Sample records for atomic structure chemical

  1. 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

  2. Atomic Structure

    NSDL National Science Digital Library

    The Concord Consortium

    2011-12-11

    In this activity students explore the structure and properties of atoms. They construct models of atoms with properties of particular mass and charge; create models of atoms with different stabilities by adding or subtracting neutrons, protons, and electrons to a model atom; and determine that the same element may have varying number of neutrons and these form isotopes.Students will be able to:

  3. 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.

  4. Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical Imaging

    E-print Network

    transformations in -Al2O3 (->- > transformation) (Determination of the structure of -Al2O3 since this phase has and morphological evolution of catalytic materials under in situ/operando conditions Develop chemical imaging: "Atomic level investigation of the phase stability of transition metal surfaces under reactive environment

  5. Atomic-scale chemical imaging and quantification of metallic alloy structures by energy-dispersive X-ray spectroscopy.

    PubMed

    Lu, Ping; Zhou, Lin; Kramer, M J; Smith, David J

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L2(1) phase with Ni0.48Co0.52 at A-sites, Al at B(?)-sites and Fe0.20Ti0.80 at B(??)-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  6. Atomic-scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-ray Spectroscopy

    PubMed Central

    Lu, Ping; Zhou, Lin; Kramer, M. J.; Smith, David J.

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L21 phase with Ni0.48Co0.52 at A-sites, Al at B?-sites and Fe0.20Ti0.80 at B??-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

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

    SciTech Connect

    Baggetto, Loic [ORNL; Bridges, Craig A [ORNL; Jumas, Dr. Jean-Claude [Institut Charles Gerhardt, University of Montpellier II, FRANCE; Mullins, David R [ORNL; Carroll, Kyler J [Massachusetts Institute of Technology (MIT); Meisner, Roberta [Oak Ridge National Laboratory (ORNL); Crumlin, Ethan [Massachusetts Institute of Technology (MIT); Liu, Xiason [Advanced Light Source, Lawrence Berkeley National Laboratory (LBNL); Yang, Wanli [Advanced Light Source, Lawrence Berkeley National Laboratory (LBNL); Veith, Gabriel M [ORNL

    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.

  8. Role of support-nanoalloy interactions in the atomic-scale structural and chemical ordering for tuning catalytic sites

    SciTech Connect

    Yang, Lefu; Shan, Shiyao; Loukrakpam, Rameshwori; Petkov, Valeri; Ren, Yang; Wanjala, Bridgid N.; Engelhard, Mark H.; Luo, Jin; Yin, Jun; Chen, Yongsheng; Zhong, Chuan-Jian

    2012-09-12

    The understanding of the atomic-scale structural and chemical ordering in supported nanosized alloy particles is fundamental for achieving active catalysts by design. This report shows how such knowledge can be obtained by a combination of techniques including x-ray photoelectron spectroscopy and synchrotron radiation based x-ray fine structure absorption spectroscopy and high-energy x-ray diffraction coupled to atomic pair distribution function analysis, and how the support-nanoalloy interaction influences the catalytic activity of a ternary nanoalloy (platinum-nickel-cobalt) particles on three different supports: carbon, silica and titania. The reaction of carbon monoxide with oxygen is employed as a probe of the catalytic activity. This ternary composition, in combination with the different support materials, is demonstrated to be capable of fine-tuning the catalytic activity and stability. The support-nanoalloy interaction is shown to influence structural and chemical ordering in the nanoparticles, leading to support-tunable active sites on the nanoalloys for oxygen activation in the catalytic oxidation of carbon monoxide. A nickel/cobalt-tuned catalytic site on the surface of nanoalloy was revealed for oxygen activation, which differs from the traditional oxygen-activation sites known for oxide-supported noble metal catalysts. The discovery of such support-nanoalloy interaction enabled oxygen-activation sites introduces a very promising strategy for designing active catalysts in heterogeneous catalysis.

  9. Direct Analysis of the Structure, Concentration, and Chemical Activity of Surface Atomic Vacancies by Specialized Low-Energy Ion-Scattering Spectroscopy: TiC(001)

    Microsoft Academic Search

    M. Aono; Y. Hou; R. Souda; C. Oshima; S. Otani; Y. Ishizawa

    1983-01-01

    The structure, concentration, and chemical activity of atomic vacancies at the TiC(001) surface have been directly analyzed by specialized low-energy ion-scattering spectroscopy. It has been found that carbon vacancies are formed at the surface under a certain condition, and they capture oxygen atoms into the vacancy holes exhibiting a very high activity.

  10. Atomic Structure: Energy in Atoms

    NSDL National Science Digital Library

    National Science Teachers Association (NSTA)

    2010-05-24

    Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the third of three Science Objects in the Atomic Structure SciPack. It investigates

  11. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  12. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

  13. Correlations of chemical structure, atomic force microscopy (AFM) morphology, and reverse osmosis (RO) characteristics in aromatic polyester high-flux RO membranes

    Microsoft Academic Search

    Seung-Yeop Kwak; Min-Oh Yeom; Il Juhn Roh; Dong Young Kim; Jae-Jin Kim

    1997-01-01

    A homologous series of thin-film composite membranes was prepared by interfacial polymerization of various bisphenols possessing structural variations and trimesoyl chloride (TMC). Correlations between the inherent chemical nature of bisphenols with methyl or halogen substitutions on the biphenyl rings, reverse osmosis (RO) characteristics, and surface features characterized by atomic force microscopy (AFM) were studied. The methyl substitutions in bisphenol phenyl

  14. Insights From Atomic-Resolution X-Ray Structures Of Chemically-Synthesized Hiv-1 Protease In Complex With Inhibitors

    PubMed Central

    Johnson, Erik C.B.; Malito, Enrico; Shen, Yuequan; Pentelute, Brad; Rich, Dan; Florián, Jan; Tang, Wei-Jen; Kent, Stephen B.H.

    2007-01-01

    Summary The HIV-1 protease is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 protease has one catalytic site formed by the homodimeric enzyme. We have chemically synthesized fully active HIV-1 protease using modern ligation methods. When complexed with the classic substrate-derived inhibitors JG-365 and MVT-101, the synthetic HIV-1 protease formed crystals that diffracted to 1.04 and 1.2Å resolution, respectively. These atomic resolution structures revealed additional structural details of the HIV-1 protease interactions with its active site ligands. Heptapeptide inhibitor JG-365, which has a hydroxyethylamine moiety in place of the scissile bond, binds in two equivalent antiparallel orientations within the catalytic groove, whereas the reduced isostere hexapeptide MVT-101 binds in a single orientation. When JG-365 was converted into the natural peptide substrate for molecular dynamic simulations, we found putative catalytically competent reactant states for both lytic water and direct nucleophilic attack mechanisms. Moreover, free energy perturbation calculations indicated that the insertion of catalytic water into the catalytic site is an energetically favorable process. PMID:17869270

  15. Atom structures August 8, 2002

    E-print Network

    Venema, Yde

    the reader is referred to Goldblatt gold:vari89. In this paper we will concentrate on atomic baosAtom structures Yde Venema August 8, 2002 Abstract The atom structure of an atomic boolean algebra with operators is some canonically defined frame or relational structure that is based on the set of atoms

  16. Quantum chemical study of atomic structure evolution of Cox/C60 (x

    PubMed

    Avramov, Pavel; Naramoto, Hiroshi; Sakai, Seiji; Narumi, Kazumasa; Lavrentiev, Vasily; Maeda, Yoshihito

    2007-03-29

    The main features of the local atomic structure of novel Cox/C60 (xatomic structure approaching the equilibrium atomic geometry. PMID:17388319

  17. FAST TRACK COMMUNICATION: Electronic structure of a graphene/hexagonal-BN heterostructure grown on Ru(0001) by chemical vapor deposition and atomic layer deposition: extrinsically doped graphene

    NASA Astrophysics Data System (ADS)

    Bjelkevig, Cameron; Mi, Zhou; Xiao, Jie; Dowben, P. A.; Wang, Lu; Mei, Wai-Ning; Kelber, Jeffry A.

    2010-08-01

    A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling microscopy/spectroscopy. The unoccupied ?*(?1 +) band dispersion yields an effective mass of 0.05 me for graphene in the graphene/h-BN(0001) heterostructure, in spite of strong perturbations to the graphene conduction band edge placement.

  18. Atomic force microscopy and chemical force microscopy of microbial cells

    Microsoft Academic Search

    Yves F Dufrêne

    2008-01-01

    Over the past years, atomic force microscopy (AFM) has emerged as a powerful tool for imaging the surface of microbial cells with nanometer resolution, and under physiological conditions. Moreover, chemical force microscopy (CFM) and single-molecule force spectroscopy have enabled researchers to map chemical groups and receptors on cell surfaces, providing valuable insight into their structure–function relationships. Here, we present protocols

  19. Chemical factors influencing selenium atomization 

    E-print Network

    Buren, Mary Sue

    1980-01-01

    by generating the hydride and introducing it into the flame (24, 29) or a tube furnace for flameless analysis. Some organics and other metals, such as copper (25), interfere. Graphite furnace atomic absorption (GFAA) using electrothermal atomizers has been... Atomization. (August 1980) Mary Sue Buren, B, S. , Angelo State University Chairman of Advisory Comm1ttee: Dr. Thomas M. Vickrey Selenium in an acid1c matrix was analyzed using graphite furnace atom1c absorption with Zeeman-effect background correct1on...

  20. Exploring Conceptual Frameworks of Models of Atomic Structures and Periodic Variations, Chemical Bonding, and Molecular Shape and Polarity: A Comparison of Undergraduate General Chemistry Students with High and Low Levels of Content Knowledge

    ERIC Educational Resources Information Center

    Wang, Chia-Yu; Barrow, Lloyd H.

    2013-01-01

    The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…

  1. N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?

    PubMed

    Garcia-Jacas, Cesar R; Marrero-Ponce, Yovani; Barigye, Stephen J; Valdes-Martini, Jose R; Rivera-Borroto, Oscar M; Olivero-Verbel, Jesus

    2014-01-01

    The present manuscript introduces, for the first time, a novel 3D-QSAR alignment free method (QuBiLS-MIDAS) based on tensor concepts through the use of the three-linear and four-linear algebraic forms as specific cases of n-linear maps. To this end, the k(th) three-tuple and four-tuple spatial-(dis)similarity matrices are defined, as tensors of order 3 and 4, respectively, to represent 3Dinformation among "three and four" atoms of the molecular structures. Several measures (multi-metrics) to establish (dis)-similarity relations among "three and four" atoms are discussed, as well as, normalization schemes proposed for the n-tuple spatial-(dis)similarity matrices based on the simple-stochastic and mutual probability algebraic transformations. To consider specific interactions among atoms, both for the global and local indices, n-tuple path and length cut-off constraints are introduced. This algebraic scaffold can also be seen as a generalization of the vector-matrix-vector multiplication procedure (which is a matrix representation of the traditional linear, quadratic and bilinear forms) for the calculation of molecular descriptors and is thus a new theoretical approach with a methodological contribution. A variability analysis based on Shannon's entropy reveals that the best distributions are achieved with the ternary and quaternary measures corresponding to the bond and dihedral angles. In addition, the proposed indices have superior entropy behavior than the descriptors calculated by other programs used in chemo-informatics studies, such as, DRAGON, PADEL, Mold2, and so on. A principal component analysis shows that the novel 3D n-tuple indices codify the same information captured by the DRAGON 3D-indices, as well as, information not codified by the latter. A QSAR study to obtain deeper criteria on the contribution of the novel molecular parameters was performed for the binding affinity to the corticosteroid-binding globulin, using Cramer's steroid database. The achieved results reveal superior statistical parameters for the Bond Angle and Dihedral Angle approaches, consistent with the results obtained in variability analysis. Finally, the obtained QuBiLS-MIDAS models yield superior performances than all 3D-QSAR methods reported in the literature using the 31 steroids as training set, and for the popular division of Cramer's database in training (1-21) and test (22-31) sets, comparable to superior results in the prediction of the activity of the steroids are obtained. From the results achieved, it can be suggested that the proposed QuBiLS-MIDAS N-tuples indices are a useful tool to be considered in chemo-informatics studies. PMID:24909423

  2. Orientation dependences of atomic structures in chemically heterogeneous Cu50Ta50/Ta glass-crystal interfaces

    NASA Astrophysics Data System (ADS)

    Yang, Guiqin; Gao, Xiaoze; Li, Jinfu; Kong, Lingti

    2015-01-01

    Molecular dynamics simulations based on an angular-dependent potential were performed to examine the structural properties of chemically heterogeneous interfaces between amorphous Cu50Ta50 and crystalline Ta. Several phenomena, namely, layering, crystallization, intermixing, and composition segregation, were observed in the Cu50Ta50 region adjacent to the Ta layers. These interfacial behaviors are found to depend on the orientation of the underlying Ta substrate: Layering induced by Ta(110) extends the farthest into Cu50Ta50, crystallization in the Cu50Ta50 region is most significant for interface against Ta(100), while inter-diffusion is most pronounced for Ta(111). It turns out that the induced layering behavior is dominated by the interlayer distances of the underlying Ta layers, while the degree of inter-diffusion is governed by the openness of the Ta crystalline layers. In addition, composition segregations are observed in all interface models, corresponding to the immiscible nature of the Cu-Ta system. Furthermore, Voronoi polyhedra ?0,5,2,6? and ?0,4,4,6? are found to be abundant in the vicinity of the interfaces for all models, whose presence is believed to facilitate the structural transition between amorphous and body centered cubic.

  3. 3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations.

    PubMed

    Page, Alister J; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A; Warr, Gregory G; Voïtchovsky, Kislon; Atkin, Rob

    2014-07-21

    In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition. PMID:24916188

  4. 3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations

    NASA Astrophysics Data System (ADS)

    Page, Alister J.; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A.; Warr, Gregory G.; Voïtchovsky, Kislon; Atkin, Rob

    2014-06-01

    In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01219d

  5. Surface atomic and chemical structure of relaxor Sr0.63Ba0.37Nb2O6(001)

    NASA Astrophysics Data System (ADS)

    Wang, J. L.; Vilquin, B.; Gautier, B.; Dezanneau, G.; Barrett, N.

    2015-06-01

    The surface atomic and chemical structures of a Sr0.63Ba0.37Nb2O6(001) single crystal are studied using the low-energy electron diffraction (LEED) and X-ray photoelectron spectroscopy. Sharp, well-defined LEED patterns are observed, consisting of the superposition of two surface reconstructions, ( ?{ 5 } × ?{ 5 } )R26.6° and ( 5 ?{ 2 } × ?{ 2 } )R45°, probably due to long-range ordering of the alkaline earth metal vacancies in A1 or A2 sites. The Sr/Ba stoichiometry is determined by high-resolution X-ray photoelectron spectroscopy. The Sr 3d core level has 2 components corresponding to the 12- and 15-fold coordinated A1 and A2 sites. The Ba 3d core level has only one component, consistent with the A2 site occupancy. The long-range order of the cation vacancies implies that it is rather the Sr/Ba occupancy of the A2 sites which is responsible for the local random fields at the origin of the relaxor behavior.

  6. Theoretical study of atomic arrangement in BXCYNZ nanotubular structures

    NASA Astrophysics Data System (ADS)

    Souza, T. A.; Silva, M. R. A.; Carvalho, A. C. M.

    A theoretical approach was used to study the atomic arrangements of boron carbonitride nanotubes with diameters from 4 to 16 The role played by nitrogen and boron doping in the structural stabilization of these molecular systems was evaluated, and the geometry of carbon and boron carbonitride nanotubes was investigated using quantum chemical methods. The atomic arrangements and chemical compositions of B-C-N tubular structures proposed in the literature (BCN, B3C2N3, and BC2N) were analyzed. The results showed that the energy associated with boron and nitrogen incorporation depends strongly on tube diameter and the B-C-N atomic distribution in the tubular structures.

  7. Atomic structure of titania nanosheet with vacancies

    PubMed Central

    Ohwada, Megumi; Kimoto, Koji; Mizoguchi, Teruyasu; Ebina, Yasuo; Sasaki, Takayoshi

    2013-01-01

    Titania nanosheets are two-dimensional single crystallites of titanium oxide with a thickness of one titanium or two oxygen atoms, and they show attractive material properties, such as photocatalytic reactions. Since a titania (Ti0.87O2) nanosheet is synthesized by the delamination of a parent layered K0.8Ti1.73Li0.27O4 crystal using a soft chemical procedure, substantial Ti vacancies are expected to be included and affect the material properties. The atomic arrangement of a titania nanosheet with vacancies has not been revealed owing to the difficulties of direct observation. Here, we have directly visualized the atomic arrangement and Ti vacancies of a titania nanosheet using advanced lower-voltage transmission electron microscopy (TEM). Analyses of the results of first-principles calculations and TEM image simulations for various Ti vacancy structure models indicate that two particular oxygen atoms around each Ti vacancy are desorbed, suggesting the sites where atomic reduction first occurs. PMID:24077611

  8. Chemical control of electrical contact to sp2 carbon atoms

    NASA Astrophysics Data System (ADS)

    Frederiksen, Thomas; Foti, Giuseppe; Scheurer, Fabrice; Speisser, Virginie; Schull, Guillaume

    2014-04-01

    Carbon-based nanostructures are attracting tremendous interest as components in ultrafast electronics and optoelectronics. The electrical interfaces to these structures play a crucial role for the electron transport, but the lack of control at the atomic scale can hamper device functionality and integration into operating circuitry. Here we study a prototype carbon-based molecular junction consisting of a single C60 molecule and probe how the electric current through the junction depends on the chemical nature of the foremost electrode atom in contact with the molecule. We find that the efficiency of charge injection to a C60 molecule varies substantially for the considered metallic species, and demonstrate that the relative strength of the metal-C bond can be extracted from our transport measurements. Our study further suggests that a single-C60 junction is a basic model to explore the properties of electrical contacts to meso- and macroscopic sp2 carbon structures.

  9. The Chemical Structure and Acid Deterioration of Paper.

    ERIC Educational Resources Information Center

    Hollinger, William K., Jr.

    1984-01-01

    Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

  10. Development of a chemical oxygen - iodine laser with production of atomic iodine in a chemical reaction

    SciTech Connect

    Censky, M; Spalek, O; Jirasek, V; Kodymova, J [Institute of Physics, Czech Academy of Sciences, Prague (Czech Republic); Jakubec, I [Institute of Inorganic Chemistry, Czech Academy of Sciences, Rez (Czech Republic)

    2009-11-30

    The alternative method of atomic iodine generation for a chemical oxygen - iodine laser (COIL) in chemical reactions with gaseous reactants is investigated experimentally. The influence of the configuration of iodine atom injection into the laser cavity on the efficiency of the atomic iodine generation and small-signal gain is studied. (lasers)

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

    SciTech Connect

    Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. [Departamento de Fisica Fundamental, Universidad Nacional de Educacion a Distancia, Apartado 60.141, E-28080 Madrid (Spain)] [Departamento de Fisica Fundamental, Universidad Nacional de Educacion a Distancia, Apartado 60.141, E-28080 Madrid (Spain); [Instituto de Ciencias de Materiales, Consejo Superior de Investigaciones Cientificas, Cantoblanco, E-28049 Madrid (Spain)

    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.}

  12. Chemical stability of positronic complexes with atoms and atomic ions

    SciTech Connect

    Karl, M.W.; Nakanishi, H.; Schrader, D.M.

    1984-10-01

    A simple theory for establishing the stability or instability of positron-atomic systems against dissociation is presented. The theory consists of assuming that Morse-potential parameters for protonic diatoms are transferrable to the corresponding positronic molecules, and making appropriate reduced-mass modifications in the calculation of binding energies. The surprisingly good reliability of the method is established by appealing to the well-known positronium affinities of atomic hydrogen and fluorine. Positronium (Ps) binding is found for about half of the 42 atoms tested. In addition, instability is indicated for all nine positron-atom systems tested, and stability is indicated for seven of eight negatively charged systems tested; e.g., PsO/sup -/.

  13. The Atomic Structure of Oxide\\/Oxide Interface

    Microsoft Academic Search

    Qi-Hui Wu

    2011-01-01

    The physical and chemical properties of thin or ultrathin oxide film deposited on another oxide bulk or thin film usually differ strongly from the bulk. The properties of the heterostructures ultimately rely on the structure and the chemistry of the oxide\\/oxide interface. Data in the literature indicated that atomically abrupt interfaces between oxides show abnormal electronic and magnetic properties. This

  14. A Thermo-Chemical Reactor for analytical atomic spectrometry

    NASA Astrophysics Data System (ADS)

    Gilmutdinov, A. Kh.; Nagulin, K. Yu.

    2009-01-01

    A novel atomization/vaporization system for analytical atomic spectrometry is developed. It consists of two electrically and thermally separated parts that can be heated separately. Unlike conventional electrothermal atomizers in which atomization occurs immediately above the vaporization site and at the same instant of time, the proposed system allows analyte atomization via an intermediate stage of fractional condensation as a two stage process: Vaporization ? Condensation ? Atomization. The condensation step is selective since vaporized matrix constituents are mainly non-condensable gases and leave the system by diffusion while analyte species are trapped on the cold surface of a condenser. This kind of sample distillation keeps all the advantages of traditional electrothermal atomization and allows significant reduction of matrix interferences. Integration into one design a vaporizer, condenser and atomizer gives much more flexibility for in situ sample treatment and thus the system is called a Thermo-Chemical Reactor (TCR). Details of the design, temperature measurements, vaporization-condensation-atomization mechanisms of various elements in variety of matrices are investigated in the TCR with spectral, temporal and spatial resolution. The ability of the TCR to significantly reduce interferences and to conduct sample pyrolysis at much higher temperatures as compared to conventional electrothermal atomizers is demonstrated. The analytical potential of the system is shown when atomic absorption determination of Cd and Pb in citrus leaves and milk powder without the use of any chemical modification.

  15. Chemical reduction of refractory oxides by atomic hydrogen

    Microsoft Academic Search

    D. Dooley; M. Balooch; D. R. Olander

    1978-01-01

    The chemical reduction of UO and AlO by atomic hydrogen was studied. Results of the UO\\/H investigation indicates that reduction of UO by atomic hydrogen proceeds by the production of water vapor and hypostoichiometric urania. Water vapor and aluminum metal are formed in the AlO\\/H system. The relative ease which UO is reduced by atomic hydrogen compared with AlO is

  16. Quantum Chemical Topology: Knowledgeable atoms in peptides

    NASA Astrophysics Data System (ADS)

    Popelier, Paul L. A.

    2012-06-01

    The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

  17. Atomic structure and mechanical properties of carbyne

    NASA Astrophysics Data System (ADS)

    Timoshevskii, A.; Kotrechko, S.; Matviychuk, Yu.

