinement were challenging. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ along a, but one of the molecules has two alternate positions related by a rotation of approximately 2°. This rotation axis is located near the edge of the central β-sheet, causing a maximum distance disparity of 1.7 Å between equivalent atoms on the diametrically opposite side of the molecule. The crystal-packing contacts are similar to two sequential combined unit cells along a of the previously determined monoclinic unit cell. Abnormally high final R{sub cryst} and R{sub free} values (20.2% and 23.7%, respectively) are not unusual for structures containing pseudo-translational symmetry and probably result from poor signal to noise in the weak h-odd data.

  6. Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

    NASA Astrophysics Data System (ADS)

    Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

    2017-02-01

    Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

  7. Theoretical investigations of the structures and electronic spectra of Zn(II) and Ni(II) complexes with cyclohexylamine-N-dithiocarbamate

    NASA Astrophysics Data System (ADS)

    Yu, Xiaohan; Wang, Na; He, Hongqing; Wang, Li

    2014-03-01

    The ground-state structures of two ligands cyclohexylamine-N-dithiocarbamate (L) and PPh3 and four complexes [Zn(L)2] (A), [Ni(L)2] (B), [Zn(L)2PPh3] (C), and [Ni(L)2PPh3] (D) are optimized by M06, B3LYP, and B3PW91 methods with the same mixed basis set. As compared with the experimental data of other complexes containing the Ni-P bond, the result obtained by M06/6-31+G(d)-LANL2DZ method is finally regarded as accurate and reliable for this project. Based on the optimized geometries, the compositions of molecular orbitals are analyzed and the absorption spectra are simulated. When one more ligand PPh3 is coordinated, the lowest-lying transition energy presents red-shift; while it shows blue-shift when the metal coordination center change from Ni to Zn with the same ligands. The detailed transition characters related with the absorption spectrum are assigned. In all the key transitions, it is hard to find the contribution from Zn atom. On the contrary, the d orbital of Ni atom contributes a lot for the HOMO and LUMO of complexes B and D. Consequently, the transition characters of Zn(II) and Ni(II) complexes are different.

  8. Prediction of atomic structure of Pt-based bimetallic nanoalloys by using genetic algorithm

    NASA Astrophysics Data System (ADS)

    Oh, Jung Soo; Nam, Ho-Seok; Choi, Jung-Hae; Lee, Seung-Cheol

    2013-05-01

    The atom-arrangements in Pt-based bimetallic nanoalloys were predicted by the combined use of genetic algorithm (GA) and molecular dynamics (MD) simulations. The nanoparticles of these nanoalloys were assumed to be a 3.5 nm-diameter truncated octahedron with Pt and noble metals of fixed composition ratio of 1:1. For the GA, a Python code, which concurrently linked with the MD method that uses the embedded atom method inter-atomic potentials, was developed for the prediction of the atom arrangements in these bimetallic nanoalloys. Successfully, the GA calculation predicted the core-shell structures for both Pt-Ag and Pt-Au nanoalloy, but an onion-like multilayered core-shell structure for Pt-Cu nanoalloy. The structural characteristics in the bimetallic nanoalloy were mainly due to the differences in the surface energy and cohesive energy between Pt and the other alloying metal elements and their miscibility gap and so on. Briefly, the prediction performance was analyzed to show the superior searching ability of GA.

  9. Influence of the plasma environment on atomic structure using an ion-sphere model

    NASA Astrophysics Data System (ADS)

    Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

    2015-09-01

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

  10. Influence of the plasma environment on atomic structure using an ion-sphere model

    DOE PAGES

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    2015-09-03

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

  11. Influence of the plasma environment on atomic structure using an ion-sphere model

    SciTech Connect

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    2015-09-03

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.

  12. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment

    PubMed Central

    Chakraborty, Sandeep; Venkatramani, Ravindra; Rao, Basuthkar J.; Asgeirsson, Bjarni; Dandekar, Abhaya M.

    2014-01-01

    The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP), which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD) of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134. PMID:25506420

  13. Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

    PubMed

    Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

    2016-05-05

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

  14. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

    PubMed

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-19

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.