    2015-06-01

    The atomic structure and mechanical properties of the carbyne (monatomic linear chains), containing from 2 to 21 carbon atoms, are theoretically investigated by ab-initio methods. We demonstrate the existence of a stable cumulene structure in the inner part of chains with the number of atoms N ?10 . We present a general stress-strain diagram of chains until the moment when they break, which enables to determine their strength, elasticity, and fragility. These diagrams can be utilized to calibrate empirical potentials, especially for large deviations of the atoms from the equilibrium positions. For chains with N ?4 , the relationship between the strength of the chain and the binding energy of the edge atom in the chain is established. The existence of scale-effect and "even-odd" effect for such properties as strength, elasticity, and fragility is observed. We demonstrate that the five-atom carbon chains show the maximum strength value.

  18. Direct chemical conversion of graphene to boron- and nitrogen- and carbon-containing atomic layers.

    PubMed

    Gong, Yongji; Shi, Gang; Zhang, Zhuhua; Zhou, Wu; Jung, Jeil; Gao, Weilu; Ma, Lulu; Yang, Yang; Yang, Shubin; You, Ge; Vajtai, Robert; Xu, Qianfan; MacDonald, Allan H; Yakobson, Boris I; Lou, Jun; Liu, Zheng; Ajayan, Pulickel M

    2014-01-01

    Graphene and hexagonal boron nitride are typical conductor and insulator, respectively, while their hybrids hexagonal boron carbonitride are promising as a semiconductor. Here we demonstrate a direct chemical conversion reaction, which systematically converts the hexagonal carbon lattice of graphene to boron nitride, making it possible to produce uniform boron nitride and boron carbonitride structures without disrupting the structural integrity of the original graphene templates. We synthesize high-quality atomic layer films with boron-, nitrogen- and carbon-containing atomic layers with full range of compositions. Using this approach, the electrical resistance, carrier mobilities and bandgaps of these atomic layers can be tuned from conductor to semiconductor to insulator. Combining this technique with lithography, local conversion could be realized at the nanometre scale, enabling the fabrication of in-plane atomic layer structures consisting of graphene, boron nitride and boron carbonitride. This is a step towards scalable synthesis of atomically thin two-dimensional integrated circuits. PMID:24458370

  19. Digital Resource Package for Teaching Atomic Structure

    NSDL National Science Digital Library

    Laura Moin

    This digital resource package is a collection of online sources to help K-12 teachers create lessons on the Chemistry subject of atomic structures. Topics include The History of the Atom, Reference Material, Tutorials, Simulations, Questions and Activities, Periodic Tables, and resources for more advanced learners.

  20. A relationship between chemical structure and the critical temperature

    NASA Technical Reports Server (NTRS)

    Fedors, R. F.

    1982-01-01

    The present investigation is concerned with the effect of both molecular weight and chemical structure on the critical temperature. Using data from the comprehensive compilation of critical constants of Kudchadker et al. (1968), a simple relationship could be developed between the critical temperature and chemical structure. This relationship does not require experimental data such as the normal boiling point. It was found that the critical temperature (Tc) is given by an expression containing m and the sum of delta-i, where m is the total number of atoms in the molecule and delta-i is a number whose value is obtained from a table of additive atomic, group, and structural constants.

  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. PHYSICAL REVIEW B 85, 205417 (2012) Chemically ordered MnPt ultrathin films on Pt(001) substrate: Growth, atomic structure, and

    E-print Network

    Paris-Sud XI, Université de

    2012-01-01

    PHYSICAL REVIEW B 85, 205417 (2012) Chemically ordered MnPt ultrathin films on Pt(001) substrate; published 10 May 2012) Ultrathin MnPt films have been grown on Pt(001) single crystals by alternate leads to a disordered and rough MnPt film. After annealing at 770 K, chemical order develops

  3. Local atomic structure in disordered and nanocrystalline catalytic materials.

    SciTech Connect

    Dmowski, W. [University of Tennessee, Knoxville (UTK); Egami, T. [University of Tennessee, Knoxville (UTK); Swider-Lyons, K. [Naval Research Laboratory, Washington, D.C.; Dai, Sheng [ORNL; Overbury, Steven {Steve} H [ORNL

    2007-01-01

    The power of the atomic pair density function method to study the local atomic structure of dispersed materials is discussed for three examples (I) supercapacitor hydrous ruthenia, (II) electroctalyst platinum-iron phosphate and (III) nanoparticle gold catalyst. Hydrous ruthenia appears to be amorphous, but was found to be nanocomposite with RuO{sub 2} nanocrystals supporting electronic and hydrous boundaries protonic conductivity. A platinum-iron phosphate electrocatalyst, that exhibits activity for the oxygen reduction reaction has platinum in a non-metallic state. In catalysts comprised of gold nanoparticles supported on TiO{sub 2}, atomic correlations in the second atomic shell were observed suggesting interaction with the support that could modify gold chemical activity.

  4. Spatial chemical distance based on atomic property fields

    Microsoft Academic Search

    A. V. Grigoryan; Irina Kufareva; Maxim Totrov; Ruben Abagyan

    2010-01-01

    Similarity of compound chemical structures often leads to close pharmacological profiles, including binding to the same protein\\u000a targets. The opposite, however, is not always true, as distinct chemical scaffolds can exhibit similar pharmacology as well.\\u000a Therefore, relying on chemical similarity to known binders in search for novel chemicals targeting the same protein artificially\\u000a narrows down the results and makes lead

  5. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grégoire A.; Pietrucci, Fabio

    2013-08-01

    We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

  6. Electrohydrodynamic atomization (EHDA) assisted wet chemical synthesis of nickel nanoparticles

    SciTech Connect

    Barzegar Vishlaghi, M. [Department of Mechanical Engineering, University of Tabriz, Tabriz (Iran, Islamic Republic of)] [Department of Mechanical Engineering, University of Tabriz, Tabriz (Iran, Islamic Republic of); Farzalipour Tabriz, M., E-mail: meisam.fa@gmail.com [Department of Mechanical Engineering, University of Tabriz, Tabriz (Iran, Islamic Republic of); Mohammad Moradi, O. [Department of Mechanical Engineering, University of Tabriz, Tabriz (Iran, Islamic Republic of)] [Department of Mechanical Engineering, University of Tabriz, Tabriz (Iran, Islamic Republic of)

    2012-07-15

    Highlights: ? Electrohydrodynamic atomization (EHDA) assisted chemical synthesis of nickel nanoparticles is reported. ? Substituting water with non-aqueous media prevents the formation of nickel hydroxide. ? Size of particles decreased from 10 to 20 nm down to 2–4 nm by using multi-jet mode. ? Synthesized nanoparticles have diffraction patterns similar to amorphous materials. -- Abstract: In this study nickel nanoparticles were prepared via chemical reduction of nickel acetate using sodium borohydride using electrohydrodynamic atomization (EHDA) technique. This technique was used to spray a finely dispersed aerosol of nickel precursor solution into the reductive bath. Obtained particles were characterized by means of X-ray diffraction (XRD), UV–Visible spectroscopy, and transmission electron microscopy (TEM). Results confirmed the formation of nickel nanoparticles and showed that applying EHDA technique to chemical reduction method results in producing smaller particles with narrower size distribution in comparison with conventional reductive precipitation method.

  7. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    E-print Network

    Labushev, Mikhail M

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  8. Chemically induced magnetism in atomically precise gold clusters.

    PubMed

    Krishna, Katla Sai; Tarakeshwar, Pilarisetty; Mujica, Vladimiro; Kumar, Challa S S R

    2014-03-12

    Comparative theoretical and experimental investigations are reported into chemically induced magnetism in atomically-precise, ligand-stabilized gold clusters Au25 , Au38 and Au55 . The results indicate that [Au25 (PPh3 )10 (SC12 H25 )5 Cl2 ](2+) and Au38 (SC12 H25 )24 are diamagnetic, Au25 (SC2 H4 Ph)18 is paramagnetic, and Au55 (PPh3 )12 Cl6 , is ferromagnetic at room temperature. Understanding the magnetic properties resulting from quantum size effects in such atomically precise gold clusters could lead to new fundamental discoveries and applications. PMID:24150895

  9. 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 ? 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.

  10. Structural materials: understanding atomic scale microstructures

    SciTech Connect

    Marquis, E A [University of Oxford; Miller, Michael K [ORNL; Blavette, D [Universite de Rouen, France; Ringer, S. P. [University of Sydney, Australia; Sudbrack, C [Northwestern University, Evanston; Smith, G.D.W. [University of Oxford

    2009-01-01

    With the ability to locate and identify atoms in three dimensions, atom-probe tomography (APT) has revolutionized our understanding of structure-property relationships in materials used for structural applications. The atomic-scale details of clusters, second phases, and microstructural defects that control alloy properties have been investigated, providing an unprecedented level of detail on the origins of aging behavior, strength, creep, fracture toughness, corrosion, and irradiation resistance. Moreover, atomic-scale microscopy combined with atomistic simulation and theoretical modeling of material behavior can guide new alloy design. In this article, selected examples highlight how APT has led to a deeper understanding of materials structures and therefore properties, starting with the phase transformations controlling the aging and strengthening behavior of complex Al-, Fe-, and Ni-based alloys systems. The chemistry of interfaces and structural defects that play a crucial role in high-temperature strengthening, fracture, and corrosion resistance are also discussed, with particular reference to Zr- and Al-alloys and FeAl intermetallics.

  11. Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Wienczek, Albert

    2015-04-01

    Nuclear structure corrections to energy levels of light muonic atoms are derived with particular attention to the nuclear mass dependence. The obtained result for the 2 P -2 S transition of 1.717 (20 ) meV serves for determination of the nuclear charge radius from the spectroscopic measurement in muonic deuterium.

  12. Atomic structure of silver clusters on silicon

    Microsoft Academic Search

    M. V. Gomoyunova; I. I. Pronin; N. S. Faradzhev

    1997-01-01

    The atomic structure of silver clusters formed on a Si(111)-77 single crystal surface by annealing a silver thin film condensed\\u000a at room temperature is investigated by the diffraction of medium-energy quasielastically scattered electrons. Simulation of\\u000a the diffraction pattern obtained within a nearly complete electron reflection hemisphere shows that the silver islands formed\\u000a on the silicon have an ordered structure and

  13. 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.

  14. Atomic Structure and the Periodic Table

    NSDL National Science Digital Library

    Dr. Steven Lower

    2005-10-12

    This is a section of an online textbook ("Chem 1 Virtual Textbook") on General Chemistry at the first-year college or advanced high-school level. It provides an introduction to the structure and properties of the elements and their relationship to the periodic table of the elements. The six lessons cover quantum theory, the properties of light, the Bohr model of the atom, the quantum model of the atom, electron configurations, and the periodic properties of the elements. Each lesson is accompanied by a concept map.

  15. PROTEIN STRUCTURE REPORT Atomic resolution structure of the

    E-print Network

    PROTEIN STRUCTURE REPORT Atomic resolution structure of the cytoplasmic domain of Yersinia pestis III secretion system (T3SS) in Yersinia pestis, have been solved by single-wavelength anomolous; YscU Introduction Yersinia pestis is the causative agent of plague, one of the most deadly diseases

  16. Local correlation measures and atomic shell structure

    NASA Astrophysics Data System (ADS)

    Sagar, Robin P.; Guevara, Nicolais L.

    2007-04-01

    The correlation coefficient and mutual information, used to measure the interdependence between two variables, are generalized to the local level and employed to examine the radial distribution of electron correlation. We compare the behavior of the two local measures with regard to their emphasis on core and valence correlation and show that while there are differences, both are able to correctly reproduce the shell structure in atomic systems.

  17. Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii

    E-print Network

    Heyrovska, Raji

    2008-01-01

    It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

  18. Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii

    E-print Network

    Raji Heyrovska

    2008-06-21

    It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

  19. Markov logic networks for optical chemical structure recognition.

    PubMed

    Frasconi, Paolo; Gabbrielli, Francesco; Lippi, Marco; Marinai, Simone

    2014-08-25

    Optical chemical structure recognition is the problem of converting a bitmap image containing a chemical structure formula into a standard structured representation of the molecule. We introduce a novel approach to this problem based on the pipelined integration of pattern recognition techniques with probabilistic knowledge representation and reasoning. Basic entities and relations (such as textual elements, points, lines, etc.) are first extracted by a low-level processing module. A probabilistic reasoning engine based on Markov logic, embodying chemical and graphical knowledge, is subsequently used to refine these pieces of information. An annotated connection table of atoms and bonds is finally assembled and converted into a standard chemical exchange format. We report a successful evaluation on two large image data sets, showing that the method compares favorably with the current state-of-the-art, especially on degraded low-resolution images. The system is available as a web server at http://mlocsr.dinfo.unifi.it. PMID:25068386

  20. Partial Atomic Charge Derivation of small molecule Partial atomic charge is very crucial for computing physical, chemical and biological

    E-print Network

    Jayaram, Bhyravabotla

    Partial Atomic Charge Derivation of small molecule Partial atomic charge is very crucial for computing physical, chemical and biological properties, and reactivity of molecules. Through the information of the atomic charge in a given species, it is possible to predict the stability, solvation energetics

  1. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  2. Atomic structure of ion tracks in Ceria

    NASA Astrophysics Data System (ADS)

    Takaki, S.; Yasuda, K.; Yamamoto, T.; Matsumura, S.; Ishikawa, N.

    2014-05-01

    We have investigated atomic structure of ion tracks in CeO2 irradiated with 200 MeV Xe ions by transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). TEM observations under inclined conditions showed continuous ion tracks with diffraction and structure factor contrast, and the decrease in the atomic density of the ion tracks was evaluated to be about 10%. High resolution STEM with high-angle annular dark-field (HAADF) technique showed that the crystal structure of the Ce cation column is retained at the core region of ion tracks, although the signal intensity of the Ce cation lattice is reduced over a region 4-5 nm in size. Annular bright field (ABF) STEM observation has detected that the O anion column is preferentially distorted at the core region of ion tracks within a diameter of 4 nm. The core region of ion track in CeO2 is determined to contain a high concentration of vacancies or small vacancy clusters and to generate interstitials in surrounding regions.

  3. Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

    NASA Astrophysics Data System (ADS)

    Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

    2014-12-01

    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-xSex 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.

  4. Direct determination of grain boundary atomic structure in SrTiO{sub 3}

    SciTech Connect

    McGibbon, M.M.; Browning, N.D.; McGibbon, A.J.; Chisholm, M.F.; Pennycook, S.J.

    1994-12-01

    In the electroceramic SrTiO{sub 3} the grain boundary atomic structure governs a variety of electrical properties such as non-linear I-V characteristics. An understanding of this atomic structure-property relationship for individual grain boundaries requires a technique which probes both composition and chemical bonding on an atomic scale. Atomic structure models for tilt boundaries in SrTiO{sub 3} bicrystals have been determined directly from experimental data, by combining high-resolution Z-contrast imagine to locate the cation columns at the boundary, with simultaneous electron energy loss spectroscopy to examine light element coordination at atomic resolution. In this paper we compare and contrast the grain boundary structure models of symmetric and asymmetric boundaries in SrTiO{sub 3}.

  5. Unraveling the chemical dynamics of bimolecular reactions of ground state boron atoms, B(2

    E-print Network

    Kaiser, Ralf I.

    Unraveling the chemical dynamics of bimolecular reactions of ground state boron atoms, B(2 PjArticle on the web 8th March 2004 The reaction dynamics of atomic boron, B(2 P), with acetylene, C2H2(X 1 Sg þ molecular beams technique. Only the atomic boron versus hydrogen atom exchange pathway was observed. Forward

  6. Chemical Reactions and Atomic Removal Dynamics during Gallium Nitride Chemical Mechanical Polishing Process: Quantum Chemical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kentaro; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2015-03-01

    The chemical mechanical polishing (CMP) is promising for efficient polishing of the GaN substrate, and it is essential for manufacturing of GaN devices. However, the detailed CMP mechanisms are unclear, and then the design of efficient and precise CMP process is difficult. We performed polishing simulations of a GaN substrate by a SiO2 abrasive grain in a solution including OH radicals in order to reveal effects of OH radicals on the polishing process. The OH radicals in the solution are adsorbed on the GaN surface and occupy the hollow sites on the surface. Then, a surface-adsorbed O atom is generated by the chemical reaction between the surface-adsorbed OH species and a OH radical in the solution. In the friction interface between the GaN substrate and the abrasive grain, the surface-adsorbed O atom is mechanically pushed into the GaN substrate by the abrasive grain. This O atom intrusion induces the dissociation of Ga-N bonds of the GaN substrate. Moreover, volatile N2 molecules and soluble Ga(OH)3 molecules are generated due to the dissociation of Ga-N bonds. Then, we suggested that the GaN CMP process efficiently proceeds by the mechanically induced chemical reactions: a surface-adsorbed O atom is generated and pushed into the GaN bulk by the abrasive grain.

  7. Automated structure elucidation system — CHEMICS

    Microsoft Academic Search

    Kimito Funatsu; Carlos A. Carpio; Shin-ichi Sasaki

    1986-01-01

    Ein rechnerunterstütztes Programm zur Strukturaufklärung organischer Substanzen, CHEMICS, wurde von den Autoren entwickelt. Es besteht im wesentlichen aus den Teilen Datenanalyse und Strukturgenerierung. Im vorliegenden Beitrag wird die gegenwärtige Form von CHEMICS und ein neuer Ansatz für die Auswertung von NMR-Daten (1H und 13C) unbekannter Verbindungen beschrieben, wobei der Schwerpunkt bei der Datenanalyse liegt. Dieses Programm kann sinnvolle Partialstrukturen, in

  8. 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.

  9. Sharing chemical relationships does not reveal structures.

    PubMed

    Matlock, Matthew; Swamidass, S Joshua

    2014-01-27

    In this study, we propose a new, secure method of sharing useful chemical information from small-molecule libraries, without revealing the structures of the libraries' molecules. Our method shares the relationship between molecules rather than structural descriptors. This is an important advance because, over the past few years, several groups have developed and published new methods of analyzing small-molecule screening data. These methods include advanced hit-picking protocols, promiscuous active filters, economic optimization algorithms, and screening visualizations, which can identify patterns in the data that might otherwise be overlooked. Application of these methods to private data requires finding strategies for sharing useful chemical data without revealing chemical structures. This problem has been examined in the context of ADME prediction models, with results from information theory suggesting it is impossible to share useful chemical information without revealing structures. In contrast, we present a new strategy for encoding the relationships between molecules instead of their structures, based on anonymized scaffold networks and trees, that safely shares enough chemical information to be useful in analyzing chemical data, while also sufficiently blinding structures from discovery. We present the details of this encoding, an analysis of the usefulness of the information it conveys, and the security of the structures it encodes. This approach makes it possible to share data across institutions, and may securely enable collaborative analysis that can yield insight into both specific projects and screening technology as a whole. PMID:24289228

  10. Structure and conductance of a gold atomic chain

    Microsoft Academic Search

    Masakuni Okamoto; Kunio Takayanagi

    1999-01-01

    The conductances of linear chains of gold atoms suspended between two electrodes were calculated while the distance between the electrodes was increased. The stable structures of the linear chains of the gold atoms at low temperature were initially determined by using the ab initio local spin-density-functional approach. As the average bond length increased, the spacings of the neighboring gold atoms

  11. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  12. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties.

    PubMed

    Dalvit, Claudio; Vulpetti, Anna

    2012-02-01

    A correlation between 19F NMR isotropic chemical shift and close intermolecular F???H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F???X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F???H distance and F???H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target. PMID:22262517

  13. The atomic structure of two intermetallic compounds

    Microsoft Academic Search

    E A Owen; G D Preston

    1923-01-01

    The two intermetallic compounds Mg2Si and AlSb have been examined by the X-ray spectrometer with the following results: - Mg2Si. - A face centred cubic lattice of silicon atoms of side 6.391Å symmetrically intermeshed with a simple cubic lattice of magnesium atoms of side 3.19Å. There are eight magnesium atoms situated within each face centred cube of silicon atoms, dividing

  14. MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES

    SciTech Connect

    D. M. PARKIN; L. CHEN; ET AL

    2000-09-01

    We explored both experimentally and theoretically the behavior of materials at stresses close to their theoretical strength. This involves the preparation of ultra fine scale structures by a variety of fabrication methods. In the past year work has concentrated on wire drawing of in situ composites such as Cu-Ag and Cu-Nb. Materials were also fabricated by melting alloys in glass and drawing them into filaments at high temperatures by a method known as Taylor wire technique. Cu-Ag microwires have been drawn by this technique to produce wires 10 {micro}m in diameter that consist of nanoscale grains of supersaturated solid solution. Organogels formed from novel organic gelators containing cholesterol tethered to squaraine dyes or trans-stilbene derivatives have been studied from several different perspectives. The two types of molecules are active toward several organic liquids, gelling in some cases at w/w percentages as low as 0.1. While relatively robust, acroscopically dry gels are formed in several cases, studies with a variety of probes indicate that much of the solvent may exist in domains that are essentially liquid-like in terms of their microenvironment. The gels have been imaged by atomic force microscopy and conventional and fluorescence microscopy, monitoring both the gelator fluorescence in the case of the stilbene-cholesterol gels and, the fluorescence of solutes dissolved in the solvent. Remarkably, our findings show that several of the gels are composed of similarly appearing fibrous structures visible at the nano-, micro-, and macroscale.

  15. Behavior of the chemical potential of neutral atoms in the limit of large nuclear charge

    Microsoft Academic Search

    José Luis Gázquez; Alberto Vela; Marcelo Galván

    1986-01-01

    It is shown that in the limit of large nuclear charge Z, the chemical potential of a neutral atom is given by mu~Z-1\\/3X periodic function of Z1\\/3. This expression accounts for the general behavior of the chemical potential of atoms in the Periodic Table.

  16. Atom-by-atom simulations of chemical vapor deposition of nanoporous hydrogenated silicon nitride

    Microsoft Academic Search

    J. Houska; J. E. Klemberg-Sapieha; L. Martinu

    2010-01-01

    Amorphous hydrogenated silicon nitride (SiNH) materials prepared by plasma-enhanced chemical vapor deposition (PECVD) are of high interest because of their suitability for diverse applications including optical coatings, gas\\/vapor permeation barriers, corrosion resistant, and protective coatings and numerous others. In addition, they are very suitable for structurally graded systems such as those with a graded refractive index. In parallel, modeling the

  17. 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.

  18. Synthesis of multiferroic Er-Fe-O thin films by atomic layer and chemical vapor deposition

    SciTech Connect

    Mantovan, R., E-mail: roberto.mantovan@mdm.imm.cnr.it; Vangelista, S.; Wiemer, C.; Lamperti, A.; Tallarida, G. [Laboratorio MDM IMM-CNR, I-20864 Agrate Brianza (MB) (Italy); Chikoidze, E.; Dumont, Y. [GEMaC, Université de Versailles St. Quentin en Yvelines-CNRS, Versailles (France); Fanciulli, M. [Laboratorio MDM IMM-CNR, I-20864 Agrate Brianza (MB) (Italy); Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Milano (Italy)

    2014-05-07

    R-Fe-O (R?=?rare earth) compounds have recently attracted high interest as potential new multiferroic materials. Here, we report a method based on the solid-state reaction between Er{sub 2}O{sub 3} and Fe layers, respectively grown by atomic layer deposition and chemical vapor deposition, to synthesize Er-Fe-O thin films. The reaction is induced by thermal annealing and evolution of the formed phases is followed by in situ grazing incidence X-ray diffraction. Dominant ErFeO{sub 3} and ErFe{sub 2}O{sub 4} phases develop following subsequent thermal annealing processes at 850?°C in air and N{sub 2}. Structural, chemical, and morphological characterization of the layers are conducted through X-ray diffraction and reflectivity, time-of-flight secondary ion-mass spectrometry, and atomic force microscopy. Magnetic properties are evaluated by magnetic force microscopy, conversion electron Mössbauer spectroscopy, and vibrating sample magnetometer, being consistent with the presence of the phases identified by X-ray diffraction. Our results constitute a first step toward the use of cost-effective chemical methods for the synthesis of this class of multiferroic thin films.

  19. Direct chemical vapor deposition growth of WS2 atomic layers on hexagonal boron nitride.

    PubMed

    Okada, Mitsuhiro; Sawazaki, Takumi; Watanabe, Kenji; Taniguch, Takashi; Hibino, Hiroki; Shinohara, Hisanori; Kitaura, Ryo

    2014-08-26

    Atomically thin transition metal dichalcogenides (TMDCs) have attracted considerable interest owing to the spin-valley coupled electronic structure and possibility in next-generation devices. Substrates are one of the most important factors to limit physical properties of atomic-layer materials, and among various substrates so far investigated, hexagonal boron nitride (hBN) is the best substrate to explore the intrinsic properties of atomic layers. Here we report direct chemical vapor deposition (CVD) growth of WS2 onto high-quality hBN using a 3-furnace CVD setup. Triangular-shaped WS2 grown on hBN have shown limited crystallographic orientation that is related to that of the underlying hBN. Photoluminescence spectra of the WS2 show an intense emission peak at 2.01 eV with a quite small fwhm of 26 meV. The sharp emission peak indicates the high quality of the present WS2 atomic layers with high crystallinity and clean interface. PMID:25093606

  20. Chemical and physical structure of coals

    Microsoft Academic Search

    R. E. Winans; R. L. McBeth; R. G. Scott; P. Thiyagarajan; R. E. Botto; R. Hayatsu

    1987-01-01

    New information on the chemical and physical structure of coals and separated coal macerals strongly suggests that polycyclic aromatics do not dominate the aromatic structure except in the very high rank coals and in inertinites. Two very different approaches have led to these conclusions. First, a very mild, selective oxidation method has been used to break down the coal macromolecular

  1. Atomic and electronic structures of an extremely fragile liquid.

    PubMed

    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

  2. Structures of Molecules at the Atomic Level: Caffeine and Related Compounds

    E-print Network

    Heyrovska, Raji

    2008-01-01

    Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.

  3. Chemical reactivity of iron atoms near room temperature

    Microsoft Academic Search

    S. A. Mitchell; P. A. Hackett

    1990-01-01

    The reactivity of ground state iron atoms with respect to atom transfer and adduct formation reactions with a variety of simple molecules in Ar buffer gas near room temperature has been investigated. Iron atoms are produced by visible multiphoton dissociation of iron pentacarbonyl or ferrocene, and their removal by added gases under pseudo-first-order conditions is monitored by resonance fluorescence excitation

  4. Atomic structure determination of carbon nanotubes by electron diffraction

    NASA Astrophysics Data System (ADS)

    Liu, Zejian

    This dissertation comprises developing and applying an electron diffraction technique to determine and map the chiral indices of carbon nanotubes which dictate their chemical and physical properties. Due to the tubular geometry of carbon nanotubes, the diffraction intensity is usually elongated to form layer lines perpendicular to the tubule axis. Based on helical diffraction theory, we show that the diffraction intensity on a layer line is modulated in dominance by the Bessel functions of the lowest order and all the other Bessel functions of higher orders contribute negligibly to the diffraction intensity. By examining the peak positions of the scattering intensities on the non-equatorial principal layer lines in the electron diffraction pattern of a single-walled carbon nanotube, we can assign unambiguously the chiral indices (u,nu) of the carbon nanotube, which define its atomic structure. A systematic procedure has been established for experimental structure determination. Electron diffraction patterns of carbon nanotubes were obtained using a modern transmission electron microscope equipped with a field emission gun. To avoid damaging the atomic structure of carbon nanotubes, the electron microscope has been operated at 80 kV above which knock-on radiation damage to the carbon nanotubes occurs. Experimentally, we have determined accurately the atomic structure of more than 200 isolated individual carbon nanotubes, and a mapping of these nanotubes in terms of their diameter, helicity and metallicity has been implemented. We have also studied in detail the symmetry properties of electron diffraction from carbon nanotubes both theoretically and experimentally. We show that the electron diffraction pattern of a single-walled carbon nanotube always has 2mm symmetry. However, for the case of multiwalled carbon nanotubes, the 2mm symmetry can break down when coherent interferences of the electron waves from two different shells take place such as when the two shells of the same helicity but their chiral indices ( u,nu) have opposite evenness/oddity. The helical electron diffraction theory has also been extended to study the structure of deformed carbon nanotubes such as elliptical and twisted carbon nanotubes. Finally, we have discussed the possibility of determining the handedness of both single-walled and multiwalled carbon nanotubes by electron diffraction.

  5. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  6. Cheminoes: A Didactic Game to Learn Chemical Relationships between Valence, Atomic Number, and Symbol

    ERIC Educational Resources Information Center

    Moreno, Luis F.; Hincapié, Gina; Alzate, María Victoria

    2014-01-01

    Cheminoes is a didactic game that enables the meaningful learning of some relations between concepts such as chemical element, valence, atomic number, and chemical symbol for the first 36 chemical elements of the periodic system. Among the students who have played the game, their opinions of the activity were positive, considering the game to be a…

  7. Structure–Activity Model of Chemicals That Cause Human Respiratory Sensitization

    Microsoft Academic Search

    Cynthia Graham; Herbert S. Rosenkranz; Meryl H. Karol

    1997-01-01

    We report a structure–activity model of chemicals with the potential to cause respiratory allergy developed through the CASE\\/MultiCASE systems. Chemicals documented to elicit a decrease in FEV1of ?20% within 24 h of inhalation provocation challenge were used to form a learning set. Additional requirements for inclusion in the learning set were that chemicals had at least two contiguous nonhydrogen atoms

  8. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    USGS Publications Warehouse

    Dowty, E.; 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.

  9. The PubChem chemical structure sketcher

    PubMed Central

    2009-01-01

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

  10. Atomic structure and physical properties of amorphous carbon and its hydrogenated analogs

    Microsoft Academic Search

    Th. Frauenheim; P. Blaudeck; U. Stephan; G. Jungnickel

    1993-01-01

    A semiempirical molecular-dynamic density-functional approach is used to perform a systematic investigation of the stability, structure, and properties of quenched pure and hydrogenated amorphous carbon dependent on the mass density and the hydrogen concentration. By comparing the total structure energies for supercell clusters of equal composition and atom number, we obtain the most stable a-C:H configurations characterized by optimal chemical

  11. 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. PMID:12089459

  12. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

    PubMed Central

    Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

  13. Atomic-scale chemical analyses of niobium oxide\\/niobium interfaces via atom-probe tomography

    Microsoft Academic Search

    Kevin E. Yoon; David N. Seidman; Claire Antoine; Pierre Bauer

    2008-01-01

    Niobium is the metal of choice for superconducting radio-frequency cavities for the future International Linear Collider. We present the results of atomic-scale characterization of the oxidation of niobium utilizing local-electrode atom-probe tomography employing picosecond laser pulsing. Laser pulsing is utilized to prevent a tip from fracturing as a buried niobium oxide\\/niobium interface is dissected on an atom-by-atom basis. The thickness

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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, AunPt38-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.

  15. Atomic and Molecular Structure Codes with Lab View

    Microsoft Academic Search

    Edward Deveney

    2005-01-01

    Atomic and molecular electronic structure (AMES) computer codes yield spectroscopic and dynamic details about atomic and molecular electron states. This information plays a fundamental and practical role in physics, chemistry, biology and industry. Advances in AMES codes have progressed in parallel with quantum theory and computer technologies yet many of the codes continue to be developed in the original scientific

  16. The atomic structure of the threefold surface of the icosahedral Ag-In-Yb quasicrystal.

    PubMed

    Cui, C; Nugent, P J; Shimoda, M; Ledieu, J; Fournée, V; Tsai, A P; McGrath, R; Sharma, H R

    2012-11-01

    We report a study of the atomic structure of the threefold icosahedral (i-)Ag-In-Yb quasicrystal surface using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). The LEED confirms that the surface exhibits quasicrystalline long-range order with the threefold symmetry expected from the bulk. The STM reveals large atomically flat terraces separated by steps of different heights. A comparison of atomically resolved STM images for the terraces and the step-height distribution with the bulk structure of isostructural i-Cd-Yb shows that the terraces are formed at bulk planes intersecting the centers of the rhombic triacontahedral clusters that make up the bulk structure of the system. However, the stability of particular terraces may be influenced by the density of atoms in the interstices (glue atoms that bind the clusters) in the terraces and also by the chemical environment in the underlying atomic plane. The surface exhibits screw dislocations, which is explained in terms of a continuous atomic density along the threefold axis. PMID:23044476

  17. Annual Report 2002. Chemical Structure & Dynamics

    Microsoft Academic Search

    Steven D. Colson; Roy E. Gephart

    2003-01-01

    This report describes the research and accomplishments of the Chemical Structure and Dynamics (CS&D) Group of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) from October 2000 through December 2001. Publications, presentations, and collaborations are listed from October 2000 to September 2002. The EMSL is a national user facility located at the Pacific Northwest National Laboratory, Richland, Washington. The

  18. Chemical automaton for crystal growth: Stable structures from non-equilibrium processes

    Microsoft Academic Search

    P. Quémerais; F. Ducastelle

    1997-01-01

    A chemical growth model for binary alloys is presented. At each step, using a simple energetic criterion, an A or B atom is aggregated to the growing cluster. Two one-dimensional models are considered. The first one is a lattice-gas model with short-range decreasing and convex chemical interactions. It is proved that the growing structures are the so-called uniform structures where

  19. Atomic Structure Prediction with Large-Scale High Performance Computing

    NASA Astrophysics Data System (ADS)

    Wang, Cai-Zhuang; Harmon, Bruce; Nguyen, Manh Cuong; Zhao, Xin; Ho, Kai-Ming; Ames Lab, US DOE Team

    2014-03-01

    Many unknown binary or ternary materials for energy applications have very complex crystal structures, containing large number of atoms in their unit cells and possible uncertainty in composition. Computational prediction for atomic structures of such complex materials is a highly demanding work. Advances in modern large-scale high performance computational resources and computational algorithms now make it feasible to perform an efficient crystal structure prediction. We developed an adaptive genetic algorithm to perform large-scale structure search on high performance supercomputer. Examples of successful structure prediction/solving of complex materials will be presented. Further applications of the adaptive genetic algorithm to aid material discoveries will be discussed.

  20. Control structure design for complete chemical plants Sigurd Skogestad +

    E-print Network

    Skogestad, Sigurd

    Control structure design for complete chemical plants Sigurd Skogestad + Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway Abstract Control structure design deals with the structural decisions of the control system, including what to control

  1. An atomic-scale analysis of catalytically-assisted chemical vapor deposition of carbon nanotubes

    E-print Network

    Grujicic, Mica

    An atomic-scale analysis of catalytically-assisted chemical vapor deposition of carbon nanotubes M Growth of carbon nanotubes during transition-metal particles catalytically-assisted thermal decomposition of the transition-metal particles and onto the surface of carbon nanotubes, carbon atom attachment to the growing

  2. Atomic Structure of Graphene on SiO 2

    Microsoft Academic Search

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

    2007-01-01

    We employ scanning probe microscopy to reveal atomic structures and nanoscale\\u000amorphology of graphene-based electronic devices (i.e. a graphene sheet\\u000asupported by an insulating silicon dioxide substrate) for the first time.\\u000aAtomic resolution STM images reveal the presence of a strong spatially\\u000adependent perturbation, which breaks the hexagonal lattice symmetry of the\\u000agraphitic lattice. Structural corrugations of the graphene sheet

  3. Cd-metallothionein: Analysis of local atomic structure

    NASA Astrophysics Data System (ADS)

    Yalovega, Galina; Smolentsev, Grigory; Soldatov, Alexander; Chan, Jayna; Stillman, Martin

    2007-05-01

    Cadmium-metallothioneins (Cd-MT) are small proteins containing seven cadmium atoms in a tetrahedral arrangement of sulfur atoms. Comparison of experimental X-ray absorption fine structure (XAFS) with theoretical full multiple-scattering XAFS spectra have been used as a tool for verification of the structural models generated using both available experimental NMR data and theoretical simulations on the basis of molecule mechanics/molecular dynamics (MM/MD) and density functional theory (DFT).

  4. Quantum chemical studies of protein structure

    PubMed Central

    Oldfield, Eric

    2004-01-01

    Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions. PMID:16147526

  5. Verification of protein structures: patterns of nonbonded atomic interactions.

    PubMed Central

    Colovos, C.; Yeates, T. O.

    1993-01-01

    A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window. PMID:8401235

  6. Chemical profiling of silicon nitride structures

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.

    1989-01-01

    X ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), and scanning electron microscopy (SEM) were used to study structural and chemical inhomogeneities in several electronic materials and device structures of relevance to radiation hard electronics. The systems studied include metal nitride oxide semiconductor (MNOS) structures, silicon oxynitride (SiO(x)N(y)) formed by the thermal nitridation of SiO2, and semiconductor on insulator (SOI) structures. Studies of MNOS structures suggest that the effect of H2 annealing is to make the Si3N4/SiO2 interface less abrupt by causing interdiffusion of silanol and silamine groups with subsequent oxynitride formation. Another effect of the annealing appears to be to relieve the strain at the SiO2/Si interface.

  7. Atomic structure of grain boundaries in iron modeled using the atomic density function

    NASA Astrophysics Data System (ADS)

    Kapikranian, O.; Zapolsky, H.; Domain, C.; Patte, R.; Pareige, C.; Radiguet, B.; Pareige, P.

    2014-01-01

    A model based on the continuous atomic density function (ADF) approach is applied to predict the atomic structure of grain boundaries (GBs) in iron. Symmetrical [100] and [110] tilt GBs in bcc iron are modeled with the ADF method and relaxed afterwards in molecular dynamics (MD) simulations. The shape of the GB energy curve obtained in the ADF model reproduces well the peculiarities of the angles of 70.53? [?3(112)] and 129.52? [?11(332)] for [110] tilt GBs. The results of MD relaxation with an embedded-atom method potential for iron confirm that the atomic GB configurations obtained in ADF modeling are very close to equilibrium ones. The developed model provides well-localized atomic positions for GBs of various geometries.

  8. Chemical vapor deposition and atomic layer deposition of metal oxide and nitride thin films

    Microsoft Academic Search

    Jeffrey Thomas Barton

    2003-01-01

    Processes for depositing thin films with various electronic, optical, mechanical, and chemical properties are indispensable in many industries today. Of the many deposition methods available, chemical vapor deposition (CVD) has proved over time to be one of the most flexible, efficient, and cost-effective. Atomic layer deposition (ALD) is a newer process that is gaining favor as a method for depositing

  9. Chemical structure and dynamics. Annual report 1994

    SciTech Connect

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  10. Gas atomized chemical reservoir ODS ferritic stainless steels

    SciTech Connect

    Rieken, J.R.; Anderson, I.E.; Kramer, M.J.

    2010-06-27

    Gas atomization reaction synthesis was used to surface oxidize ferritic stainless steel powders (i.e., Fe-16.0Cr-(0.1-0.2)Y-(0.1-0.5)(Ti or Hf) at.%) during the primary break-up and solidification of the molten alloy. This rapid surface reaction resulted in envelopment of the powders by an ultra thin (i.e., t < 100nm) metastable Cr-enriched oxide shell. This metastable oxide phase was subsequently dissociated, and used as an oxygen reservoir for the formation of more thermodynamically favored Y-(Ti,Hf) nano-metric oxide precipitates during elevated temperature heat treatment of the as-consolidated powders. This oxygen exchange reaction promoted the formation of nano-metric oxide dispersoids throughout the alloy microstructure. The atomization processing parameters were adjusted to tailor the oxygen content in as-atomized powders. Microstructure phase analysis was completed using transmission electron microscopy and X-ray powder diffraction.

  11. Atomic structure calculations using MCHF and BSR

    NASA Astrophysics Data System (ADS)

    Zatsarinny, Oleg; Froese Fischer, Charlotte

    2009-11-01

    Theoretical results of high accuracy can be obtained using B-spline R-matrix methods implemented in BSR codes. These require a description of targets and perturbers that include correlation. They can be computed efficiently using the multi-configuration Hartree-Fock (MCHF) program. This write-up describes the computational procedure for determining a variety of atomic properties by combining these two codes. Special attention is given to the calculation of transition probabilities for Rydberg series and to photoionization cross-sections.

  12. [Electronic structure of hemoglobin's heme complexes with nitric oxide and dynamics of atomic base under physiological temperature].

    PubMed

    Romanova, T A; Krasnov, P O; Avramov, P V

    2001-01-01

    The comparative study of atomic and electronic structure of hem complexes of hemoglobin with molecular oxygen and nitric oxide has been performed by semiempirical quantum chemical PM3 method. It has been shown that the length of chemical bonding in oxygen molecule coordinated with hem increases by 0.046 A and the length of chemical bonding in nitrogen oxide coordinated with hem increases by 0.064 A in comparison with pure substances. This fact indicates that chemical bonding between nitric oxide and Fe atom of hem is stronger that one with oxygen molecule. Analysis of charge of the molecules indicates that NO bounded with Fe by covalent chemical bonding and oxygen molecule bounded with Fe by weak dipole interaction. Atomic orbitals of ligand atoms in oxygen complex play small part in high occupied (HOMO) and low vacant (LVMO) molecular orbitals in comparison with HOMO and LVMO of complex with NO. In the last one unpaired electron of NO molecule moves from ligand to d-orbitals of Fe atom and creates d7-configuration. Molecular dynamics simulation under physiological temperature (310 K) indicates visible difference in atomic and electronic structure of the complexes in comparison with ones under low (from 77 up to 0 K) temperatures. PMID:11558313

  13. Atomic structure of highly ordered pyrolytic graphite doped with boron

    E-print Network

    Kwak, Juhyoun

    Atomic structure of highly ordered pyrolytic graphite doped with boron Eunkyung Kim, Ilwhan Oh 3 September 2001; accepted 3 September 2001 Abstract Boron-doped carbon was prepared by the high of the boron doping on the HOPG structure, several experimental tools were employed such as X-ray photoelectron

  14. Direct experimental determination of the atomic structure at internal interfaces

    SciTech Connect

    Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

    1995-07-01

    A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

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

    Microsoft Academic Search

    Jürgen Eschner; Alessandra Gatti; Agnès Maître; Giovanna Morigi

    2003-01-01

    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.

  16. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  17. Fine-structure-changing collisions in atomic titanium

    NASA Astrophysics Data System (ADS)

    Lu, Mei-Ju; Hardman, Kyle S.; Weinstein, Jonathan D.; Zygelman, Bernard

    2008-06-01

    We have measured cold titanium-helium collisions that cause transitions between the fine-structure levels of the [3d24s2]FJ3 electronic ground state of atomic titanium, over a temperature range from 5 to 20K . The Ti-He inelastic collision cross section is significantly smaller than cross sections measured for collisions of non-transition-metal atoms with noble gas atoms. Our theoretical calculations of the inelastic cross sections reproduce the magnitude and temperature dependence of the measurements, and attribute the suppression of inelastic collisions to titanium’s “submerged” d -shell valence electrons.

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

    Microsoft Academic Search

    Muhammad Usman

    2010-01-01

    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

  19. Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data.

    PubMed Central

    Dolinnaya, N G; Tsytovich, A V; Sergeev, V N; Oretskaya, T S; Shabarova, Z A

    1991-01-01

    Chemical ligation of oligonucleotides in double-stranded helices has been considered in its structural-kinetic aspect. A study was made of (i) two series of DNA duplexes with various arrangements of reacting groups in the ligation junction induced by mispairing or by alteration of furanose structure (the replacement of dT unit with rU, aU, IU, xU, dxT ones) and of (ii) eight synthetic water-soluble carbodiimides with different substituents at N1 and N3 atoms. We assumed that some information on the local structure of modified sites in the duplex can be obtained from kinetic parameters of oligonucleotide coupling reaction. The ratio of kinetic constants k3/(k2 + k3) for productive and nonproductive decomposition of the activated phosphomonoester derivative apparently reflects the reaction site structure: for a given duplex this parameter is virtually independent of the condensing agent composition. Based on the analysis of the chemical ligation kinetics a suggestion has been made about the conformation of some modified units in the double helix. Images PMID:2057363

  20. Surface Modification and Chemical Sputtering of Graphite Induced by Low Energy Atomic and Molecular Deuterium Ions

    SciTech Connect

    Zhang, Hengda [ORNL; Meyer, Fred W [ORNL; Meyer III, Harry M [ORNL; Lance, Michael J [ORNL

    2008-01-01

    The surface morphology, and chemical/structural modifications induced during chemical sputtering of ATJ graphite by low-energy (<200 eV/D) deuterium atomic and molecular ions are explored by Scanning Electron Microscopy (SEM), Raman and Auger Electron Spectroscopy (AES) diagnostics. At the lowest impact energies, the ion range may become less than the probe depth of Raman and AES spectroscopy diagnostics. We show that such diagnostics are still useful probes at these energies. As demonstration, we used these surface diagnostics to confirm the characteristic changes of surface texture, increased amorphization, enhanced surface reactivity to impurity species, and increased sp{sup 3} content that low-energy deuterium ion bombardment to steady-state chemical sputtering conditions produces. To put these studies into proper context, we also present new chemical sputtering yields for methane production of ATJ graphite at room temperature by impact of D{sub 2}{sup +} in the energy range 10-250 eV/D, and by impact of D{sup +} and D{sub 3}{sup +} at 30 eV/D and 125 eV/D, obtained using a Quadrupole Mass Spectroscopy (QMS) approach. Below 100 eV/D, the methane production in ATJ graphite is larger than that in HOPG by a factor of {approx} 2. In the energy range 10-60 eV/D, the methane production yield is almost independent of energy and then decreases with increasing ion energies. The results are in good agreement with recent molecular dynamics simulations.