  15. Electrical conductance and structure of copper atomic junctions in the presence of water molecules.

    PubMed

    Li, Yu; Demir, Firuz; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Saffarzadeh, Alireza; Kirczenow, George; Kiguchi, Manabu

    2015-12-28

    We have investigated Cu atomic contacts in the presence of H2O both experimentally and theoretically. The conductance measurements showed the formation of H2O/Cu junctions with a fixed conductance value of around 0.1 G0 (G0 = 2e(2)/h). These structures were found to be stable and could be stretched over 0.5 nm, indicating the formation of an atomic or molecular chain. In agreement with the experimental findings, theoretical calculations revealed that the conductance of H2O/Cu junctions decreases in stages as the junction is stretched, with the formation of a H2O/Cu atomic chain with a conductance of ca. 0.1 G0 prior to junction rupture. Conversely, in the absence of H2O, the conductance of the Cu junction remains close to 1 G0 prior to the junction rupture and abrupt conductance drop.

  16. Structural, magnetic and electronic properties of single Iron atom at graphene edges

    NASA Astrophysics Data System (ADS)

    Zhang, Junfeng; Hao, Yanjun; Xu, Xiaohong

    2017-02-01

    A systemic theoretical study of one iron atom on graphene ribbon edges (Fe/GR) has been carried out by using density functional theory. Thermodynamic stabilities, electronic and magnetic properties of Fe/GR with different edge types and adsorption locations were investigated. According to the Clar's aromatic sextet rule, the formation energies and density of states of Fe atom are found to rely tightly on the ribbon's periodic length. Moreover, Fe atoms on reconstructed zz edges are also stable with low formation energies and semiconducting properties. Finally, the magnetic properties are found sensitive with the structural details, especially the local bond environment. The present theoretical results constitute a useful picture for the deep comprehending on the interface details of the lateral Fe/graphene heterostructures.

  17. Approximants of icosahedral quasicrystals: Atomic structure, inherent defects, and superstructural ordering

    SciTech Connect

    Dmitrienko, V. E. Chizhikov, V. A.

    2006-07-15

    The structural features of approximants of icosahedral and decagonal quasicrystals and new unusual approximants (rhombohedral AlPd and cubic Al{sub 68}Pd{sub 20}Ru{sub 12}) are considered. It is shown that most approximants can be described in terms of universal local ordering of atoms, in which the nearest neighbors of each atom occupy the vertices of an almost ideal dodecahedron: the so-called dodecahedral local ordering. A set of general atomic motifs in the approximants of different orders is found for quasicrystals of different types. It is shown that the dodecahedral local ordering can be easily described by the project method, in which the basis vectors directed along icosahedral threefold axes are used. Different types of defects inherent in dodecahedral local ordering are analyzed.

  18. TUNABLE Band Structures of 2d Multi-Atom Archimedean-Like Phononic Crystals

    NASA Astrophysics Data System (ADS)

    Xu, Y. L.; Chen, C. Q.; Tian, X. G.

    2012-06-01

    Two dimensional multi-atom Archimedean-like phononic crystals (MAPCs) can be obtained by adding "atoms" at suitable positions in primitive cells of traditional simple lattices. Band structures of solid-solid and solid-air MAPCs are computed by the finite element method in conjunction with the Bloch theory. For the solid-solid system, our results show that the MAPCs can be suitably designed to split and shift band gaps of the corresponding traditional simple phononic crystal (i.e., with only one scatterer inside a primitive cell). For the solid-air system, the MAPCs have more and wider band gaps than the corresponding traditional simple phononic crystal. Numerical calculations for both solid-solid and solid-air MAPCs show that the band gap of traditional simple phononic crystal can be tuned by appropriately adding "atoms" into its primitive cell.

  19. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  20. Changes in the Atomic Structure through Glass Transition Observed by X-Ray Scattering

    SciTech Connect

    Egami, Takeshi

    2012-01-01

    The glass transition involves a minor change in the internal energy, and yet the physical and mechanical properties of a glass change dramatically. In order to determine the evolution of the atomic structure through the glass transition, we employed in-situ synchrotron X-ray scattering measurements as a function of temperature on a model material: Zr-Cu-Al metallic glass. We found that the thermal expansion at the atomic level is smaller than the macroscopic thermal expansion, and significantly increases above the glass transition temperature. The observed changes in the pair-distribution function (PDF) are explained in terms of the fluctuations in the local atomic volume and their change through the glass transition.