  1. Design and implementation of a novel portable atomic layer deposition/chemical vapor deposition hybrid reactor.

    PubMed

    Selvaraj, Sathees Kannan; Jursich, Gregory; Takoudis, Christos G

    2013-09-01

    We report the development of a novel portable atomic layer deposition chemical vapor deposition (ALD/CVD) hybrid reactor setup. Unique feature of this reactor is the use of ALD/CVD mode in a single portable deposition system to fabricate multi-layer thin films over a broad range from "bulk-like" multi-micrometer to nanometer atomic dimensions. The precursor delivery system and control-architecture are designed so that continuous reactant flows for CVD and cyclic pulsating flows for ALD mode are facilitated. A custom-written LabVIEW program controls the valve sequencing to allow synthesis of different kinds of film structures under either ALD or CVD mode or both. The entire reactor setup weighs less than 40 lb and has a relatively small footprint of 8 × 9 in., making it compact and easy for transportation. The reactor is tested in the ALD mode with titanium oxide (TiO2) ALD using tetrakis(diethylamino)titanium and water vapor. The resulting growth rate of 0.04 nm/cycle and purity of the films are in good agreement with literature values. The ALD/CVD hybrid mode is demonstrated with ALD of TiO2 and CVD of tin oxide (SnOx). Transmission electron microscopy images of the resulting films confirm the formation of successive distinct TiO2-ALD and SnO(x)-CVD layers. PMID:24089868

  2. Design and implementation of a novel portable atomic layer deposition/chemical vapor deposition hybrid reactor

    NASA Astrophysics Data System (ADS)

    Selvaraj, Sathees Kannan; Jursich, Gregory; Takoudis, Christos G.

    2013-09-01

    We report the development of a novel portable atomic layer deposition chemical vapor deposition (ALD/CVD) hybrid reactor setup. Unique feature of this reactor is the use of ALD/CVD mode in a single portable deposition system to fabricate multi-layer thin films over a broad range from "bulk-like" multi-micrometer to nanometer atomic dimensions. The precursor delivery system and control-architecture are designed so that continuous reactant flows for CVD and cyclic pulsating flows for ALD mode are facilitated. A custom-written LabVIEW program controls the valve sequencing to allow synthesis of different kinds of film structures under either ALD or CVD mode or both. The entire reactor setup weighs less than 40 lb and has a relatively small footprint of 8 × 9 in., making it compact and easy for transportation. The reactor is tested in the ALD mode with titanium oxide (TiO2) ALD using tetrakis(diethylamino)titanium and water vapor. The resulting growth rate of 0.04 nm/cycle and purity of the films are in good agreement with literature values. The ALD/CVD hybrid mode is demonstrated with ALD of TiO2 and CVD of tin oxide (SnOx). Transmission electron microscopy images of the resulting films confirm the formation of successive distinct TiO2-ALD and SnOx-CVD layers.

  3. Chemical Applications of Metastable Argon Atoms. III. Production of Krypton and Xenon Metastable Atoms

    Microsoft Academic Search

    D. H. Stedman; D. W. SETSERt

    1970-01-01

    An inexpensive experimental technique has been developed for the production of argon, krypton, and xenon metastable atoms using a discharge-flow system. The reactions of these metastable atoms with N2, CO, and N2O were investigated in the pressure range 0.3–10 torr, and the emission spectra resulting from the reactions were identified. These spectra gave information about the collision event and also

  4. Static and Dynamic Structural Modeling Analysis of Atomic Force Microscope

    Microsoft Academic Search

    Yin Zhang; Kevin D Murphy

    2010-01-01

    As a cantilever structure, atomic force microscope (AFM) can be either modeled as a beam, plate or a simple one degree-of-freedom\\u000a (DOF) system depending on its geometry and application scenario. The AFM structure can experience the deformation shapes of\\u000a vertical bending, lateral bending, torsion, extension and couplings between these four deformations depending on the excitation\\u000a mode. As a small structure

  5. Single-atom based coherent quantum interference device structure.

    PubMed

    Naydenov, Borislav; Rungger, Ivan; Mantega, Mauro; Sanvito, Stefano; Boland, John J

    2015-05-13

    We describe the fabrication, operation principles, and simulation of a coherent single-atom quantum interference device (QID) structure on Si(100) controlled by the properties of single atoms. The energy and spatial distribution of the wave functions associated with the device are visualized by scanning tunneling spectroscopy and the amplitude and phase of the evanescent wave functions that couple into the quantum well states are directly measured, including the action of an electrostatic gate. Density functional theory simulations were employed to simulate the electronic structure of the device structure, which is in excellent agreement with the measurements. Simulations of device transmission demonstrate that our coherent single-atom QID can have ON-OFF ratios in excess of 10(3) with potentially minimal power dissipation. PMID:25826690

  6. Ageing of impregnating liquids with different chemical structure for polypropylene capacitor dielectric

    Microsoft Academic Search

    A. Andreyev; M. Jevti?; N. Zhuravleva

    2003-01-01

    The results of an ageing test of power capacitor dielectrics consisting of polypropylene film and impregnating liquids with different chemical structure (phenylxilylethan, monobenzyltoluol\\/dibenzyltoluol, polybuten, dodecylbenzol and perfluorcarbon) are presented in the paper. The testing was carried out on the specimens that modelled capacitor dielectric systems. The effects of aromaticity of synthetic hydrocarbon liquids and substitution of hydrogen atom by fluor

  7. Atomic structure analysis of stabilized toxic wastes

    Microsoft Academic Search

    C. Poon; A. I. Clark; R. Perry

    1986-01-01

    Experimental results of a microstruetural study based on an extended X?ray absorption fine structure (EXAFS) technique to investigate the mechanism involved in the immobilisation of heavy metal wastes by cement based stabilisation\\/solidification processes are presented. This study verifies the differential mode of interaction between heavy metals and the cementitious matrix and provides supportive evidence to the protective coating theory proposed

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

    NASA Astrophysics Data System (ADS)

    Osmera, Pavel

    2010-06-01

    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.

  9. Imaging surface atomic structure by means of Auger electrons

    NASA Astrophysics Data System (ADS)

    Frank, Douglas G.; Batina, Nikola; Golden, Teresa; Lu, Frank; Hubbard, Arthur T.

    1990-01-01

    Measurements of the complete angular distribution of Auger electrons emitted from well-defined platinum 111-orientation single-crystals surfaces have led to the discovery that the distributions are composed of 'silhouettes' of surface atoms 'back-lit' by emission from atoms deeper in the solid. Theoretical simulations of Auger electron angular distributions based upon atomic point emitters and spherical atomic scatterers of uniform cross section are in close agreement with these experimental results, but opposite to previous theoretical predictions. In view of the definitive results obtained and the straightforward agreement between theory and experiment, angular distribution Auger microscopy (ADAM) is useful for direct imaging of interfacial structure and investigation of electron-solid interactions in the physical and biological sciences and engineering. Applicability of ADAM is illustrated by images obtained for monolayers of silver and iodine on platinum of 111-orientation.

  10. Chemical mapping of mammalian cells by atom probe tomography

    PubMed Central

    Narayan, Kedar; Prosa, Ty; Fu, Jing; Kelly, Thomas F; Subramaniam, Sriram

    2012-01-01

    In atom probe tomography (APT), a technique that has been used to determine 3D maps of ion compositions of metals and semiconductors at sub-nanometer resolution, controlled emissions of ions can be induced from needle-shaped specimens in the vicinity of a strong electric field. Detection of these ions in the plane of a position sensitive detector provides two-dimensional compositional information while the sequence of ion arrival at the detector provides information in the third dimension. However, the applicability of APT to imaging unstained cells has not been explored. Here, we report the use of APT to obtain 3D spatial distributions of cellular ions and metabolites from unstained, freeze-dried mammalian cells. Multiple peaks were reliably obtained in the mass spectrum from tips with diameters of ~ 50 nm and heights of ~ 200 nm, with mass-to-charge ratios (m/z) ranging from 1 to 80. Peaks at m/z 12, 23, 28 and 39, corresponding to carbon, sodium, carbonyl and potassium ions respectively, showed distinct patterns of spatial distribution within the cell. Our studies establish that APT could become a powerful tool for mapping the sub-cellular distribution of atomic species, such as labeled metabolites, at 3D spatial resolutions as high as ~ 1 nm. PMID:22245777

  11. InChI - the worldwide chemical structure identifier standard

    PubMed Central

    2013-01-01

    Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the extensive use and dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community, the chemical information community, and major publishers and disseminators of chemical and related scientific offerings in manuscripts and databases. PMID:23343401

  12. Insight into Amyloid Structure Using Chemical Probes

    PubMed Central

    Reinke, Ashley A.; Gestwicki, Jason E.

    2011-01-01

    Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-? (A?) peptide. Over the past decade, it has become clear that these A? amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of A? peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

  13. Following Ostwald ripening in nanoalloys by high-resolution imaging with single-atom chemical sensitivity

    SciTech Connect

    Alloyeau, D.; Nelayah, J.; Wang, G.; Ricolleau, C. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); Oikawa, T. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558 (Japan)

    2012-09-17

    Several studies have shown that substantial compositional changes can occur during the coarsening of bimetallic nanoparticles (CoPt, AuPd). To explain this phenomenon that could dramatically impacts all the technologically relevant properties of nanoalloys, we have exploited the sensitivity of the latest generation of electron microscope to prove that during the beam-induced coarsening of CoPt nanoparticles, the dynamic of atom exchanges between the particles is different for Co and Pt. By distinguishing the chemical nature of individual atoms of Co and Pt, while they are diffusing on a carbon film, we have clearly shown that Co atoms have a higher mobility than Pt atoms because of their higher evaporation rate from the particles. These atomic-scale observations bring the experimental evidence on the origin of the compositional changes in nanoalloys induced by Ostwald ripening mechanisms.

  14. 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 has been generated by the application of concepts from wave optics to matter waves. An example is the contribution by Franke-Arnold et al. The authors investigate the coherence properties of two trapped cold atoms using concepts developed in wave optics. Nevertheless, novel features appear in this system due to the quantum statistics - as atoms may be bosons or fermions - and due to interactions. Matter waves find a spectacular manifestation in Bose-Einstein condensates (BECs) of cold dilute atomic gases. Several concepts of wave optics, like the laser, have been discussed in relation to BECs, and the .eld of atom optics with BECs is rapidly developing. The similarity between the theoretical description of a weakly interacting BEC with that of a non-linear optical system has motivated a series of experiments that led to the observation of, e.g., solitons, vortices and vortex crystallization in matter waves. In this context, the paper by Josopait et al. describes the dynamics of a Bose-Einstein condensate containing a vortex. The vortex stability is discussed as a function of the interparticle interaction, which can be tuned using Feshbach resonances, and the dynamics of the BEC reflected by an atomic mirror is investigated. Non-linear optics merges with atomic physics also in a relatively new research area which aims at quantum non-linear optics with cold atomic gases. Labeyrie et al. use a dense, laser-cooled atomic gas as a non-linear medium for light propagation, and discuss the conditions for observing optical patterns in the transmitted beam. Pattern formation in non-linear optical media is one of the numerous forms of self-organization that these systems display, including also turbulence and optical solitons. With respects to other physical systems, where these phenomena are commonly observed, optical systems are however special: at optical frequencies thermal .uctuations are negligible and do not hide the presence of quantum .uctuations, even at room temperature. Remarkably, the interplay between non-linearity and quantum noise leads to novel

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Solid state 93Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. 93Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni60Nb35Sn5 has been found to be ˜100 ppm lower than that of Ni60Nb35Zr5 MG, which is correlated with their intrinsic fracture toughness. The evolution of 93Nb 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. Crambin: a direct solution for a 400-atom structure.

    PubMed

    Weeks, C M; Hauptman, H A; Smith, G D; Blessing, R H; Teeter, M M; Miller R

    1995-01-01

    The crystal structure of crambin, a 46-residue protein containing the equivalent of approximately 400 fully occupied non-H-atom positions, was originally solved at 1.5 A by exploiting the anomalous scattering of its six S atoms at a single wavelength far removed from the absorption edge of sulfur. The crambin structure has now been resolved without the use of any anomalous-dispersion measurements. The technique employed was an ab initio 'shake-and-bake' method, consisting of a phase-refinement procedure based on the minimal function alternated with Fourier refinement. This method has successfully yielded solutions for a smaller molecule (28 atoms) using 1.2 A data, and a crambin solution was obtained at 1.1 A. PMID:15299333

  17. Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

    PubMed

    Berns, Veronica M; Fredrickson, Daniel C

    2014-10-01

    Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity. PMID:25238606

  18. Hydrogen atom initiated chemistry. [chemical evolution in planetary atmospheres

    NASA Technical Reports Server (NTRS)

    Hong, J. H.; Becker, R. S.

    1979-01-01

    H Atoms have been created by the photolysis of H2S. These then initiated reactions in mixtures involving acetylene-ammonia-water and ethylene-ammonia-water. In the case of the acetylene system, the products consisted of two amino acids, ethylene and a group of primarily cyclic thio-compounds, but no free sulfur. In the case of the ethylene systems, seven amino acids, including an aromatic one, ethane, free sulfur, and a group of solely linear thio-compounds were produced. Total quantum yields for the production of amino acids were about 3 x 10 to the -5th and about 2 x 10 to the -4th with ethylene and acetylene respectively as carbon substrates. Consideration is given of the mechanism for the formation of some of the products and implications regarding planetary atmosphere chemistry, particularly that of Jupiter, are explored.

  19. 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.

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

    SciTech Connect

    Not Available

    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)

  1. Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure

    E-print Network

    Davis, James C.

    Chapter 3 Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure and Symmetry in Underdoped Cuprates Kazuhiro Fujita, Mohammad Hamidian, Inês Firmo, Sourin Mukhopadhyay, Chung) phases of underdoped cuprates, two distinct types of electronic states are observed K. Fujita (B) · M

  2. Atomic-scale structure: From surfaces to nanomaterials

    Microsoft Academic Search

    M. A. Van Hove

    2009-01-01

    This brief overview is dedicated to Professor G. Ertl’s profound influence on shaping the field of surface science. I sketch recent accomplishments toward the determination and understanding of the atomic-scale structure of nanostructures. I argue that, to properly understand nanoscience and develop nanotechnology, there is a dire need to determine many more than the ?1,000 detailed surface structures known today.

  3. Atomic structure of quantum gold nanowires: quantification of the lattice strain.

    PubMed

    Kundu, Paromita; Turner, Stuart; Van Aert, Sandra; Ravishankar, N; Van Tendeloo, Gustaaf

    2014-01-28

    Theoretical studies exist to compute the atomic arrangement in gold nanowires and the influence on their electronic behavior with decreasing diameter. Experimental studies, e.g., by transmission electron microscopy, on chemically synthesized ultrafine wires are however lacking owing to the unavailability of suitable protocols for sample preparation and the stability of the wires under electron beam irradiation. In this work, we present an atomic scale structural investigation on quantum single crystalline gold nanowires of 2 nm diameter, chemically prepared on a carbon film grid. Using low dose aberration-corrected high resolution (S)TEM, we observe an inhomogeneous strain distribution in the crystal, largely concentrated at the twin boundaries and the surface along with the presence of facets and surface steps leading to a noncircular cross section of the wires. These structural aspects are critical inputs needed to determine their unique electronic character and their potential as a suitable catalyst material. Furthermore, electron-beam-induced structural changes at the atomic scale, having implications on their mechanical behavior and their suitability as interconnects, are discussed. PMID:24289167

  4. Recent ORNL measurements of chemical sputtering of ATJ graphite by slow atomic and molecular D ions

    Microsoft Academic Search

    F W Meyer; L I Vergara; H F Krause

    2006-01-01

    We describe here an ORNL Physics Division research activity whose focus is the investigation of chemical sputtering of graphite by atomic and molecular D ions at very low energies that have so far been unexplored. Our initial experimental approach is based on the use of a quadrupole mass spectrometer (QMS) which samples the partial pressure of selected mass species produced

  5. Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics

    E-print Network

    Takada, Shoji

    Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics Kengo,Myodaiji, Okazaki 444. Japan (Received 28 September 1993; accepted 8 December 1993) The constant centrifugal of such practically useful approxima- tions the constant centrifugal potential approximation (CCPA) (or the energy

  6. Structural chaos in reversible spontaneous emission of moving atoms

    SciTech Connect

    Prants, Sergei V; Yusupov, V I [V.I. Il'ichev Pacific Oceanological Institute, Far-Eastern Division of the Russian Academy of Sciences, Vladivostok (Russian Federation)

    2000-07-31

    t is proved analytically and numerically that, under certain conditions, the reversible spontaneous emission of two-level atoms moving in a high-Q resonator and described quantum-classically can be chaotic in the sense of the exponential sensitivity with respect to the initial conditions. The wavelet analysis of the vacuum Rabi oscillations showed that this chaos is structural. The numerical estimates showed that a Rydberg atom maser with a superconducting microwave resonator operating in a strong coupling mode is a promising device for detecting mani-festations of the dynamic chaos in the reversible spontaneous emission. (laser applications and other topics in quantum electronics)

  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. Metal Oxide Nanoparticle Growth on Graphene via Chemical Activation with Atomic Oxygen

    PubMed Central

    Johns, James E.; Alaboson, Justice M. P.; Patwardhan, Sameer; Ryder, Christopher R.; Schatz, George C.

    2013-01-01

    Chemically interfacing the inert basal plane of graphene with other materials has limited the development of graphene-based catalysts, composite materials, and devices. Here, we overcome this limitation by chemically activating epitaxial graphene on SiC(0001) using atomic oxygen. Atomic oxygen produces epoxide groups on graphene, which act as reactive nucleation sites for zinc oxide nanoparticle growth using the atomic layer deposition precursor diethyl zinc. In particular, exposure of epoxidized graphene to diethyl zinc abstracts oxygen, creating mobile species which diffuse on the surface to form metal oxide clusters. This mechanism is corroborated with a combination of scanning probe microscopy, Raman spectroscopy, and density functional theory, and can likely be generalized to a wide variety of related surface reactions on graphene. PMID:24206242

  9. Atomic structure variations of mechanically stable fcc-bcc interfaces

    NASA Astrophysics Data System (ADS)

    Kang, K.; Wang, J.; Beyerlein, I. J.

    2012-03-01

    It has recently been shown that under severe plastic deformation processing bi-metal fcc/bcc composites develop a mechanically stable heterophase interface that joins the {112}fcc//{112}bcc planes in the Kurdjumov-Sachs orientation relationship. In this article, we study variations in the relaxed equilibrium atomic structure of this interface with changes in fcc stacking fault energy (SFE) and lattice mismatch between the two crystals. Using molecular statics/dynamics simulations for three fcc/bcc systems, Cu-Nb, Al-Fe, and Al-Nb, we find that the number of distinct sets of intrinsic interfacial dislocations and their core structures vary significantly among these three systems. The impact of these atomic-scale structural differences on interfacial properties is demonstrated through their interactions with point defects. The interfaces studied here are shown to exhibit a wide variation in ability, ranging from being a poor to an excellent sink for vacancies.

  10. Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

    PubMed Central

    2013-01-01

    Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

  11. 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.

  12. Chemical potential, Teller's theorem, and the scaling of atomic and molecular energies

    PubMed Central

    March, Norman H.; Parr, Robert G.

    1980-01-01

    For atoms and homonuclear diatomic molecules, it is argued that the electronic energies have the forms [Formula: see text] and [Formula: see text] [Formula: see text], respectively,where Z is the atomic number, N is the number of electrons, and R is the internuclear distance. By using the Lieb-Simon theorem that the Thomas-Fermi theory is exact in the limit of large atomic number and the Teller theorem that molecules are not bound in the Thomas-Fermi theory, it is then shown, among other results, that the electron-electron repulsion energy for neutral systems has no term in Z2 and that the nucleus-nucleus repulsion energy for neutral molecules is probably [unk](Z5/3). For neutral atoms, it is predicted and verified that the chemical potential (electronegativity) is [unk](Z-1/3) for large Z. Tetrahedral and octahedral molecules are briefly discussed. PMID:16592908

  13. Conservation-dissipation structure of chemical reaction systems.

    PubMed

    Yong, Wen-An

    2012-12-01

    In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics. PMID:23368081

  14. Delta-doping of boron atoms by photoexcited chemical vapor deposition

    SciTech Connect

    Akazawa, Housei [NTT Microsystem Integration Laboratories, 3-1 Morinosato Wakamiya, Atsugi, Kanagawa 243-0198 (Japan)

    2012-03-15

    Boron delta-doped structures in Si crystals were fabricated by means of photoexcited chemical vapor deposition (CVD). Core electronic excitation with high-energy photons ranging from vacuum ultraviolet to soft x rays decomposes B{sub 2}H{sub 6} molecules into fragments. Combined with in situ monitoring by spectroscopic ellipsometry, limited number of boron hydrides can be delivered onto a Si(100) surface by using the incubation period before the formation of a solid boron film. The boron-covered surface is subsequently embedded in a Si cap layer by Si{sub 2}H{sub 6} photo-excited CVD. The crystallinity of the Si cap layer depended on its thickness and the substrate temperature. The evaluation of the boron depth profile by secondary ion mass spectroscopy revealed that boron atoms were confined within the delta-doped layer at a concentration of 2.5 x 10{sup 20} cm{sup -3} with a full width at half maximum of less than 9 nm, while the epitaxial growth of a 130-nm-thick Si cap layer was sustained at 420 deg. C.

  15. We present a unique approach to the design and synthesis of "giant molecules" based on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic properties.

    E-print Network

    Pennycook, Steve

    a remarkable sensitivity of their self-assembled structures to the primary chemical structures. Unconventional on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic-defined chemical structures and surface functionalities that can serve as elemental building blocks

  16. ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

    PubMed

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

    Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu . PMID:24160861

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

    NASA Astrophysics Data System (ADS)

    K?c, M.; Morgiel, J.; Polit, A.; Zabila, Y.; Marsza?ek, 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.

  18. 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.

  19. Catalyst-free growth of mono- and few-atomic-layer boron nitride sheets by chemical vapor deposition.

    PubMed

    Qin, Li; Yu, Jie; Li, Mingyu; Liu, Fei; Bai, Xuedong

    2011-05-27

    Boron nitride (BN) is a wide bandgap semiconductor with a structure analogous to graphite. Mono- and few-atomic-layer BN sheets have been grown on silicon substrates by microwave plasma chemical vapor deposition from a gas mixture of BF(3)-H(2)-N(2) without using any catalysts. Growth of the BN sheets can be ascribed to the etching effects of the fluorine-containing gases and the thickness control down to mono- and few-atomic-layers was realized by decreasing the concentrations of BF(3) and H(2) in N(2). A large decrease of the BF(3) and H(2) concentrations was achieved by increasing the gas flow rate of N(2) and keeping the BF(3) and H(2) flow rates constant and the mono- and few-atomic-layered BN sheets were obtained at the BF(3), H(2) and N(2) flow rates of 3, 10, and 1200 sccm. The present mono- and few-atomic-layer BN sheets are promising for applications in catalyst supports, composites, gas adsorption, nanoelectronics, etc. PMID:21451227

  20. 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.

  1. Chemical structures and electrical properties of atomic layer deposited HfO2 thin films grown at an extremely low temperature (?100 °C) using O3 as an oxygen source

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Hwan; Park, Tae Joo; Kim, Seong Keun; Cho, Deok-Yong; Jung, Hyung-Suk; Lee, Sang Young; Hwang, Cheol Seong

    2014-02-01

    The properties of atomic layer deposited (ALD) HfO2 films grown at low temperatures (?100 °C) were examined for potential applications in flexible display and bioelectronics. A saturated ALD growth behavior was observed even at an extremely low temperature (30 °C) due to the strong oxidizing potential of O3. However, HfO2 films grown at low temperatures showed a low film density and high impurity concentration, because the thermal energy during film growth was insufficient to remove ligands completely from Hf ions in precursor molecule. This resulted in low dielectric constant and high leakage current density of the films. Nevertheless, HfO2 film grown at 100 °C using O3 gas with a high concentration (390 g/Nm3) showed a tolerable impurity concentration with the dielectric constant of ?16 and breakdown field of ?4 MV/cm, which are approximately two-thirds of those of HfO2 film grown at 250 °C.

  2. The local atomic structure of superconducting Fe-Se-Te

    Microsoft Academic Search

    Martin C. Lehman; Despina Louca; Kazumasa Horigane; Anna Llobet; Ryotaro Arita; Sungdae Ji; Naoyuki Katayama; Shun Konbu; Kazuma Nakamura; Peng Tong; Tae-Yeong Koo; Kazuyoshi Yamada

    2009-01-01

    We report on the first local atomic structure study via the pair density function (PDF) analysis of neutron diffraction data and show a direct correlation of local coordinates to TC in the newly discovered superconducting FeSe1-xTex. The isovalent substitution of Te for Se such as in FeSe0.5Te0.5 increases Tc by twofold in comparison to a-FeSe without changing the carrier concentration

  3. Atomic structure of amorphous particles produced by spark erosion

    Microsoft Academic Search

    S. Aur; T. Egami; A. E. Berkowitz; J. L. Walter

    1982-01-01

    The atomic structure of amorphous particles of composition Fe75Si15B10 produced by spark erosion was studied by the energy-dispersive x-ray diffraction technique and was compared to that of the amorphous ribbon of the same composition produced by melt spinning. It was found that the nearest-neighbor Fe-Fe correlation is almost identical for the ribbon and the particles of different sizes, whereas the

  4. Atomic-scale recognition of surface structure and intercalation mechanism of Ti3C2X.

    PubMed

    Wang, Xuefeng; Shen, Xi; Gao, Yurui; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

    2015-02-25

    MXenes represent a large family of functionalized two-dimensional (2D) transition-metal carbides and carbonitrides. However, most of the understanding on their unique structures and applications stops at the theoretical suggestion and lack of experimental support. Herein, the surface structure and intercalation chemistry of Ti3C2X are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope (STEM) and density functional theory (DFT) calculations. The STEM studies show that the functional groups (e.g., OH(-), F(-), O(-)) and the intercalated sodium (Na) ions prefer to stay on the top sites of the centro-Ti atoms and the C atoms of the Ti3C2 monolayer, respectively. Double Na-atomic layers are found within the Ti3C2X interlayer upon extensive Na intercalation via two-phase transition and solid-solution reactions. In addition, aluminum (Al)-ion intercalation leads to horizontal sliding of the Ti3C2X monolayer. On the basis of these observations, the previous monolayer surface model of Ti3C2X is modified. DFT calculations using the new modeling help to understand more about their physical and chemical properties. These findings enrich the understanding of the MXenes and shed light on future material design and applications. Moreover, the Ti3C2X exhibits prominent rate performance and long-term cycling stability as an anode material for Na-ion batteries. PMID:25688582

  5. How to Make an Atomic Blog in Your Own Kitchen. Summary of the Workshop: Uncertainties in Atomic Data and How They Propagate in Chemical Abundances

    E-print Network

    Luridiana, Valentina; Aggarwal, Kanti; Bautista, Manuel; Bergemann, Maria; Delahaye, Franck; del Zanna, Giulio; Ferland, Gary; Lind, Karin; Manchado, Arturo; Mendoza, Claudio; Delgado, Adal Mesa; Díaz, Manuel Núñez; Shaw, Richard A; Wesson, Roger

    2011-01-01

    This workshop brought together scientists (including atomic physicists, theoretical astrophysicists and astronomers) concerned with the completeness and accuracy of atomic data for astrophysical applications. The topics covered in the workshop included the evaluation of uncertainties in atomic data, the propagation of such uncertainties in chemical abundances, and the feedback between observations and calculations. On a different level, we also discussed communication issues such as how to ensure that atomic data are correctly understood and used, and which forum is the best one for a fluid interaction between all communities involved in the production and use of atomic data. This paper reports on the discussions held during the workshop and introduces AstroAtom, a blog created as a platform for timely and open discussions on the needs and concerns over atomic data, and their effects on astronomical research. The complete proceedings will be published on http://astroatom.wordpress.com/.

  6. Sub-micron period lattice structures of magnetic microtraps for ultracold atoms on an atom chip

    NASA Astrophysics Data System (ADS)

    Herrera, I.; Wang, Y.; Michaux, P.; Nissen, D.; Surendran, P.; Juodkazis, S.; Whitlock, S.; McLean, R. J.; Sidorov, A.; Albrecht, M.; Hannaford, P.

    2015-03-01

    We report on the design, fabrication and characterization of magnetic nanostructures to create a lattice of magnetic traps with sub-micron period for trapping ultracold atoms. These magnetic nanostructures were fabricated by patterning a Co/Pd multilayered magnetic film grown on a silicon substrate using high precision e-beam lithography and reactive ion etching. The Co/Pd film was chosen for its small grain size and high remanent magnetization and coercivity. The fabricated structures are designed to magnetically trap 87Rb atoms above the surface of the magnetic film with one-dimensional and two-dimensional (triangular and square) lattice geometries and sub-micron period. Such magnetic lattices can be used for quantum tunneling and quantum simulation experiments, including using geometries and periods that may be inaccessible with optical lattices.

  7. Chemical Reaction of Ultracold Atoms and Ions in a Hybrid Trap

    E-print Network

    Rellergert, Wade G; Kotochigova, Svetlana; Petrov, Alexander; Chen, Kuang; Schowalter, Steven J; Hudson, Eric R

    2011-01-01

    Interactions between cold ions and atoms have been proposed for use in implementing quantum gates\\cite{Idziaszek2007}, probing quantum gases\\cite{Sherkunov2009}, observing novel charge-transport dynamics\\cite{Cote2000}, and sympathetically cooling atomic and molecular systems which cannot be laser cooled\\cite{Smith2005,Hudson2009}. Furthermore, the chemistry between cold ions and atoms is foundational to issues in modern astrophysics, including the formation of stars, planets, and interstellar clouds\\cite{Smith1992}, the diffuse interstellar bands\\cite{Reddy2010}, and the post-recombination epoch of the early universe\\cite{Stancil1996b}. However, as pointed out in refs 9 and 10, both experimental data and a theoretical description of the ion-atom interaction at low temperatures, reached in these modern atomic physics experiments and the interstellar environment, are still largely missing. Here we observe a chemical reaction between ultracold $^{174}$Yb$^+$ ions and $^{40}$Ca atoms held in a hybrid trap. We me...

  8. Structural and chemical derivatization of graphene for electronics and sensing

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    Graphene - a single atom thick two dimensional sheet of sp 2 bonded carbon atoms arranged in a honeycomb lattice - has shown great promise for both fundamental research & applications because of its unique electrical, optical, thermal, mechanical and chemical properties. Derivatization of graphene unlocks a plethora of novel properties unavailable to their pristine parent "graphene". In this dissertation we have synthesized various structural and chemical derivatives of graphene; characterized them in detail; and leveraged their exotic properties for diverse applications. We have synthesized protein/DNA/ethylenediamine functionalized derivatives of graphene via a HATU catalyzed amide reaction of primary-amine-containing moieties with graphene oxide (GO) -- an oxyfunctional graphene derivative. In contrast to non-specificity of graphene, this functionalization of GO has enabled highly specific interactions with analytes. Devices fabricated from the protein (concanavalin -- A) and DNA functionalized graphene derivatives were demonstrated to enable label-free, specific detection of bacteria and DNA molecules, respectively, with single quanta sensitivity. Room temperature electrical characterization of the sensors showed a generation of ˜ 1400 charge carriers for single bacterium attachment and an increase of 5.6 X 1012 charge carriers / cm2 for attachment of a single complementary strand of DNA. This work has shown for the first time the viability of graphene for bio-electronics and sensing at single quanta level. Taking the bio-interfacing of graphene to the next level, we demonstrate the instantaneous swaddling of a single live bacterium (Bacillus subtilis ) with several hundred sq. micron (˜ 600 mum2) areal protein-functionalized graphene sheets. The atomic impermeability and high yield strength of graphene resulted in hermetic compartmentalization of bacteria. This enabled preservation of the dimensional and topological characteristics of the bacterium against the degrading effects of harsh environments such as the ultrahigh vacuum (˜ 10-5 Torr) and high intensity electron beam (˜ 150 A/cm2) in a transmission electron microscope (TEM) column. While an unwrapped bacterium shrank by ˜ 76% and displayed significant charge buildup in the TEM column; a wrapped bacterium remained uncontracted and undamaged owing to the graphenic wraps. This work has shown for the first time an impermeable graphenic encasement of bacteria and its application in high vacuum TEM imaging without using any lengthy traditional biological TEM sample preparation techniques. In an inch-scale, we fabricated robust free-standing paper composed of TWEEN/Graphene composite which exhibited excellent chemical stability and mechanical strength. This paper displayed excellent biocompatibility towards three mammalian cell lines while inhibiting the non-specific binding of bacteria (Bacillus cereus). We predict this composite and its derivatives to have excellent applications in biomedical engineering for transplant devices, invasive instrument coatings and implants. We also demonstrate a novel, ultra-fast and high yield process for reducing GO to reduced graphene oxide (RGO) using a facile hydride-based chemistry. The RGO sheets thus-produced exhibited high carrier mobilities (˜ 100-600 cm2/V·s) and reinstatement of the ambipolar characteristic of graphene. Raman spectra and UV-Vis spectroscopy on the RGO sheets displayed a high degree of restoration of the crystalline sp2 lattice with relatively low defects. We fabricated graphene nanoribbons (GNRs) -- 1D structural derivatives of graphene -- using a nano-scale cutting process from highly oriented pyrolytic graphite (HOPG) blocks, with widths pre-determinable between 5 nm to 600 nm. The as-produced GNRs had very high aspect ratio in the longitudinal direction (˜ 0.01); exhibited predominantly mono-layered structure (< 10% bilayer); and smooth edges (Raman ID/G ˜ 0.25 -0.28). Low temperature electrical transport measurements on back-gated thin film GNR devices were performed and a ca

  9. 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 stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

  10. Mechanical and structural characterization of atomic layer deposition-based ZnO films

    NASA Astrophysics Data System (ADS)

    Tapily, K.; Gu, D.; Baumgart, H.; Namkoong, G.; Stegall, D.; Elmustafa, A. A.

    2011-11-01

    Zinc oxide thin films were deposited by atomic layer deposition (ALD). The structural and mechanical properties of the thin films were investigated by x-ray diffraction, transmission electron microscopy, atomic force microscopy, and nanoindentation. Diethyl zinc was used as the chemical precursor for zinc and water vapor was used as the oxidation agent. The samples were deposited at 150 °C and at a pressure of 2.1 × 10-1 Torr in the ALD reactor. A growth rate of 2 Å per cycle was calculated in the ALD process window. The Nano Indenter XP was used in conjunction with the continuous stiffness method in depth control mode in order to measure and to analyze the mechanical properties of hardness and modulus of ALD ZnO thin film samples. For comparison, we benchmarked the mechanical properties of single crystal bulk ZnO samples against those of our ALD ZnO thin films.

  11. Confirmation of the Carbon Chemical Shifts of Ethylenic Carbon Atoms in Methyl Ricinoleate and Methyl Ricinelaidate

    Microsoft Academic Search

    A. K. L. Cheng

    1993-01-01

    The carbon chemical shifts of the ethylenic carbon atoms of methyl ricinoleate (12-hydroxy-9-cis-octadecenoate) are 133.32, C-9; 125.28, C-10 and those of methyl ricinelaidate (12-hydroxy-9-trans-octadecenoate) are 134.56, C-9 and 125.97, C-10. The shift values were confirmed by double irradiation (spin decoupling) and H-C COSY nuclear magnetic resonance techique.

  12. 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 (?)-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 ?-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. PMID:25778700

  13. 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.

  14. Chemical shifts of atomic core levels and structure of K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4}, x=0-0.23, solid solutions

    SciTech Connect

    Atuchin, V.V. [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation)]. E-mail: atuchin@thermo.isp.nsc.ru; Alekseeva, O.A. [X-ray Laboratory, Institute of Crystallography, RAS, Moscow 119333 (Russian Federation); Kesler, V.G. [Technical Centre, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Pokrovsky, L.D. [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Sorokina, N.I. [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Voronkova, V.I. [Department of Physics, Moscow State University, Moscow 117234 (Russian Federation)

    2006-08-15

    Antimony-doped K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4}, x=0.23, crystals have been prepared by spontaneous nucleation from the flux in the quaternary system K{sub 2}O-TiO{sub 2}-P{sub 2}O{sub 5}-Sb{sub 2}O{sub 5}. Crystal structure observation with TEM method reveals the presence of superstructure ordering. Core level electronic parameters have been studied by X-ray photoelectron spectroscopy. Strong effect of Sb doping has been detected for inner shells of Ti{sup 4+} ions. Prominent decreasing of the binding energy difference {delta}(O 1s-Ti 2p{sub 3/2}) correlates with the shortening of mean oxide bond length L(Ti-O) at x=0.23 that suggests increased ionicity of Ti-O bonds in K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4} solid solutions.

  15. Ordering of carbon atoms in boron carbide structure

    SciTech Connect

    Ponomarev, V. I., E-mail: i2212@yandex.ru; Kovalev, I. D.; Konovalikhin, S. V.; Vershinnikov, V. I. [Russian Academy of Sciences, Institute of Structural Macrokinetics and Materials Science (Russian Federation)

    2013-05-15

    Boron carbide crystals have been obtained in the entire compositional range according to the phase diagram by self-propagating high-temperature synthesis (SHS). Based on the results of X-ray diffraction investigations, the samples were characterized by the unit-cell metric and reflection half-width in the entire range of carbon concentrations. A significant spread in the boron carbide unit-cell parameters for the same carbon content is found in the data in the literature; this spread contradicts the structural concepts for covalent compounds. The SHS samples have not revealed any significant spread in the unit-cell parameters. Structural analysis suggests that the spread of parameters in the literary data is related to the unique process of ordering of carbon atoms in the boron carbide structure.

  16. GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles.

    PubMed

    Chimichi, Stefano; Boccalini, Marco; Matteucci, Alessandra; Kharlamov, Sergey V; Latypov, Shamil K; Sinyashin, Oleg G

    2010-08-01

    The combined use of two-dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in (13)C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated (15)N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to (13)C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison. PMID:20589725

  17. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

    The manifestation of novel phenomena upon scaling to finite size has inspired a paradigm shift in materials science that takes advantage of the distinctive electrical and physical properties of nanomaterials. Remarkably, the simple honeycomb arrangement of carbon atoms in a single atomic layer has become renowned for exhibiting never-before-seen electronic and physical phenomena. This archetypal 2-dimensional nanomaterial is known as graphene, a single layer of graphite. Early reports in the 1950's eluded to graphene-like nanostructures that were evidenced from exfoliation of oxidized graphite followed by chemical reduction, absorbed carbon on transition metals, and thermal decomposition of SiC. Furthermore, the earliest tight binding approximation calculations in the 1950's held clues that a single-layer of graphite would behave drastically different than bulk graphite. Not until 2004, when Giem and Novoselov first synthesized graphene by mechanical exfoliation from highly-oriented pyrolytic graphite did the field of graphene-based research bloom within the scientific community. Since 2004, the availability and relatively straight forward synthesis of single-layer graphene (SLG) enabled the observation of remarkable phenomena including: massless Dirac fermions, extremely high mobilities of its charge carriers, room temperature half-integer quantum Hall effect, the Rashba effect, and the potential for ballistic conduction over macroscopic distances. These enticing electronic properties produce the drive to study graphene for use in truly nanoscale electrical interconnects, integrated circuits, transparent conducting electrodes, ultra-high frequency transistors, and spintronic devices, just to name a few. Yet, for almost all real world applications graphene will need to be interfaced with other materials, metals, dielectrics, organics, or any combination thereof that in turn are constituted from various inorganic and organic components. Interfacing graphene, a nanomaterial with lateral dimensions in the hundreds of microns if not larger, with a corresponding atomic vertical thickness poses significant difficulties. Graphene's unique structure is dominated by surface area or potentially hybridized interfaces; consequently, the true realization of this remarkable nanomaterial in device constructs relies on engineering graphene interfaces at the surface in order to controllably mold the electronic structure. Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy and the transmission mode analogue scanning transmission X-ray microscopy (STXM) are particularly useful tools to study the unoccupied states of graphene and graphene interfaces. In addition, polarized NEXAFS and STXM studies provide information on surface orientation, bond sterics, and the extent of substrate alignment before and after interfacial hybridization. The work presented in this dissertation is fundamentally informed by NEXAFS and STXM measurements on graphene/metal, graphene/dielectric, and graphene/organic interfaces. We start with a general review of the electronic structure of freestanding graphene and graphene interfaces in Chapter 1. In Chapter 2, we investigate freestanding single-layer graphene via STXM and NEXAFS demonstrating that electronic structure heterogeneities from synthesis and processing are ubiquitous in 2-dimensional graphene. We show the mapping of discrete charge transfer regions as a result of doped impurities that decorate the surfaces of graphene and that transfer processing imparts local electronic corrugations or ripples. In corroboration with density functional theory, definitive assignments to the spectral features, global steric orientations of the localized domains, and quantitative charge transfer schemes are evidenced. In the following chapters, we deliberately (Chapter 3) incorporate substitutional nitrogen into reduced graphene oxide to induce C--N charge redistribution and improve global conductivity, (Chapter 4) fabricate graphene/metal interfaces and metal/graphene/metal sandwich structures evidencing classic

  18. Chemical structure of vanadium-based contact formation on n-AlN

    SciTech Connect

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  19. Accelerating atomic orbital-based electronic structure calculation via pole expansion and selected inversion.

    PubMed

    Lin, Lin; Chen, Mohan; Yang, Chao; He, Lixin

    2013-07-24

    We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellmann-Feynman force and the Pulay force) 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 PEXSI is that it has a computational complexity much lower than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI 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 PEXSI are modest. This even makes it possible to perform Kohn-Sham DFT calculations for 10?000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8, 0) boron nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of the accuracy required in a practical DFT calculation. PMID:23803312

  20. Atomic structure of amorphous particles produced by spark erosion

    NASA Astrophysics Data System (ADS)

    Aur, S.; Egami, T.; Berkowitz, A. E.; Walter, J. L.

    1982-12-01

    The atomic structure of amorphous particles of composition Fe75Si15B10 produced by spark erosion was studied by the energy-dispersive x-ray diffraction technique and was compared to that of the amorphous ribbon of the same composition produced by melt spinning. It was found that the nearest-neighbor Fe-Fe correlation is almost identical for the ribbon and the particles of different sizes, whereas the second peak of the radial distribution function shows considerable differences among the samples. The result is consistent with decreased metal-metalloid compositional short-range order in the particles compared to that in the ribbon sample.

  1. Chemical structure representations and applications in computational toxicity.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2012-01-01

    Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies. PMID:23007430

  2. Measurement of a Large Chemical Reaction Rate between Ultracold Closed-Shell {sup 40}Ca Atoms and Open-Shell {sup 174}Yb{sup +} Ions Held in a Hybrid Atom-Ion Trap

    SciTech Connect

    Rellergert, Wade G.; Sullivan, Scott T.; Chen Kuang; Schowalter, Steven J.; Hudson, Eric R. [Department of Physics and Astronomy, University of California, Los Angeles, California 90095 (United States); Kotochigova, Svetlana; Petrov, Alexander [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States)

    2011-12-09

    Ultracold {sup 174}Yb{sup +} ions and {sup 40}Ca atoms are confined in a hybrid trap. The charge exchange chemical reaction rate constant between these two species is measured and found to be 4 orders of magnitude larger than recent measurements in other heteronuclear systems. The structure of the CaYb{sup +} molecule is determined and used in a calculation that explains the fast chemical reaction as a consequence of strong radiative charge transfer. A possible explanation is offered for the apparent contradiction between typical theoretical predictions and measurements of the radiative association process in this and other recent experiments.

  3. PPM_One: a static protein structure based chemical shift predictor.

    PubMed

    Li, Dawei; Brüschweiler, Rafael

    2015-07-01

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs. PMID:26091586

  4. THE JOURNAL OF CHEMICAL PHYSICS 137, 214302 (2012) Ultrafast probing of ejection dynamics of Rydberg atoms and molecular

    E-print Network

    Neumark, Daniel M.

    2012-01-01

    on a similar time scale as the n = 3 Rydberg atoms. © 2012 American Institute of Physics. [http://dx.doi.org/10THE JOURNAL OF CHEMICAL PHYSICS 137, 214302 (2012) Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets Oliver Bünermann,1

  5. Temperature Dependence in Atom-Surface Scattering Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovoth, Israel

    E-print Network

    Manson, Joseph R.

    Temperature Dependence in Atom-Surface Scattering Eli Pollak Chemical Physics Department, Weizmann measure of the temperature dependence of energy resolved atom-surface scattering spectra measured under conditions of higher translational energies, larger surface temperatures and partic- ularly for heavier mass

  6. 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. PMID:26064629

  7. 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.

  8. Entanglement dynamics of three interacting two-level atoms within a common structured environment

    SciTech Connect

    An, Nguyen Ba; Kim, Jaewan; Kim, Kisik [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Hanoi (Viet Nam) and School of Computational Sciences, Korea Institute for Advanced Study, 207-43 Cheongryangni 2-dong, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of); Department of Physics, Inha University, 253 Yonghyun-Dong, Nam-Gu, Incheon 402-751 (Korea, Republic of)

    2011-08-15

    We derive exact time evolution of three two-level atoms coupled to a common environment. The environment is structured and is modeled by a leaky cavity with Lorentzian spectral density. The atoms are initially prepared in a generalized W state and later on experience pairwise dipole-dipole interactions and couplings to the cavity. We study tripartite disentangling and entangling dynamics as well as protecting bipartite entanglement with both atom-atom interactions and atom-cavity couplings taken simultaneously into account.

  9. Nature of Atomic Bonding and Atomic Structure in the Phase-Change Ge2Sb2Te5 Glass

    NASA Astrophysics Data System (ADS)

    Xu, M.; Cheng, Y. Q.; Sheng, H. W.; Ma, E.