  1. Longitudinal structure in atomic oxygen concentrations observed with WINDII on UARS. [Wind Imaging Interferometer

    NASA Technical Reports Server (NTRS)

    Shepherd, G. G.; Thuillier, G.; Solheim, B. H.; Chandra, S.; Cogger, L. L.; Duboin, M. L.; Evans, W. F. J.; Gattinger, R. L.; Gault, W. A.; Herse, M.

    1993-01-01

    WINDII, the Wind Imaging Interferometer on the Upper Atmosphere Research Satellite, began atmospheric observations on September 28, 1991 and since then has been collecting data on winds, temperatures and emissions rates from atomic, molecular and ionized oxygen species, as well as hydroxyl. The validation of winds and temperatures is not yet complete, and scientific interpretation has barely begun, but the dominant characteristic of these data so far is the remarkable structure in the emission rate from the excited species produced by the recombination of atomic oxygen. The latitudinal and temporal variability has been noted before by many others. In this preliminary report on WINDII results we draw attention to the dramatic longitudinal variations of planetary wave character in atomic oxygen concentration, as reflected in the OI 557.7 nm emission, and to similar variations seen in the Meine1 hydroxyl band emission.

  2. Structure-property-relationship of p-toluidinium tetrachloromercurate(II)

    SciTech Connect

    Dinesh; Kumar, Mukesh; Dalela, S.

    2014-04-24

    The single crystals of p-toluidinium tetrachloromercurate(II) hybrid materials have been grown with perfect crystal of size 0.35 × 0.30 × 0.27 mm. The hybrid material is exposed to X-rays for 3D intensity data which is used to refine the crystal structure upto reliability-factor of 0.034. The phenyl ring has planar conformation with skeletal torsion angle of 0.003(6)° and the aromatic ring (C1-C6) forms an angle of 78.7(1)° to the plane of inorganic layer. The N-H...Cl hydrogen bonded tetramer pattern is observed in p-toluidinium tetrachloromercurate(II) and the two tetramer layers are separated by a distance of 3.925(6)Å and the minimum distance between two mercury atoms is 4.112(1)Å which is quite larger for any metallophilic interaction. The inorganic layers form zig-zag ribbons which are separated by a distance of 12.987(5)Å.

  3. Theoretical investigation of atomic and electronic structures of Ga2O3(ZnO)6

    NASA Astrophysics Data System (ADS)

    da Silva, Juarez L. F.; Walsh, Aron; Wei, Su-Huai

    2009-12-01

    Transparent conducting oxides (TCO) are widely used in technological applications ranging from photovoltaics to thin-film transparent field-effect transistors. In this work we report a first-principles investigation, based on density-functional theory, of the atomic and electronic properties of Ga2O3(ZnO)6 (GZO6) , which is a promising candidate to be used as host oxide for wide band gap TCO applications. We identify a low-energy configuration for the coherent distribution of the Ga and Zn atoms in the cation positions within the experimentally reported orthorhombic GZO6 structure. Four Ga atoms are located in four-fold sites, while the remaining 12 Ga atoms in the unit cell form four shared Ga agglomerates (a motif of four atoms). The Zn atoms are distributed in the remaining cation sites with effective coordination numbers from 3.90 to 4.50. Furthermore, we identify the natural formation of twin-boundaries in GZO6 , which can explain the zigzag modulations observed experimentally by high-resolution transmission electron microscopy in GZOn (n=9) . Due to the intrinsic twin-boundary formation, polarity inversion in the ZnO tetrahedrons is present which is facilitated by the formation of the Ga agglomerates. Our analysis shows that the formation of fourfold Ga sites and Ga agglomerates are stabilized by the electronic octet rule, while the distribution of Ga atoms and the formation of the twin-boundary help alleviate excess strain. Finally we identify that the electronic properties of GZO6 are essentially determined by the electronic properties of ZnO, i.e., there are slight changes in the band gap and optical absorption properties.

  4. Atomic structure and magnetic properties of Cu 80Co 20 nanocrystalline compound produced by mechanical alloying

    NASA Astrophysics Data System (ADS)

    Ivchenko, V. A.; Uimin, M. A.; Yermakov, A. Ye; Korobeinikov, A. Yu

    1999-10-01

    Direct observation of the atomic structure of the mechanically alloyed Cu 80Co 20 compounds has been made using the field ion microscope (FIM). Phase composition, defect structure and morphology of material on the atomic scale have been determined. It has been established that the studied material is chemically inhomogeneous, presenting a mixture of two main phases: heterogeneous solid solution of cobalt in copper, and pure cobalt. Phase volume ratios, particle and cluster sizes have been estimated. An evaluation of Co content in CuCo solid solution has been made. The width of interfaces in this mechanically alloyed material was revealed to be at least twice the width of phase boundaries in metals and alloys. Superparamagnetism of the compound studied at elevated temperatures and saturation magnetization deficit at low temperatures are discussed on the basis of the above-mentioned structural data.

  5. Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

    NASA Astrophysics Data System (ADS)

    Gründer, Yvonne; Markovic, Nenad M.; Thompson, Paul; Lucas, Christopher A.

    2015-01-01

    The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface, and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.

  6. Atomic-scale observation of dynamical fluctuation and three-dimensional structure of gold clusters

    SciTech Connect

    Li, Junjie; Yin, Deqiang; Chen, Chunlin; Lin, Liyang; Wang, Zhongchang; Li, Qiang; Sun, Rong; Huang, Sumei

    2015-02-28

    Unravelling three-dimensional structures and dynamical fluctuation of metal nanoclusters is critical to understanding reaction process and the origin of catalytic activity in many heterogeneous catalytic systems. We obtain three-dimensional structures of ultra-small Au clusters by combining aberration-corrected scanning transmission electron microscopy, density functional theory calculations, and imaging simulations. The configurations of unique Au clusters are revealed at the atomic scale and the corresponding electronic states are given. The sequential observations reveal a transition of ultra-small Au clusters with about 25 atoms from a near-square to an elongated structure. We also find a transition from two dimensions to three dimensions for the Au clusters. The obtained three-dimensional geometry and associated electronic states help to clarify atomistic mechanism of shape- and number-dependent catalytic activities of Au clusters.

  7. Atomic Structure of the Anatase TiO2(001) Surface

    SciTech Connect

    Xia, Yaobiao; Zhu, Ke; Kaspar, Tiffany C.; Du, Yingge; Birmingham, Blake; Park, Kenneth T.; Zhang, Zhenrong

    2013-08-16

    Understanding the structure of well-defined anatase TiO2 surfaces is critical for deciphering site-specific thermal and photo- reaction mechanisms on anatase TiO2. Using UHV scanning tunneling microscopy (STM), we have studied the atomic structure of anatase TiO2(001) epitaxial thin films grown by oxygen plasma assisted molecular beam epitaxy. Bright rows of the (1×4) reconstructed surface are resolved as three types of features with different sizes. High-resolution STM images taken from the same area at different bias voltages show that these individual features are originated from combinations of two basic atomic building blocks. We propose a modified added molecule model for the anatase TiO2 (001) surface structure.

  8. Hierarchical surface atomic structure of a manganese-based spinel cathode for lithium-ion batteries.

    PubMed

    Lee, Sanghan; Yoon, Gabin; Jeong, Minseul; Lee, Min-Joon; Kang, Kisuk; Cho, Jaephil

    2015-01-19

    The increasing use of lithium-ion batteries (LIBs) in high-power applications requires improvement of their high-temperature electrochemical performance, including their cyclability and rate capability. Spinel lithium manganese oxide (LiMn2O4) is a promising cathode material because of its high stability and abundance. However, it exhibits poor cycling performance at high temperatures owing to Mn dissolution. Herein we show that when stoichiometric lithium manganese oxide is coated with highly doped spinels, the resulting epitaxial coating has a hierarchical atomic structure consisting of cubic-spinel, tetragonal-spinel, and layered structures, and no interfacial phase is formed. In a practical application of the coating to doped spinel, the material retained 90% of its capacity after 800 cycles at 60 °C. Thus, the formation of an epitaxial coating with a hierarchical atomic structure could enhance the electrochemical performance of LIB cathode materials while preventing large losses in capacity.

  9. Cation-poor complex metallic alloys in Ba(Eu)–Au–Al(Ga) systems: Identifying the keys that control structural arrangements and atom distributions at the atomic level

    DOE PAGES

    Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; ...