    2009-11-01

    Using electronic structure calculations, we demonstrate a global valence alternation in the amorphous Ge2Sb2Te5, a prototype phase-change alloy for data storage. The resulting p bonding profoundly influences the local atomic structure, leading to right-angle components similar to those in the crystalline counterpart of this chalcogenide glass. The dominance of p bonding is revealed by (i) distributions of the coordination number (CN) and the bond angle, for truly bonded atoms determined based on the electron localization function, and (ii) a direct evaluation of the p (and s) orbital occupation probability for the CN=3 Ge atoms that form 90° bonds with neighbors.

  10. Nature of atomic bonding and atomic structure in the phase-change Ge2Sb2Te5 glass.

    PubMed

    Xu, M; Cheng, Y Q; Sheng, H W; Ma, E

    2009-11-01

    Using electronic structure calculations, we demonstrate a global valence alternation in the amorphous Ge2Sb2Te5, a prototype phase-change alloy for data storage. The resulting p bonding profoundly influences the local atomic structure, leading to right-angle components similar to those in the crystalline counterpart of this chalcogenide glass. The dominance of p bonding is revealed by (i) distributions of the coordination number (CN) and the bond angle, for truly bonded atoms determined based on the electron localization function, and (ii) a direct evaluation of the p (and s) orbital occupation probability for the CN=3 Ge atoms that form 90 degree bonds with neighbors. PMID:20365937

  11. Confluence of structural and chemical biology: plant polyketide synthases as biocatalysts for a bio-based future.

    PubMed

    Stewart, Charles; Vickery, Christopher R; Burkart, Michael D; Noel, Joseph P

    2013-06-01

    Type III plant polyketide synthases (PKSs) biosynthesize a dazzling array of polyphenolic products that serve important roles in both plant and human health. Recent advances in structural characterization of these enzymes and new tools from the field of chemical biology have facilitated exquisite probing of plant PKS iterative catalysis. These tools have also been used to exploit type III PKSs as biocatalysts to generate new chemicals. Going forward, chemical, structural and biochemical analyses will provide an atomic resolution understanding of plant PKSs and will serve as a springboard for bioengineering and scalable production of valuable molecules in vitro, by fermentation and in planta. PMID:23481348

  12. Patents, licensing, and market structure in the chemical industry

    Microsoft Academic Search

    Ashish Arora

    1997-01-01

    The strategies of rent appropriation and industry structure are inter-dependent. How firms use patents depends upon industry structure, and in turn, affects industry structure. In the 19th century, market leaders in the chemical industry combined patents and secrecy to deter entry. Within cartels, patents were used to stabilize cartels and organize technology licensing. The role of patents changed in the

  13. PATENTS, LICENSING, AND MARKET STRUCTURE IN THE CHEMICAL INDUSTRY

    Microsoft Academic Search

    Ashish Arora

    1996-01-01

    The strategies of rent appropriation and market structure are inter- dependent. How firms use patents depends upon industry structure, and in turn, affects industry structure. In the early part of the history of the chemical industry, market leaders combined patents and secrecy to deter entry. Patents were also used to within cartels to organize technology licensing. The role of patents

  14. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  15. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  16. Few-atomic-layered boron carbonitride nanosheets prepared by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Qin, Li; Yu, Jie; Kuang, Shengyong; Xiao, Chang; Bai, Xuedong

    2011-12-01

    Few-atomic-layered boron carbonitride (BCN) nanosheets have been grown on Si substrate by microwave plasma chemical vapor deposition from a gas mixture of CH4-N2-H2-BF3. The grown BCN nanosheets are oriented with their base planes perpendicular to the substrate surface. Ultrathin BCN nanosheets with thickness from 2 to a few atomic layers account for a considerable portion of the products, although many of them have more than 10 layers. Photoluminescence is measured for the BCN nanosheets and intense emission at 3.27 eV with very weak defect-related emission is observed for the nanosheets with the composition of B0.38C0.27N0.35. The present BCN nanosheets are promising for applications in nanoelectronics, catalyst supports, gas adsorption, etc.

  17. Few-atomic-layered boron carbonitride nanosheets prepared by chemical vapor deposition.

    PubMed

    Qin, Li; Yu, Jie; Kuang, Shengyong; Xiao, Chang; Bai, Xuedong

    2012-01-01

    Few-atomic-layered boron carbonitride (BCN) nanosheets have been grown on Si substrate by microwave plasma chemical vapor deposition from a gas mixture of CH(4)-N(2)-H(2)-BF(3). The grown BCN nanosheets are oriented with their base planes perpendicular to the substrate surface. Ultrathin BCN nanosheets with thickness from 2 to a few atomic layers account for a considerable portion of the products, although many of them have more than 10 layers. Photoluminescence is measured for the BCN nanosheets and intense emission at 3.27 eV with very weak defect-related emission is observed for the nanosheets with the composition of B(0.38)C(0.27)N(0.35). The present BCN nanosheets are promising for applications in nanoelectronics, catalyst supports, gas adsorption, etc. PMID:22064967

  18. Quantum simulation of a triatomic chemical reaction with ultracold atoms on a waveguide

    E-print Network

    E. Torrontegui; A. Ruschhaupt; D. Guéry-Odelin; J. G. Muga

    2011-02-23

    We study the scaling and coordinate transformation to physically simulate quantum three-body collinear chemical reactions of the type A+BC $\\rightarrow$ AB+C by the motion of single ultracold atoms or a weakly interacting Bose-Einstein condensate on an $L$-shaped waveguide. As an example we show that the parameters to model the reaction F+HH $\\to$ H+HF with lithium are at reach with current technology. This mapping provides also an inverse scattering tool to find an unknown potential, and a way to transfer the knowledge on molecular reaction dynamics to design beam splitters for cold atoms with control of the channel outcome and vibrational excitation.

  19. The Understanding and Structure Analyzing for Online Handwritten Chemical Formulas

    Microsoft Academic Search

    Xin Wang; Guangshun Shi; Jufeng Yang

    2009-01-01

    In this paper, we propose a novel approach for understanding and analyzing the online handwritten chemical formulas. With the structural characteristics, semantic rules, and more importantly grammatical rules, the analyzing process is divided into 3 levels: formula level, molecule level, and text level. A formal description of the chemical formula based-on the grammatical rules is summed up and applied to

  20. Sensitivity of chemical reaction networks: a structural approach.

    E-print Network

    Fiedler, Bernold

    Sensitivity of chemical reaction networks: a structural approach. 2. Regular monomolecular systems to perturbations of reaction rates in chemical reaction networks. Strong motivation for our study comes from recent For the deceptively innocent case of monomolecular reactions, only, we embark on a systematic mathematical analysis

  1. Chromosome structure investigated with the atomic-force microscope

    NASA Astrophysics Data System (ADS)

    de Grooth, Bart G.; Putman, Constant A.; van der Werf, Kees O.; van Hulst, Niko F.; van Oort, Geeske; Greve, Jan

    1992-05-01

    We have developed an atomic force microscope (AFM) with an integrated optical microscope. The optical microscope consists of an inverted epi-illumination system that yields images in reflection or fluorescence of the sample. With this system it is possible to quickly locate an object of interest. A high-resolution image of the object thus selected can then be obtained with the AFM that is built on top of the optical microscope. In addition, the combined microscopes enable a direct comparison between the optical image and the topography of the same object. The microscope is used to study the structure of metaphase chromosomes of eukaryotic cells. The topography of metaphase chromosomes reveal grooved structures that might indicate spiral structure of the chromatin. High resolution images reveal structures that can be ascribed to the end loops of the chromatin. The resolution of the AFM images was improved by using sharper tips obtained by carbon deposition on the Si3N4 cantilevers using a scanning electron microscope. Chromosomes which are treated to reveal the G- banding pattern in the optical microscope display a similar pattern when viewed with the AFM, as is shown by a direct comparison.

  2. Atomic structure of nanoclusters in oxide-dispersion-strengthened steels

    NASA Astrophysics Data System (ADS)

    Hirata, A.; Fujita, T.; Wen, Y. R.; Schneibel, J. H.; Liu, C. T.; Chen, M. W.

    2011-12-01

    Oxide-dispersion-strengthened steels are the most promising structural materials for next-generation nuclear energy systems because of their excellent resistance to both irradiation damage and high-temperature creep. Although it has been known for a decade that the extraordinary mechanical properties of oxide-dispersion-strengthened steels originate from highly stabilized oxide nanoclusters with a size smaller than 5?nm, the structure of these nanoclusters has not been clarified and remains as one of the most important scientific issues in nuclear materials research. Here we report the atomic-scale characterization of the oxide nanoclusters using state-of-the-art Cs-corrected transmission electron microscopy. This study provides compelling evidence that the nanoclusters have a defective NaCl structure with a high lattice coherency with the bcc steel matrix. Plenty of point defects as well as strong structural affinity of nanoclusters with the steel matrix seem to be the most important reasons for the unusual stability of the clusters at high temperatures and in intensive neutron irradiation fields.

  3. An atomic force microscopy investigation of cyanophage structure.

    PubMed

    Kuznetsov, Yurii G; Chang, Sheng-Chieh; Credaroli, Arielle; Martiny, Jennifer; McPherson, Alexander

    2012-12-01

    Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of some of the different architectures and novel structural features that emerge from even a very limited investigation, one focused on cyanophages, viruses that infect cyanobacteria (blue-green algae). These were isolated by phage selection of viruses collected from California coastal waters. We present AFM images of tailed, spherical, filamentous, rod shaped viruses, and others of eccentric form. Among the tailed phages numerous myoviruses were observed, some having long tail fibers, some other none, and some having no visible baseplate. Syphoviruses and a podovirus were also seen. We also describe a unique structural features found on some tailed marine phages that appear to have no terrestrial homolog. These are long, 450 nm, complex helical tail fibers terminating in a unique pattern of 3+1 globular units made up of about 20 small proteins. PMID:22424715

  4. Physical and chemical evidence for metallofullerenes with metal atoms as part of the cage

    NASA Astrophysics Data System (ADS)

    Clemmer, David E.; Hunter, Joanna M.; Shelimov, Konstantin B.; Jarrold, Martin F.

    1994-11-01

    SINCE the discovery of fullerenes1, efforts have been made to trap metal atoms inside fullerene cages2, and both endohedral3,4 and exohedral5,6 metallofullerenes have been synthesized. There is, however, a third possibility: a 'networked' metallofullerene, where the metal atom is incorporated into the carbon cage. Here we report the results of experiments to study the structure and reactivity of gas-phase fullerenes doped with niobium (NbCn+ with n = 28-50). These experiments, which use injected-ion drift-tube tech-niques, indicate that for fullerenes containing an even number of carbon atoms the metal is endohedral, but for fullerenes with an odd number of carbon atoms, the niobium metal is bound as a part of the carbon cage. Thus, networked metallofullerenes appear to be a stable class of metallofullerene. We suggest that such metallo-fullerenes can form if the metal atom retains sufficient electron density to form several strong covalent metal-carbon bonds.

  5. Note: Mechanically and chemically stable colloidal probes from silica particles for atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Kuznetsov, V.; Papastavrou, G.

    2012-11-01

    In this note we present a novel approach to prepare colloidal probes for atomic force microscopy by sintering. A central element of this procedure is the introduction of an inorganic "fixation neck" between the cantilever and a micrometer-sized silica particle that is acting as probe. This procedure overcomes previous restrictions for the probe particles, which had to be low melting point materials, such as borosilicate glass or latex particles. The here-presented colloidal probes from silica can withstand large mechanical forces. Additionally, they have high chemical resistivity due to the absence of adhesives and the well-studied surface chemistry of colloidal silica.

  6. Note: mechanically and chemically stable colloidal probes from silica particles for atomic force microscopy.

    PubMed

    Kuznetsov, V; Papastavrou, G

    2012-11-01

    In this note we present a novel approach to prepare colloidal probes for atomic force microscopy by sintering. A central element of this procedure is the introduction of an inorganic "fixation neck" between the cantilever and a micrometer-sized silica particle that is acting as probe. This procedure overcomes previous restrictions for the probe particles, which had to be low melting point materials, such as borosilicate glass or latex particles. The here-presented colloidal probes from silica can withstand large mechanical forces. Additionally, they have high chemical resistivity due to the absence of adhesives and the well-studied surface chemistry of colloidal silica. PMID:23206110

  7. Resonance enhanced multiphoton ionization probing of H atoms and CH3 radicals in a hot lament chemical vapour deposition reactor

    E-print Network

    Bristol, University of

    hot ®lament (HF) reactor, or plasma (e.g. microwave) enhanced. The formation of H atoms chemical vapour deposition reactor James A. Smith, Moray A. Cook, Stephen R. Langford, Stephen A. Redman reactor used for diamond chemical vapour deposition (CVD). Parameters varied include the hydrocarbon (CH4

  8. From Petascale to Exascale: Prospects for Transforming Atomic, Molecular, and Chemical Dynamics with Leadership Computing

    NASA Astrophysics Data System (ADS)

    Wells, Jack

    2013-05-01

    Modeling and simulation with petascale computing has supercharged the process of innovation and understanding, dramatically accelerating time-to-insight and time-to-discovery. From petascale modeling of combustion for advanced engines, to designing bio-inspired catalysts for renewable energy, to exploring the evolution of complex systems such as our earth's climate, or breakthroughs gained from quantum many-body applications in chemical and nuclear physics, petascale computing is delivering high impact results that are transforming science and engineering. This presentation will provide an overview of the unique computational resources and user programs at the Oak Ridge Leadership Computing Facility (OLCF) at DOE's Oak Ridge National Laboratory, discuss a range of ambitious computational research projects underway in atomic, molecular, and chemical physics, and discuss scientific opportunities and challenges associated with advancing computational capabilities to the exascale. Modeling and simulation with petascale computing has supercharged the process of innovation and understanding, dramatically accelerating time-to-insight and time-to-discovery. From petascale modeling of combustion for advanced engines, to designing bio-inspired catalysts for renewable energy, to exploring the evolution of complex systems such as our earth's climate, or breakthroughs gained from quantum many-body applications in chemical and nuclear physics, petascale computing is delivering high impact results that are transforming science and engineering. This presentation will provide an overview of the unique computational resources and user programs at the Oak Ridge Leadership Computing Facility (OLCF) at DOE's Oak Ridge National Laboratory, discuss a range of ambitious computational research projects underway in atomic, molecular, and chemical physics, and discuss scientific opportunities and challenges associated with advancing computational capabilities to the exascale. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

  9. Structure Correlation Methods in Chemical Crystallography

    Microsoft Academic Search

    Valeria Ferretti; Paola Gilli; Valerio Bertolasi; Gastone Gilli

    1996-01-01

    The structural information collected by X-ray (or neutron) diffraction studies of metallic, ionic, molecular and macromolecular crystals has increased beyond any previously imagined limit. Data are presently compiled in computer-based crystal structure databases. Making particular reference to molecular crystals, it is shown that the information collected may possess a great heuristic value, that is a great potential for guiding the

  10. Probing interface structure and bonding at atomic resolution by STEM

    SciTech Connect

    Pennycook, S.J.; Browning, N.D.; Jesson, D.E.; Chisholm, M.F.

    1993-06-01

    Advantage of STEM is that no model structures are required to interpret the images to first order, so that unexpected interfacial phenomena will be immediately apparent, such as in CoSi{sub 2}/Si(100) interface made by Co implantation/annealing. By depositing two monolayer Ge marker layers during growth of Si{sub 0. 5}Ge{sub 0.5} alloy layer, a misfit dislocation was found to nucleate to relieve the strain. Hole concentration profiles can be measured in YBCO superconductor, using the pre-edge of the oxygen K EELS spectrum. Future directions of this combination of atomic-resolution imaging and analysis on a single microscope are discussed briefly.

  11. Exafs studies of nanocrystalline materials exhibiting a new solid state structure with randomly arranged atoms

    Microsoft Academic Search

    T. Haubold; R. Birringer; B. Lengeler; H. Gleiter

    1989-01-01

    Nanocrystalline materials are polycrystals with a typical crystallite diameter of 5 to 15 nm. They structurally consist of two components with comparable volume fractions: a crystalline component and a grain boundary component, which is shown by means of EXAFS to exhibit a new solid state structure with random atomic arrangement to exhibit a new solid state structure with random atomic

  12. Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    E-print Network

    Zhang, Jiapu

    2010-01-01

    To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has amyloid fibril forming properties. This region belongs to the N-terminal unstructured region (1-123) of prions, the structure of which has proved hard to determine using NMR or X-ray crystallography. Computational optimization approaches, however, allow us to obtain a description of prion 113-120 peptide at a microscopic level. Zhang (J. Mol. Model., 2010, DOI: 10.1007/s00894-010-0691-y) using the traditional local optimization search steepest descent and conjugate gradient methods hybridized with the standard global optimization search simulated annealing method successfully constructed three atomic-resolution structures of prion AGAAAAGA amyloid fibrils. Zhang pointed out, basing on the NNQNTF peptide of elk prion 173--178 (3FVA.pdb released on 30-JUN-2009 in the Protein Data Bank), new models for prion AGAAAAG...

  13. Unusual DNA structures formed on bare highly oriented pyrolytic graphite surfaces studied by atomic force microscopy.

    PubMed

    Liu, Zhiguo; Zhao, Lin; Zu, Yuangang; Tan, Shengnan; Wang, Yuanlin; Zhang, Yiming

    2013-06-01

    It is important to know the detailed DNA structure on carbonaceous surfaces for further application of DNA-functionalized carbonaceous materials in diverse research areas. In this study, the topographic and structural characteristics of the separated single DNA molecules and their assembly on highly oriented pyrolytic graphite (HOPG) surfaces have been investigated by atomic force microscopy (AFM). AFM results indicate that both circular and linear DNA molecules tend to form hexagonal patterns along with some unusual structures that include node, protrusion, cruciform, parallel single-stranded DNA (ssDNA), and compact zigzag. Furthermore, parallel ssDNA patterns and their crossed structures have been obtained under high-temperature conditions. Our AFM results reveal that a bare HOPG surface can induce DNA molecules to form various unusual structures. This finding is helpful for understanding the adsorption behavior of DNA on other carbonaceous surfaces such as carbon nanotubes and graphene. In addition, the hexagonal DNA patterns in this study are similar to those formed on the alkylamine-modified HOPG surface, which implies that a bare HOPG, without any chemical modification, has a strong ability to align biomolecules. This study could expand our knowledge of the diversities of DNA structures and the aligning ability of carbonaceous surfaces. PMID:23534938

  14. Chemical Stability of Titania and Alumina Thin Films Formed by Atomic Layer Deposition.

    PubMed

    Correa, Gabriela C; Bao, Bo; Strandwitz, Nicholas C

    2015-07-15

    Thin films formed by atomic layer deposition (ALD) are being examined for a variety of chemical protection and diffusion barrier applications, yet their stability in various fluid environments is not well characterized. The chemical stability of titania and alumina thin films in air, 18 M? water, 1 M KCl, 1 M HNO3, 1 M H2SO4, 1 M HCl, 1 M KOH, and mercury was studied. Films were deposited at 150 °C using trimethylaluminum-H2O and tetrakis(dimethylamido)titanium-H2O chemistries for alumina and titania, respectively. A subset of samples were heated to 450 and 900 °C in inert atmosphere. Films were examined using spectroscopic ellipsometry, atomic force microscopy, optical microscopy, scanning electron microscopy, and X-ray diffraction. Notably, alumina samples were found to be unstable in pure water, acid, and basic environments in the as-synthesized state and after 450 °C thermal treatment. In pure water, a dissolution-precipitation mechanism is hypothesized to cause surface roughening. The stability of alumina films was greatly enhanced after annealing at 900 °C in acidic and basic solutions. Titania films were found to be stable in acid after annealing at or above 450 °C. All films showed a composition-independent increase in measured thickness when immersed in mercury. These results provide stability-processing relationships that are important for controlled etching and protective barrier layers. PMID:26107803

  15. Atomic optical clocks and search for variation of the fine-structure constant

    Microsoft Academic Search

    V. A. Dzuba; V. V. Flambaum

    2000-01-01

    Theories unifying gravity and other interactions suggest the possibility of spatial and temporal variations of physical ``constants.'' Accuracy achieved for atomic optical frequency standards (optical clocks) approaches the level when possible time evolution of the fine-structure constant alpha can be studied by comparisons of rates between clocks based on different atomic transitions in different atoms. The sensitivity to variation of

  16. Author's personal copy Lowest-energy structures of 13-atom binary clusters: Do

    E-print Network

    of interest for the well-known fact that the atoms in a close-packed liquid are surrounded on average by 12Author's personal copy Lowest-energy structures of 13-atom binary clusters: Do icosahedral clusters Abstract Although the existence of 13-atom icosahedral clusters in one-component close-packed undercooled

  17. 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 Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectra—atomic energy levels, oscillator strengths, and radiative decay rates—using a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator ?=??. Configuration state functions (CSFs) are linear combinations of Slater determinants of atomic orbitals, and are simultaneous eigenfunctions of the atomic electronic angular momentum operator, J, and the atomic parity operator, P. Approximate atomic state functions (ASFs) are linear combinations of CSFs. A variational functional may be constructed by combining expressions for the energies of one or more ASFs. Average energy level (EAL) functionals are weighted sums of energies of all possible ASFs that may be constructed from a set of CSFs; the number of ASFs is then the same as the number of CSFs. Extended optimal level (EOL) functionals are weighted sums of energies of some subset of ASFs. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Hartree-Fock (MCDHF) equations that define an extremum of the variational functional by the self-consistent-field (SCF) method. Lists of CSFs are generated from a set of reference CSFs and rules for deriving other CSFs from these. Expansion coefficients are obtained using sparse-matrix methods for solving the relativistic configuration interaction (CI) problem. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. Biorthogonal transformation methods are employed so that all matrix elements between CSFs can be evaluated using Racah algebra. Restrictions: The maximum number of radial orbitals is limited to 120 by the packing algorithm used for 32-bit integers. The maximum size of a multiconfiguration (MC) calculation, as measured by the length of the configuration state function (CSF) list, is limited by numerical st

  18. Recent Strategies for Retrieving Chemical Structure Information on the Web.

    ERIC Educational Resources Information Center

    Lo, Mei Ling

    1997-01-01

    Various methods for retrieving chemical structure information on the World Wide Web are discussed. Although graphical plug-in programs provide more search capabilities, users first have to obtain a copy of the programs. Tripos's WebSketch and ACD Interactive Lab adopt a different approach; using JAVA applets, users create and display a structure…

  19. Protein Structures Total Chemical Synthesis and X-ray Crystal

    E-print Network

    Bang, Duhee

    in Scheme 1b. Data for the synthesis of native ubiquitin are shown in Figure 1. The C-terminal peptide and the peptide-a thioesters were prepared by solid-phase peptide synthesis by using manual stepwise BocProtein Structures Total Chemical Synthesis and X-ray Crystal Structure of a Protein Diastereomer

  20. Chemically-selective imaging of brain structures with CARS microscopy

    E-print Network

    Xie, Xiaoliang Sunney

    Chemically-selective imaging of brain structures with CARS microscopy Conor L. Evans1§ , Xiaoyin Xu anti-Stokes Raman scattering (CARS) microscopy to image brain structure and pathology ex vivo. Although. Definitive diagnosis still requires brain biopsy in a significant number of cases. CARS microscopy

  1. Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy

    PubMed Central

    Pennycook, Timothy J.; Jones, Lewys; Pettersson, Henrik; Coelho, João; Canavan, Megan; Mendoza-Sanchez, Beatriz; Nicolosi, Valeria; Nellist, Peter D.

    2014-01-01

    Dynamic processes, such as solid-state chemical reactions and phase changes, are ubiquitous in materials science, and developing a capability to observe the mechanisms of such processes on the atomic scale can offer new insights across a wide range of materials systems. Aberration correction in scanning transmission electron microscopy (STEM) has enabled atomic resolution imaging at significantly reduced beam energies and electron doses. It has also made possible the quantitative determination of the composition and occupancy of atomic columns using the atomic number (Z)-contrast annular dark-field (ADF) imaging available in STEM. Here we combine these benefits to record the motions and quantitative changes in the occupancy of individual atomic columns during a solid-state chemical reaction in manganese oxides. These oxides are of great interest for energy-storage applications such as for electrode materials in pseudocapacitors. We employ rapid scanning in STEM to both drive and directly observe the atomic scale dynamics behind the transformation of Mn3O4 into MnO. The results demonstrate we now have the experimental capability to understand the complex atomic mechanisms involved in phase changes and solid state chemical reactions. PMID:25532123

  2. Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy.

    PubMed

    Pennycook, Timothy J; Jones, Lewys; Pettersson, Henrik; Coelho, João; Canavan, Megan; Mendoza-Sanchez, Beatriz; Nicolosi, Valeria; Nellist, Peter D

    2014-01-01

    Dynamic processes, such as solid-state chemical reactions and phase changes, are ubiquitous in materials science, and developing a capability to observe the mechanisms of such processes on the atomic scale can offer new insights across a wide range of materials systems. Aberration correction in scanning transmission electron microscopy (STEM) has enabled atomic resolution imaging at significantly reduced beam energies and electron doses. It has also made possible the quantitative determination of the composition and occupancy of atomic columns using the atomic number (Z)-contrast annular dark-field (ADF) imaging available in STEM. Here we combine these benefits to record the motions and quantitative changes in the occupancy of individual atomic columns during a solid-state chemical reaction in manganese oxides. These oxides are of great interest for energy-storage applications such as for electrode materials in pseudocapacitors. We employ rapid scanning in STEM to both drive and directly observe the atomic scale dynamics behind the transformation of Mn3O4 into MnO. The results demonstrate we now have the experimental capability to understand the complex atomic mechanisms involved in phase changes and solid state chemical reactions. PMID:25532123

  3. Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy

    NASA Astrophysics Data System (ADS)

    Pennycook, Timothy J.; Jones, Lewys; Pettersson, Henrik; Coelho, João; Canavan, Megan; Mendoza-Sanchez, Beatriz; Nicolosi, Valeria; Nellist, Peter D.

    2014-12-01

    Dynamic processes, such as solid-state chemical reactions and phase changes, are ubiquitous in materials science, and developing a capability to observe the mechanisms of such processes on the atomic scale can offer new insights across a wide range of materials systems. Aberration correction in scanning transmission electron microscopy (STEM) has enabled atomic resolution imaging at significantly reduced beam energies and electron doses. It has also made possible the quantitative determination of the composition and occupancy of atomic columns using the atomic number (Z)-contrast annular dark-field (ADF) imaging available in STEM. Here we combine these benefits to record the motions and quantitative changes in the occupancy of individual atomic columns during a solid-state chemical reaction in manganese oxides. These oxides are of great interest for energy-storage applications such as for electrode materials in pseudocapacitors. We employ rapid scanning in STEM to both drive and directly observe the atomic scale dynamics behind the transformation of Mn3O4 into MnO. The results demonstrate we now have the experimental capability to understand the complex atomic mechanisms involved in phase changes and solid state chemical reactions.

  4. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

    PubMed Central

    2011-01-01

    Background Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations. Results Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest. Conclusions The current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo. PMID:21801404

  5. Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.

    PubMed

    Thaimattam, Ram; Tykarska, Ewa; Bierzynski, Andrzej; Sheldrick, George M; Jaskolski, Mariusz

    2002-09-01

    CMTI-I, a small-protein trypsin inhibitor, has been crystallized as a 4:1 protein-zinc complex. The metal is coordinated in a symmetric tetrahedral fashion by glutamate/glutamic acid side chains. The structure was solved by direct methods in the absence of prior knowledge of the special position metal centre and refined with anisotropic displacement parameters using diffraction data extending to 1.03 A. In the final calculations, the main-chain atoms of low B(eq) values were refined without restraint control. The two molecules in the asymmetric unit have a conformation that is very similar to that reported earlier for CMTI-I in complex with trypsin, despite the Met8Leu mutation of the present variant. The only significant differences are in the enzyme-binding epitope (including the Arg5 residue) and in a higher mobility loop around Glu24. The present crystal structure contains organic solvent molecules (glycerol, MPD) that interact with the inhibitor molecules in an area that is at the enzyme-inhibitor interface in the CMTI-I-trypsin complex. A perfectly ordered residue (Ala18) has an unusual Ramachandran conformation as a result of geometrical strain introduced by the three disulfide bridges that clamp the protein fold. The results confirm deficiencies of some stereochemical restraints, such as peptide planarity or the N-C(alpha)-C angle, and suggest a link between their violations and hydrogen bonding. PMID:12198301

  6. Collagen structure deciphered CAMBRIDGE, Mass.--For the first time, an MIT researcher's atom-by-atom study of the

    E-print Network

    Buehler, Markus J.

    connection between quantum chemistry, molecular structure, material properties and collagen's physiological that begin at the atomistic scale treating individual chemical interactions based on quantum mechanical's work represents a breakthrough in understanding how molecular and tissue properties are linked

  7. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

  8. Frequent Sub-Structure-Based Approaches for Classifying Chemical Compounds

    Microsoft Academic Search

    Mukund Deshpande; Michihiro Kuramochi; George Karypis

    2003-01-01

    In this paper we study the problem of classifying chemical com- pound datasets. We present a sub-structure-based classifica- tion algorithm that decouples the sub-structure discovery pro- cess from the classification model construction and uses frequent subgraph discovery algorithms to find all topological and geo- metric sub-structures present in the dataset. The advantage of our approach is that during classification model

  9. Chemical, structural, and chemical-structural varieties of minerals and once again on ways to rationalize mineralogical nomenclature

    NASA Astrophysics Data System (ADS)

    Bulakh, A. G.

    2008-12-01

    The names of minerals are mostly irrational with respect to their chemical composition and crystal structure. The division of mineral species into structural and chemical-structural subspecies or varieties is proposed to simplify and rationalize mineral nomenclature. Special modifiers could be used and written after the root name of an initial mineral. For example, the eudialyte-group minerals could be divided into eudialyte-(CaMn), -(CaFe), -(MnCa), -(CaSr), and -(CaH) and alluaivite. The format of such modifiers should be a matter of discussion and approval.

  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. Spatially resolved atomic hydrogen concentrations and molecular hydrogen temperature profiles in the chemical-vapor deposition of diamond

    Microsoft Academic Search

    L. L. Connell; J. W. Fleming; H.-N. Chu; D. J. Vestyck; E. Jensen; J. E. Butler

    1995-01-01

    We report here a direct measurement of the spatially resolved atomic hydrogen concentration profiles during hot-filament-assisted chemical-vapor deposition (HFCVD) of diamond films. The ground-state hydrogen (1s 2S1\\/2) atoms generated in this process are monitored by an optical four-wave-mixing technique, third-harmonic generation (THG). For THG, a 364.6 nm dye laser beam is focused into the HFCVD reactor and the third-harmonic radiation

  12. Extracting and connecting chemical structures from text sources using chemicalize.org

    PubMed Central

    2013-01-01

    Background Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Results Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. Conclusion This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and databases, including structure searches in PubChem, InChIKey searches in Google and the chemicalize.org archive. It has the flexibility to extract text from any internal, external or Web source. It synergizes with other open tools and the application is undergoing continued development. It should thus facilitate progress in medicinal chemistry, chemical biology and other bioactive chemistry domains. PMID:23618056

  13. Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

    PubMed

    Stashans, Arvids; Chamba, Gaston; Pinto, Henry

    2008-02-01

    The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. PMID:17654648

  14. Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*,

    E-print Network

    Shull, Kenneth R.

    Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*, Zili Wu, Jianguo Wen ABSTRACT: Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear of the (100), (110), and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has

  15. Quantitative Surface Atomic Structure Analysis by Low-Energy Ion Scattering Spectroscopy (ISS)

    Microsoft Academic Search

    Masakazu Aono; Ryutaro Souda

    1985-01-01

    Surface atomic structure analysis by low-energy ion scattering spectroscopy (ISS) is reviewed, with particular emphasis on quantitative surface atomic structure analysis by ISS. The important differences between ISS and Rutherford backscattering spectroscopy (RBS), some basic characteristics of ISS, a special type of ISS called impact-collision ion scattering spectroscopy (ICISS), and the general features of the shadow cone in the energy

  16. Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-modulated

    E-print Network

    Zhu, Xiangdong

    Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-dimensional nano-structure arrays by passing a pulsed atomic beam through an intensity-modulated continuous of ``cooling'' along the longitudinal direction. This enables fabrication of vertically heterogeneous nano

  17. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    PubMed

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of NMR crystallography applied to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the ?-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

  18. Correlating atomic structure and transport in suspended graphene nanoribbons.

    PubMed

    Qi, Zhengqing John; Rodríguez-Manzo, Julio A; Botello-Méndez, Andrés R; Hong, Sung Ju; Stach, Eric A; Park, Yung Woo; Charlier, Jean-Christophe; Drndi?, Marija; Johnson, A T Charlie

    2014-08-13

    Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (<10 nm). We report on the controlled fabrication of pristine, freestanding GNRs with widths as small as 0.7 nm, paired with simultaneous lattice-resolution imaging and electrical transport characterization, all conducted within an aberration-corrected transmission electron microscope. Few-layer GNRs very frequently formed bonded-bilayers and were remarkably robust, sustaining currents in excess of 1.5 ?A per carbon bond across a 5 atom-wide ribbon. We found that the intrinsic conductance of a sub-10 nm bonded bilayer GNR scaled with width as GBL(w) ? 3/4(e(2)/h)w, where w is the width in nanometers, while a monolayer GNR was roughly five times less conductive. Nanosculpted, crystalline monolayer GNRs exhibited armchair-terminated edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations. PMID:24954396

  19. Correlating Atomic Structure and Transport in Suspended Graphene Nanoribbons

    PubMed Central

    2015-01-01

    Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (<10 nm). We report on the controlled fabrication of pristine, freestanding GNRs with widths as small as 0.7 nm, paired with simultaneous lattice-resolution imaging and electrical transport characterization, all conducted within an aberration-corrected transmission electron microscope. Few-layer GNRs very frequently formed bonded-bilayers and were remarkably robust, sustaining currents in excess of 1.5 ?A per carbon bond across a 5 atom-wide ribbon. We found that the intrinsic conductance of a sub-10 nm bonded bilayer GNR scaled with width as GBL(w) ? 3/4(e2/h)w, where w is the width in nanometers, while a monolayer GNR was roughly five times less conductive. Nanosculpted, crystalline monolayer GNRs exhibited armchair-terminated edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations. PMID:24954396

  20. Lens capsule structure assessed with atomic force microscopy

    PubMed Central

    Sueiras, Vivian M.; Moy, Vincent T.

    2015-01-01

    Purpose To image the ultrastructure of the anterior lens capsule at the nanoscale level using atomic force microscopy (AFM). Methods Experiments were performed on anterior lens capsules maintained in their in situ location surrounding the lens from six human cadavers (donor age range: 44–88 years), four cynomolgus monkeys (Macaca fascicularis age range: 4.83–8.92 years), and seven pigs (<6 months). Hydration of all samples was maintained using Dulbecco’s Modified Eagle Medium (DMEM). Whole lenses were removed from the eye and placed anterior side up in agarose gel before gel hardening where only the posterior half of the lens was contained within the gel. After the gel hardened, the Petri dish was filled with DMEM until the point where the intact lens was fully submerged. AFM was used to image the anterior lens surface in contact mode. An integrated analysis program was used to calculate the interfibrillar spacing, fiber diameter, and surface roughness of the samples. Results The AFM images depict a highly ordered fibrous structure at the surface of the lens capsule in all three species. The interfibrillar spacing for the porcine, cynomolgus monkey, and human lens capsules was 0.68±0.25, 1.80±0.39, and 1.08±0.25 ?m, respectively. In the primate, interfibrillar spacing significantly decreased linearly as a function of age. The fiber diameters ranged from 50 to 950 nm. Comparison of the root mean square (RMS) and average deviation demonstrate that the surface of the porcine lens capsule is the smoothest, and that the human and cynomolgus monkey capsules are significantly rougher. Conclusions AFM was successful in providing high-resolution images of the nanostructure of the lens capsule samples. Species-dependent differences were observed in the overall structure and surface roughness. PMID:25814829

  1. Core-shell photonic band gap structures fabricated using laser-assisted chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Wang, H.; Lu, Y. F.

    2008-01-01

    Laser-assisted chemical vapor deposition (LCVD), in combination with three-dimensional (3D) self-assembly of colloidal silica particles, was used to fabricate 3D core-shell photonic band gap (PBG) structures. Self-assembled multilayer silica particles were formed on silicon substrates using the isothermal heating evaporation approach. A continuous-wave CO2 laser (10.6 ?m wavelength) was used as the energy source in the LCVD to fabricate a silica-core-silicon-shell PBG structure. This technique is capable of fabricating structures with various PBGs by adjusting the silica particle size and Si-shell thickness using different LCVD parameters. This capability enables us to engineer positions and widths of PBGs by flexibly controlling the particle size and shell thicknesses. In the fabricated PBG structures, face-centered cubic structures consist of silica-core-silicon-shell "effective atoms." A series of PBG structures with designed PBGs was obtained under different experimental conditions. Incidence-angle-resolved spectroscopic ellipsometry was used to identify specific PBGs. The refractive indices of the effective atoms with different Si-shell thicknesses were calculated using the Bruggeman composite model. The plain-wave expansion method was used to simulate the photonic dispersion diagrams, which supported the experimental results.

  2. Nanoscale structural order from the atomic pair distribution function (PDF): There's plenty of room in the middle

    SciTech Connect

    Billinge, Simon J.L. [Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027 (United States); Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)], E-mail: sb2896@columbia.edu

    2008-07-15

    Emerging materials of scientific and technological interest are generally complex and often nanostructured: they have atomic orderings that extend on nanometer length-scales. These can be discrete nanoparticles; bulk crystals with nanoscale chemical or displacive order within them; mesoporous materials that are bulk materials containing nanoscale holes; and nanocomposites that are intimate heterogeneous mixtures of nano-sized constituents. As always, a quantitative knowledge of the atomic structure within these materials is a prerequisite to understanding and engineering their properties. Traditional crystallographic methods for obtaining this information break down at the nanoscale, sometimes referred to as 'the nanostructure problem'. We describe here some emerging methods for studying nanoscale structure. We present some examples of recent successes. Finally, we discuss future directions and opportunities and draw attention to limitations and potential problems. -.

  3. Role of chemical potential in relaxation of faceted crystal structure.

    PubMed

    Schneider, Joshua P; Nakamura, Kanna; Margetis, Dionisios

    2014-06-01

    Below the roughening transition, crystal surfaces have macroscopic plateaus, facets, whose evolution is driven by the microscale dynamics of steps. A long-standing puzzle was how to reconcile discrete effects in facet motion with fully continuum approaches. We propose a resolution of this issue via connecting, through a jump condition, the continuum-scale surface chemical potential away from the facet, characterized by variations of the continuum surface free energy, with a chemical potential originating from the decay of atomic steps on top of the facet. The proposed condition accounts for step flow inside a discrete boundary layer near the facet. To validate this approach, we implement in a radial geometry a hybrid discrete-continuum scheme in which the continuum theory is coupled with only a few, minimally three, steps in diffusion-limited kinetics with conical initial data. PMID:25019795

  4. Role of chemical potential in relaxation of faceted crystal structure

    NASA Astrophysics Data System (ADS)

    Schneider, Joshua P.; Nakamura, Kanna; Margetis, Dionisios

    2014-06-01

    Below the roughening transition, crystal surfaces have macroscopic plateaus, facets, whose evolution is driven by the microscale dynamics of steps. A long-standing puzzle was how to reconcile discrete effects in facet motion with fully continuum approaches. We propose a resolution of this issue via connecting, through a jump condition, the continuum-scale surface chemical potential away from the facet, characterized by variations of the continuum surface free energy, with a chemical potential originating from the decay of atomic steps on top of the facet. The proposed condition accounts for step flow inside a discrete boundary layer near the facet. To validate this approach, we implement in a radial geometry a hybrid discrete-continuum scheme in which the continuum theory is coupled with only a few, minimally three, steps in diffusion-limited kinetics with conical initial data.

  5. FAST TRACK COMMUNICATION: Finding the atomic configuration with a required physical property in multi-atom structures

    Microsoft Academic Search

    Mayeul d’Avezac; Alex Zunger

    2007-01-01

    In many problems in molecular and solid state structures one seeks to determine the energy-minimizing decoration of sites with different atom types. In other problems, one is interested in finding a decoration with a target physical property (e.g. alloy band gap) within a certain range. In both cases, the sheer size of the configurational space can be horrendous. We present

  6. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Zhong, Cheng; Douglas, Jack F.; Wang, Xiaodong; Cao, Qingping; Zhang, Dongxian; Jiang, Jian-Zhong

    2015-04-01

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ?Ga with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time ?? can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

  7. Analysis of Nanometer Structure for Chromium Atoms in Gauss Standing Laser Wave

    NASA Astrophysics Data System (ADS)

    Zhang, Wen-Tao; Zhu, Bao-Hua; Xiong, Xian-Ming

    2010-12-01

    The equation of motion of two-level chromium atoms in Gauss standing laser wave is discussed and the distribution of chromium atoms is given under different transverse velocity conditions. The results show that the focusing position of atoms will be affected by the transverse velocity of atoms. Based on the four-order Runge-Kutta method, the locus of chromium atoms in Gauss standing laser wave is simulated. The three-dimensional characteristics of nanometer structures are stimulated under perfect and emanative conditions.

  8. Chemical force microscopy of microcontact-printed self-assembled monolayers by pulsed-force-mode atomic force microscopy

    Microsoft Academic Search

    Yoh Okabe; Manabu Furugori; Yuki Tani; Uichi Akiba; Masamichi Fujihira

    2000-01-01

    A novel chemically sensitive imaging mode based on adhesive force detection by previously developed pulsed-force-mode atomic force microscopy (PFM-AFM) is presented. PFM-AFM enables simultaneous imaging of surface topography and adhesive force between tip and sample surfaces. Since the adhesive forces are directly related to interaction between chemical functional groups on tip and sample surfaces, we combined the adhesive force mapping

  9. Atomic structure of Au-nanoparticles on silica support by X-ray PDF study

    SciTech Connect

    Dmowski, W. [University of Tennessee, Knoxville (UTK); Yin, Hongfeng [ORNL; Dai, Sheng [ORNL; Overbury, Steven {Steve} H [ORNL; Egami, T. [University of Tennessee, Knoxville (UTK)

    2010-01-01

    We investigated the atomic structure of gold nanoparticles with an average size of 5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

  10. Atomic Structure of Au Nanoparticles on a Silica Support by an X-ray PDF Study

    SciTech Connect

    Dmowski, Wojtek; Yin, Hongfeng; Dai, Sheng; Overbury, Steven H.; Egami, Takeshi (Tennessee-K); (ORNL)

    2010-05-04

    We investigated the atomic structure of gold nanoparticles with an average size of {approx}5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

  11. Improved atomic force microscope infrared spectroscopy for rapid nanometer-scale chemical identification.

    PubMed

    Cho, Hanna; Felts, Jonathan R; Yu, Min-Feng; Bergman, Lawrence A; Vakakis, Alexander F; King, William P

    2013-11-01

    Atomic force microscope infrared spectroscopy (AFM-IR) can perform IR spectroscopic chemical identification with sub-100 nm spatial resolution, but is relatively slow due to its low signal-to-noise ratio (SNR). In AFM-IR, tunable IR laser light is incident upon a sample, which results in a rise in temperature and thermomechanical expansion of the sample. An AFM tip in contact with the sample senses this nanometer-scale photothermal expansion. The tip motion induces cantilever vibrations, which are measured either in terms of the peak-to-peak amplitude of time-domain data or the integrated magnitude of frequency-domain data. Using a continuous Morlet wavelet transform to the cantilever dynamic response, we show that the cantilever dynamics during AFM-IR vary as a function of both time and frequency. Based on the observed cantilever response, we tailor a time-frequency-domain filter to identify the region of highest vibrational energy. This approach can increase the SNR of the AFM cantilever signal, such that the throughput is increased 32-fold compared to state-of-the art procedures. We further demonstrate significant increases in AFM-IR imaging speed and chemical identification of nanometer-scale domains in polymer films. PMID:24113150

  12. Heavy atom tunneling in chemical reactions: Study of H +LiF collisions

    NASA Astrophysics Data System (ADS)

    Weck, P. F.; Balakrishnan, N.

    2005-06-01

    The H +LiF(X?+1,?=0-2,j=0)?HF(X?+1,?',j')+Li(S2) bimolecular process is investigated by means of quantum scattering calculations on the chemically accurate XA'2 LiHF potential energy surface of Aguado et al. [A. Aguado, M. Paniagua, C. Sanz, and J. Roncero, J. Chem. Phys. 119, 10088 (2003)]. Calculations have been performed for zero total angular momentum for translational energies from 10-7 to 10-1eV. Initial-state selected reaction probabilities and cross sections are characterized by resonances originating from the decay of metastable states of the H⋯F-Li and Li⋯F-H van der Waals complexes. Extensive assignment of the resonances has been carried out by performing quasibound states calculations in the entrance and exit channel wells. Chemical reactivity is found to be significantly enhanced by vibrational excitation at low temperatures, although reactivity appears much less favorable than nonreactive processes due to the inefficient tunneling of the relatively heavy fluorine atom strongly bound in van der Waals complexes.