    2015-10-19

    Four complex intermetallic compounds BaAu6±xGa6±y (x = 1, y = 0.9) (I), BaAu6±xAl6±y (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104–112, Fm3C), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successivemore » decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution (“coloring scheme”). Chemical bonding analyses for two different “EuAu6Tr6” models reveal maximization of the number of heteroatomic Au–Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the “EuAu6Tr6” models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. As a result, the effective moments of 8.3 μB/f.u., determined from Curie–Weiss fits, point to divalent oxidation states for europium in both III and IV.« less

  10. Size and shape of grain boundary network components and their atomic structures in polycrystalline nanoscale materials

    SciTech Connect

    Xu, Tao; Li, Mo

    2015-10-28

    Microstructure in polycrystalline materials is composed of grain boundary plane, triple junction line, and vertex point. They are the integral parts of the grain boundary network structure and the foundation for the structure-property relations. In polycrystalline, especially nanocrystalline, materials, it becomes increasingly difficult to probe the atomistic structure of the microstructure components directly in experiment due to the size limitation. Here, we present a numerical approach using pair correlation function from atomistic simulation to obtain the detailed information for atomic order and disorder in the grain boundary network in nanocrystalline materials. We show that the atomic structures in the different microstructural components are related closely to their geometric size and shape, leading to unique signatures for atomic structure in microstructural characterization at nanoscales. The dependence varies systematically with the characteristic dimension of the microstructural component: liquid-like disorder is found in vertex points, but a certain order persists in triple junctions and grain boundaries along the extended dimensions of these microstructure components.

  11. Structure prediction for CASP8 with all-atom refinement using Rosetta.

    PubMed

    Raman, Srivatsan; Vernon, Robert; Thompson, James; Tyka, Michael; Sadreyev, Ruslan; Pei, Jimin; Kim, David; Kellogg, Elizabeth; DiMaio, Frank; Lange, Oliver; Kinch, Lisa; Sheffler, Will; Kim, Bong-Hyun; Das, Rhiju; Grishin, Nick V; Baker, David

    2009-01-01

    We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.

  12. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    SciTech Connect

    Lin, Lin; Chen, Mohan; Yang, Chao; He, Lixin

    2012-02-10

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEpSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes on a single processor. We also show that the use of PEpSI does not lead to loss of accuracy required in a practical DFT calculation.

  13. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.

    PubMed Central

    García De La Torre, J; Huertas, M L; Carrasco, B

    2000-01-01

    The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program. PMID:10653785

  14. Enhanced water removal in a fuel cell stack by droplet atomization using structural and acoustic excitation

    NASA Astrophysics Data System (ADS)

    Palan, Vikrant; Shepard, W. Steve

    This work examines new methods for enhancing product water removal in fuel cell stacks. Vibration and acoustic based methods are proposed to atomize condensed water droplets in the channels of a bipolar plate or on a membrane electrode assembly (MEA). The vibration levels required to atomize water droplets of different sizes are first examined using two different approaches: (1) exciting the droplet at the same energy level required to form that droplet; and (2) by using a method called 'vibration induced droplet atomization', or VIDA. It is shown analytically that a 2 mm radius droplet resting on a bipolar-like plate can be atomized by inducing acceleration levels as low as 250 g at a certain frequency. By modeling the direct structural excitation of a simplified bipolar plate using a realistic source, the response levels that can be achieved are then compared with those required levels. Furthermore, a two-cell fuel cell finite element model and a boundary element model of the MEA were developed to demonstrate that the acceleration levels required for droplet atomization may be achieved in both the bipolar plate as well as the MEA through proper choice of excitation frequency and source strength.

  15. Vapour phase growth and grain boundary structure of molybdenum disulphide atomic layers.

    PubMed

    Najmaei, Sina; Liu, Zheng; Zhou, Wu; Zou, Xiaolong; Shi, Gang; Lei, Sidong; Yakobson, Boris I; Idrobo, Juan-Carlos; Ajayan, Pulickel M; Lou, Jun

    2013-08-01

    Single-layered molybdenum disulphide with a direct bandgap is a promising two-dimensional material that goes beyond graphene for the next generation of nanoelectronics. Here, we report the controlled vapour phase synthesis of molybdenum disulphide atomic layers and elucidate a fundamental mechanism for the nucleation, growth, and grain boundary formation in its crystalline monolayers. Furthermore, a nucleation-controlled strategy is established to systematically promote the formation of large-area, single- and few-layered films. Using high-resolution electron microscopy imaging, the atomic structure and morphology of the grains and their boundaries in the polycrystalline molybdenum disulphide atomic layers are examined, and the primary mechanisms for grain boundary formation are evaluated. Grain boundaries consisting of 5- and 7- member rings are directly observed with atomic resolution, and their energy landscape is investigated via first-principles calculations. The uniformity in thickness, large grain sizes, and excellent electrical performance signify the high quality and scalable synthesis of the molybdenum disulphide atomic layers.

  16. The Factor Structure of the CIBS-II-Readiness Assessment

    ERIC Educational Resources Information Center

    Gotch, Chad M.; French, Brian F.

    2011-01-01

    The Brigance Comprehensive Inventory of Basic Skills-II (CIBS-II)-Readiness form is a diagnostic battery intended for children aged 5 and 6 years. The CIBS-II-Readiness is a new version of the CIBS-Revised-Readiness and includes updated normative information on a larger representative sample in comparison to the CIBS-Revised-Readiness. Empirical…

  17. Interaction of light with an atom near the surface of a superlattice. II. Quasiperiodic case

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Shen; Gong, Chang-De

    1989-04-01

    Spontaneous-emission properties and resonance fluorescence for a two-level adatom near the surface of a semi-infinite superlattice with quasiperiodic structure are studied by use of surface-dressed optical Bloch equations and Maxwell's equations. Effects of dielectric properties and the geometric structure of this superlattice on spontaneous-decay rate and frequency shift, resonance-fluorescence spectrum, time evolution of adatomic inversion, and fluctuations of the dipole moment for this adatom are discussed and some novel phenomena are discovered.

  18. Aerosol cluster impact and break-up : II. Atomic and Cluster Scale Models.

    SciTech Connect

    Lechman, Jeremy B.; Takato, Yoichi

    2010-09-01

    Understanding the interaction of aerosol particle clusters/flocs with surfaces is an area of interest for a number of processes in chemical, pharmaceutical, and powder manufacturing as well as in steam-tube rupture in nuclear power plants. Developing predictive capabilities for these applications involves coupled phenomena on multiple length and timescales from the process macroscopic scale ({approx}1m) to the multi-cluster interaction scale (1mm-0.1m) to the single cluster scale ({approx}1000 - 10000 particles) to the particle scale (10nm-10{micro}m) interactions, and on down to the sub-particle, atomic scale interactions. The focus of this report is on the single cluster scale; although work directed toward developing better models of particle-particle interactions by considering sub-particle scale interactions and phenomena is also described. In particular, results of mesoscale (i.e., particle to single cluster scale) discrete element method (DEM) simulations for aerosol cluster impact with rigid walls are presented. The particle-particle interaction model is based on JKR adhesion theory and is implemented as an enhancement to the granular package in the LAMMPS code. The theory behind the model is outlined and preliminary results are shown. Additionally, as mentioned, results from atomistic classical molecular dynamics simulations are also described as a means of developing higher fidelity models of particle-particle interactions. Ultimately, the results from these and other studies at various scales must be collated to provide systems level models with accurate 'sub-grid' information for design, analysis and control of the underlying systems processes.

  19. Structure, spectroscopy, and theory calculations of mononuclear mixed-ligand copper(II) complex with malonate and 2-propylimidazole, [Cu(mal)(PIM) 2(H 2O)

    NASA Astrophysics Data System (ADS)

    Peng, Xian; Cui, Guang-Hua; Li, De-Jie; Wu, Shang-Zhuo; Yu, Ya-Mei

    2010-05-01

    A mononuclear copper(II) complex, [Cu(mal)(PIM) 2(H 2O)] (1) [mal = malonate dianion, PIM = 2-propylimidazole] has been synthesized and characterized by elemental analysis, IR, UV-Vis, TG-DTA, and single crystal X-ray diffraction. The center Cu(II) atom in the complex has a distorted square-pyramidal geometry, being coordinated by two nitrogen atoms and three oxygen atoms. Density Functional Theory (DFT) with the B3LYP method and time-dependent DFT calculations were performed to provide insight into the structural, electronic, and electronic spectroscopic properties of the complex 1, and the UV-Vis spectrum of the title compound has been discussed on this basis. All the absorption bands in UV-Vis spectrum are mostly π/( P, σ) → d x2-y2 ligand-to-metal charge transfer (LMCT) transition, together with partial d → d ligand field (LF) transition.

  20. Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites

    PubMed Central

    Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina

    2014-01-01

    Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671