  13. Relating Chemical Activity to Structure: An Examination of ILP Successes

    Microsoft Academic Search

    Ross D. King; Michael J. E. Sternberg; Ashwin Srinivasan

    1995-01-01

    An important test-bed for Inductive Logic Programming (ILP) systemshas been the task of relating the activity of chemical compounds totheir structure. In this paper we examine the structure-activity problemsthat have been addressed by ILP, and evaluate empirically the extent towhich a first-order representation was required. This is done by comparingILP theories against those constructed by standard linear regressionand a decision-tree

  14. The bulk and interfacial electronic and chemical structure of amorphous hydrogenated boron carbide

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

    The chemical and electronic structure, as related to the surface, interface and bulk of amorphous hydrogenated boron carbide (a-BxC:H y), is of interest in neutron detection and microelectronics. This dissertation investigates the chemical and electronic structure of semiconducting thin-film a-BxC:Hy grown by plasma enhanced chemical vapor deposition (PECVD) of ortho-carborane (1,2-C2B10H12). Experimental methods used include: x-ray and ultraviolet photoelectron spectroscopies (XPS/UPS) and x-ray absorption/emission spectroscopies (XAS/XES). These methods were used to investigate the chemical species, bonding and hybridizations, and band gaps of a-BxC:Hy prepared or treated under varying conditions. Additionally, a detailed examination of the formation of Schottky barriers was implemented. Throughout this dissertation the chemical structure was studied. One study was to understand various growth conditions. The effects of the PECVD growth parameters were evaluated by comparing changes in atomic percentages (at.%'s) between thin-films from various substrate temperatures. Additionally, detailed studies of the photoelectron core level under two different growth conditions were undertaken to evaluate the effects of pre-/post- argon ion etching (Ar+) for the following: the chemical structural change for both an as grown (AG) and in-situ thermal treatment (500°C), and post Ar+ etch of samples thermally treated ranging from as grown to 850°C. The as grown and in-situ treated samples were used in conjunction to determine the formation of the Schottky barrier. The electronic structure was determined by the changes within the valence band of the thermally treated samples and formation of Schottky barrier. Thermally treated samples (as grown to 850°C) were further evaluated with respect to their occupied and unoccupied electronic states. The atomic percentage gave a stoichiometry range for a-B xC:Hy (given as x=1.5 to 3.0 with y= decreases with thermal treatment and Oz: z= 0.2 to 0.5). Studies of films with respect to thermal treatment reveal two discrete state changes that occur at 400°C and 850°C These changes are due to segregation of carbon and oxygen by the reorganization of the hydrocarbon chains between icosahedra. Additionally, the Schottky barrier study indicates that a clean surface was necessary before deposition of an ohmic contact and from the metals studied. Such studies are important to applications for high temperature thermoelectric converters, high-efficiency direct-conversion solid-state neutron detectors and microelectronics.

  15. Data quality in predictive toxicology: identification of chemical structures and calculation of chemical properties.

    PubMed Central

    Helma, C; Kramer, S; Pfahringer, B; Gottmann, E

    2000-01-01

    Every technique for toxicity prediction and for the detection of structure-activity relationships relies on the accurate estimation and representation of chemical and toxicologic properties. In this paper we discuss the potential sources of errors associated with the identification of compounds, the representation of their structures, and the calculation of chemical descriptors. It is based on a case study where machine learning techniques were applied to data from noncongeneric compounds and a complex toxicologic end point (carcinogenicity). We propose methods applicable to the routine quality control of large chemical datasets, but our main intention is to raise awareness about this topic and to open a discussion about quality assurance in predictive toxicology. The accuracy and reproducibility of toxicity data will be reported in another paper. PMID:11102292

  16. The hydrodynamics of drop impact onto chemically structured surfaces

    Microsoft Academic Search

    T. Michel; U. Mock; I. V. Roisman; J. Rühe; C. Tropea

    2005-01-01

    The normal and inclined impact of liquid drops onto chemically structured surfaces has been studied experimentally and theoretically. The surface functionalization comprised a self-assembly process of a covalently bound monochlorosilane on a silicon substrate, followed by a photochemical attachment of a polymer of defined hydrophilicity and a subsequent deep UV ablation step to create a local spot of high wettability

  17. Effect of Chemical Structure on Elastohydrodynamic Traction Coefficient

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The elastohydrodynamic traction properties of a series of biobased and petroleum based oils of varying chemical structures in steel-steel contact were investigated. Traction was measured on a ball-on disk type elastohydrodynamic traction instrument. Elastohydrodynamic traction coefficient (tc) was m...

  18. Predicting Modes of Toxic Action from Chemical Structure: An Overview

    Microsoft Academic Search

    S. P. Bradbury

    1994-01-01

    In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARs) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. A basic and fundamental understanding of toxicological principles has been considered crucial to the continued acceptance and application of these techniques as biologically relevant. As a

  19. Chemical probing of RNA with the hydroxyl radical at single-atom resolution

    PubMed Central

    Ingle, Shakti; Azad, Robert N.; Jain, Swapan S.; Tullius, Thomas D.

    2014-01-01

    While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5?-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5?-aldehyde. We conclude that hydroxyl radical abstracts a 5?-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5? deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2?-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple. PMID:25313156

  20. Heterocrystal and bicrystal structures of ZnS nanowires synthesized by plasma enhanced chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Jie, J. S.; Zhang, W. J.; Jiang, Y.; Meng, X. M.; Zapien, J. A.; Shao, M. W.; Lee, S. T.

    2006-06-01

    ZnS nanowires with heterocrystal and bicrystal structures were successfully synthesized using the DC-plasma chemical vapour deposition (CVD) method. The heterocrystalline ZnS nanowires have the zinc blende (ZB) and wurtzite (WZ) zones aligned alternately in the transverse direction but without an obvious period. The bicrystal ZnS nanowires are composed of two ZB fractions separated by a clear grain boundary along the length. Significantly, the grain boundaries in both the heterocrystal and bicrystal structures are atomically sharp without any visible lattice distortion. The effects of plasma species, ion bombardment, and silicon impurities in the formation of these distinctive structures are discussed. A defect-induced red-shift and broadening of the band-gap emission are revealed in photoluminescence (PL) and cathodoluminescence (CL) measurements.

  1. Learning about Atoms, Molecules, and Chemical Bonds: A Case Study of Multiple-Model Use in Grade 11 Chemistry.

    ERIC Educational Resources Information Center

    Harrison, Allan G.; Treagust, David F.

    2000-01-01

    Reports in detail on a year-long case study of multiple-model use at grade 11. Suggests that students who socially negotiated the shared and unshared attributes of common analogical models for atoms, molecules, and chemical bonds used these models more consistently in their explanations. (Author/CCM)

  2. Chemical characterisation of ancient pottery from south of Italy by Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES)

    Microsoft Academic Search

    P Bruno; M Caselli; M. L Curri; A Genga; R Striccoli; A Traini

    2000-01-01

    Chemical characterisation has been carried out on 58 fragments of archaeological pottery from pre-classical sites in Apulia and Lucania, regions in southern Italy. Fourteen elements were determined by atomic emission spectroscopy by using inductively coupled plasma source. Statistical techniques, such as principal component analysis and clustering analysis, have been utilised to define grouping of different pottery items. Tests performed showed

  3. THE JOURNAL OF CHEMICAL PHYSICS 135, 054705 (2011) Atomic imaging of nucleation of trimethylaluminum on clean and H2O

    E-print Network

    Kummel, Andrew C.

    2011-01-01

    THE JOURNAL OF CHEMICAL PHYSICS 135, 054705 (2011) Atomic imaging of nucleation August 2011) The direct reaction of trimethylaluminum (TMA) on a Ge(100) surface and the effects­17 The lowest interface trap densities have been obtained using a stoichiometric GeO2 layer typically formed

  4. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    SciTech Connect

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

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

    SciTech Connect

    Silva, Piotr de, E-mail: piotr.desilva@unige.ch [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland); Korchowiec, Jacek [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland)] [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Wesolowski, Tomasz A. [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)] [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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.

  7. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  8. Intermixing and chemical structure at the interface between n-GaN and V-based contacts

    SciTech Connect

    Pookpanratana, S.; France, R.; Bar, M.; Weinhardt, L.; Fuchs, O.; Blum, M.; Yang, W.; Denlinger, J. D.; Moustakas, T. D.; Heske, C.

    2008-06-30

    The interface between n-type GaN and V-based contacts was characterized by soft x-ray spectroscopy. We have investigated the chemical interface structure before and after a rapid thermal annealing (RTA) step, which is crucial for the formation of an Ohmic contact. X-ray photoelectron and x-ray excited Auger electron spectra suggestthat RTA induces an accumulation of metallic Ga at the surface. Using x-ray emission spectroscopy, we find that the probed nitrogen atoms are in a VN-like environment, indicating that vanadium interacts with nitrogen atoms from the GaN to form VN.

  9. Structural properties of ZnS\\/GaAs epilayers grown by atomic-layer epitaxy

    Microsoft Academic Search

    Y. G. Kim; Y. S. Nam; K. S. Baek; S. K. Chang

    2009-01-01

    ZnS epilayers were grown on (100) semi-insulating GaAs substrates using an atmospheric pressure metal-organic chemical vapor deposition (CVD) technique under the atomic-layer epitaxy (ALE) mode. Atomic force microscopy (AFM) and photoluminescence (PL) measurements were carried out to find the effect of the II–VI ratio of the 30-nm thick ZnS epilayers and to investigate the thickness-dependent characteristics of ZnS epilayers with

  10. Precise Atomic Structure Measurements in Thallium at 378 nm using a Frequency-doubled Diode Laser

    Microsoft Academic Search

    Protik Majumder; Robert Lyman; Paul Friedberg; David Richardson

    2001-01-01

    Using both a heated thallium vapor cell and a recently constructed atomic beam apparatus, we have undertaken a series of precise atomic structure measurements within the 378 nm 6P_1\\/2 - 7S_1\\/2 E1 transition in atomic thallium. These measurements provide important, independent cross-checks on the accuracy of ongoing calculations of parity nonconservation in thallium. For these experiments, we use an external

  11. Mössbauer spectroscopy and the structure of interfaces on the atomic scale in metallic nanosystems

    Microsoft Academic Search

    V. M. Uzdin

    2007-01-01

    A microscopic model of the formation of an alloy on the interface has been constructed, which takes into account the exchange\\u000a of atoms with the substrate atoms and the “floating up” of the latter into the upper layers in the process of epitaxial growth.\\u000a The self-consistent calculations of atomic magnetic moments of spatially inhomogeneous structures obtained in this case are

  12. Atomic structure of defects in anion-deficient perovskite-based ferrites with a crystallographic shear structure.

    PubMed

    Batuk, Maria; Turner, Stuart; Abakumov, Artem M; Batuk, Dmitry; Hadermann, Joke; Van Tendeloo, Gustaaf

    2014-02-17

    Crystallographic shear (CS) planes provide a new structure-generation mechanism in the anion-deficient perovskites containing lone-pair cations. Pb2Sr2Bi2Fe6O16, a new n = 6 representative of the A(n)B(n)O(3n-2) homologous series of the perovskite-based ferrites with the CS structure, has been synthesized using the solid-state technique. The structure is built of perovskite blocks with a thickness of four FeO6 octahedra spaced by double columns of FeO5 edge-sharing distorted tetragonal pyramids, forming 1/2[110](101)p CS planes (space group Pnma, a = 5.6690(2) Å, b = 3.9108(1) Å, c = 32.643(1) Å). Pb2Sr2Bi2Fe6O16 features a wealth of microstructural phenomena caused by the flexibility of the CS planes due to the variable ratio and length of the constituting fragments with {101}p and {001}p orientation. This leads to the formation of "waves", "hairpins", "?-shaped" defects, and inclusions of the hitherto unknown layered anion-deficient perovskites Bi2(Sr,Pb)Fe3O8.5 and Bi3(Sr,Pb)Fe4O11.5. Using a combination of diffraction, imaging, and spectroscopic transmission electron microscopy techniques this complex microstructure was fully characterized, including direct determination of positions, chemical composition, and coordination number of individual atomic species. The complex defect structure makes these perovskites particularly similar to the CS structures in ReO3-type oxides. The flexibility of the CS planes appears to be a specific feature of the Sr-based system, related to the geometric match between the SrO perovskite layers and the {100}p segments of the CS planes. PMID:24479580

  13. Structure of adsorbed monolayers. The surface chemical bond

    SciTech Connect

    Somorjai, G.A.; Bent, B.E.

    1984-06-01

    This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table.

  14. Atomic structure and magnetic properties of Fe1-xCox alloys

    SciTech Connect

    Nguyen, Manh Cuong; Zhao, Xin; Ji, Min; Wang, Cai-Zhuang; Harmon, Bruce; Ho, Kai-Ming

    2012-03-09

    Using genetic algorithm with first-principle calculations, we searched for low-energy crystal structures of Fe1?xCox alloys. We found that Fe1?xCox alloys are highly configurationally degenerate with many additional off-stoichiometric stable structures to the well-known B2 structure. The average magnetic moment of Fe atom increases with concentration of Co in the alloy, while that of Co atom is almost constant, which are consistent with experiments and earlier studies. The magnetic moment of Fe atom is strongly dependent on the number of Co nearest neighbor and it increases with this number.

  15. Atomic-Scale Chemical Imaging of Composition and Bonding at Perovskite Oxide Interfaces

    NASA Astrophysics Data System (ADS)

    Fitting Kourkoutis, L.

    2010-03-01

    Scanning transmission electron microscopy (STEM) in combination with electron energy loss spectroscopy (EELS) has proven to be a powerful technique to study buried perovskite oxide heterointerfaces. With the recent addition of 3^rd order and now 5^th order aberration correction, which provides a factor of 100x increase in signal over an uncorrected system, we are now able to record 2D maps of composition and bonding of oxide interfaces at atomic resolution [1]. Here, we present studies of the microscopic structure of oxide/oxide multilayers and heterostructures by STEM in combination with EELS and its effect on the properties of the film. Using atomic-resolution spectroscopic imaging we show that the degradation of the magnetic and transport properties of La0.7Sr0.3MnO3/SrTiO3 multilayers correlates with atomic intermixing at the interfaces and the presence of extended defects in the La0.7Sr0.3MnO3 layers. When these defects are eliminated, metallic ferromagnetism at room temperature can be stabilized in 5 unit cell thick manganite layers, almost 40% thinner than the previously reported critical thickness of 3-5 nm for sustaining metallic ferromagnetism below Tc in La0.7Sr0.3MnO3 thin films grown on SrTiO3.[4pt] [1] D.A. Muller, L. Fitting Kourkoutis, M. Murfitt, J.H. Song, H.Y. Hwang, J. Silcox, N. Dellby, O.L. Krivanek, Science 319, 1073-1076 (2008).

  16. Ultrafast electron diffraction and direct observation of transient structures in a chemical reaction.

    PubMed

    Cao, J; Ihee, H; Zewail, A H

    1999-01-19

    Ultrafast electron diffraction is a unique method for the studies of structural changes of complex molecular systems. In this contribution, we report direct ultrafast electron diffraction study of the evolution of short-lived intermediates in the course of a chemical change. Specifically, we observe the transient intermediate in the elimination reaction of 1,2-diiodotetrafluoroethane (C2F4I2) to produce the corresponding ethylene derivative by the breakage of two carbon-iodine, C---I, bonds. The evolution of the ground-state intermediate (C2F4I radical) is directly revealed in the population change of a single chemical bond, namely the second C---I bond. The elimination of two iodine atoms was shown to be nonconcerted, with reaction time of the second C---I bond breakage being 17 +/- 2 ps. The structure of the short-lived C2F4I radical is more favorable to the classical radical structure than to the bridged radical structure. This leap in our ability to record structural changes on the ps and shorter time scales bodes well for many future applications in complex molecular systems. PMID:9892634

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

    PubMed Central

    Tan, J.; Wang, G.; Liu, Z. Y.; Bednar?ík, J.; Gao, Y. L.; Zhai, Q. J.; Mattern, N.; Eckert, J.

    2014-01-01

    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. PMID:24469299

  18. Investigation of plasma-doped fin structure and characterization of dopants by atom probe tomography

    SciTech Connect

    Kim, B. H.; Park, S. M. [Department of Materials Science and Engineering, POSTECH, Pohang (Korea, Republic of); Park, S. W.; Park, Y. B.; Kim, H. J. [Research and Development Division, SK Hynix, 2091, Gyeongchung-daero, Bubal-eub, Ichon-si, Gyeonggi-do (Korea, Republic of); Park, C. G. [Department of Materials Science and Engineering, POSTECH, Pohang (Korea, Republic of); National Center for Nanomaterials Technology (NCNT), Pohang 790-784 (Korea, Republic of)

    2012-11-19

    As and P dopants in a plasma-doped Si-based fin structure were analyzed using atom probe tomography. The distributions and concentrations of As and P atoms in various regions of the fin structure and the oxidation levels for different dopants were determined. Most dopants were segregated at the fin boundary, and the As and P concentrations exceeded 9 Multiplication-Sign 10{sup 20} atoms/cm{sup 3} and 2 Multiplication-Sign 10{sup 20} atoms/cm{sup 3}, respectively. The atomic oxygen and SiO{sub 2} concentrations depended on the dopant type. The larger and heavier As dopant severely damaged the surface of the fin structure and could cause more severe oxidation.

  19. Racing Carbon Atoms. Atomic Motion Reaction Coordinates and Structural Effects on Newtonian Kinetic Isotope Effects

    PubMed Central

    Andujar-De Sanctis, Ivonne L.

    2012-01-01

    Intramolecular 13C 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. PMID:23025278

  20. Atomic structure of {\\\\{112\\\\} Sigma = 3} twin boundary in beta SiC

    Microsoft Academic Search

    C. Ragaru; M. Lancin; C. Godon

    1999-01-01

    We study the atomic structure of \\\\{112\\\\} Sigma = 3 twin boundaries consisting of a stacking of six \\\\{111\\\\} planes and characterized by a resulting Burger vector equal to zero. The twins were imaged by HRTEM. We develop image processing to localize the silicon and carbon atoms in each grain and thus to deduce their stacking and to calculate the

  1. Structures of ultra-thin atomic-layer-deposited TaNx films

    Microsoft Academic Search

    Y. Y. Wu; A. Kohn; M. Eizenberg

    2004-01-01

    Atomic layer deposition (ALD) is an attractive technique in fabrication of microelectronics presently and in the future, for its accurate thickness control in atomic scale, excellent conformality, and uniformity over large areas at low temperature. It has been adapted and used in deposition of ultrathin TaNx films as diffusion barriers for Cu metallization. In this study, composition, structure, and stability

  2. Hyperfine Structures of Silver and Gold by the Atomic Beam Magnetic Resonance Method

    Microsoft Academic Search

    Günter Wessel; Hin Lew

    1953-01-01

    An ionizer of the electron bombardment type has been applied to a beam of atoms in a magnetic resonance apparatus. The ionization efficiency for potassium atoms has been found to be 1 part in 3000. The new ionizer has made it possible to study the hyperfine structures and the g factors of the ground states of silver and gold, two

  3. Conductivity of DNA probed by conducting-atomic force microscopy: effects of contact electrode, DNA structure,

    E-print Network

    Boyer, Edmond

    - 1 - Conductivity of DNA probed by conducting-atomic force microscopy: effects of contact electrode, DNA structure, surface interactions Thomas Heim, Dominique Deresmes and Dominique Vuillaumea.fr #12;- 2 - Abstract We studied the electrical conductivity of DNA molecules with conducting atomic

  4. Characterization of chemically and enzymatically treated hemp fibres using atomic force microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    George, Michael; Mussone, Paolo G.; Abboud, Zeinab; Bressler, David C.

    2014-09-01

    The mechanical and moisture resistance properties of natural fibre reinforced composites are dependent on the adhesion between the matrix of choice and the fibre. The main goal of this study was to investigate the effect of NaOH swelling of hemp fibres prior to enzymatic treatment and a novel chemical sulfonic acid method on the physical properties of hemp fibres. The colloidal properties of treated hemp fibres were studied exclusively using an atomic force microscope. AFM imaging in tapping mode revealed that each treatment rendered the surface topography of the hemp fibres clean and exposed the individual fibre bundles. Hemp fibres treated with laccase had no effect on the surface adhesion forces measured. Interestingly, mercerization prior to xylanase + cellulase and laccase treatments resulted in greater enzyme access evident in the increased adhesion force measurements. Hemp fibres treated with sulfonic acid showed an increase in surface de-fibrillation and smoothness. A decrease in adhesion forces for 4-aminotoulene-3-sulfonic acid (AT3S) treated fibres suggested a reduction in surface polarity. This work demonstrated that AFM can be used as a tool to estimate the surface forces and roughness for modified fibres and that enzymatic coupled with chemical methods can be used to improve the surface properties of natural fibres for composite applications. Further, this work is one of the first that offers some insight into the effect of mercerization prior to enzymes and the effect on the surface topography. AFM will be used to selectively screen treated fibres for composite applications based on the adhesion forces associated with the colloidal interface between the AFM tip and the fibre surfaces.

  5. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13C? and 15N (peptide backbone) groups in a protein, the ?1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13C? and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13C?. The orientations of the 13C? CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in ?-helical versus ?-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13C? CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 ? (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 ? agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-? crystal structures, based upon empirical metrics such as Ramachandran geometries and ?1/?2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  6. Atomic and electronic structure of bismuth-bilayer-terminated Bi2Se3 (0001) prepared by atomic hydrogen etching

    NASA Astrophysics Data System (ADS)

    Shokri, Roozbeh; Meyerheim, Holger L.; Roy, Sumalay; Mohseni, Katayoon; Ernst, A.; Otrokov, M. M.; Chulkov, E. V.; Kirschner, J.

    2015-05-01

    A bilayer of bismuth is recognized as a prototype two-dimensional topological insulator. Here we present a simple and well reproducible top-down approach to prepare a flat and well ordered bismuth bilayer with a lateral size of several hundred nanometers on Bi2Se3 (0001). Using scanning tunneling microscopy, surface x-ray diffraction, and Auger electron spectroscopy we show that exposure of Bi2Se3 (0001) to atomic hydrogen completely removes selenium from the top quintuple layer. The band structure of the system, calculated from first principles for the experimentally derived atomic structure, is in excellent agreement with recent photoemission data. Our results open interesting perspectives for the study of topological insulators in general.

  7. Structural Characterization of Micromechanical Properties in Asphalt Using Atomic Force Microscopy 

    E-print Network

    Allen, Robert Grover

    2012-02-14

    The purpose of this study was to characterize the micromechanical properties of various structural components in asphalt using Atomic Force Microscopy (AFM). The focus of the study was based on nano-indentation experiments ...

  8. Electronic and chemical structure of metal-silicon interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, P. J.; Grunthaner, F. J.

    1984-01-01

    This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

  9. Unique structure\\/properties of chemical vapor deposited parylene E

    Microsoft Academic Search

    Jay J. Senkevich; Christopher J. Mitchell; Aravind Vijayaraghavan; Edward V. Barnat; John F. McDonald; Toh-Ming Lu

    2002-01-01

    Parylene E, a low kappa polymer thin film, with the approximate composition 69% diethylated and 25% monoethylated poly(p-xylylene), has been chemical vapor deposited via a cyclophane precursor at room temperature. It has a dielectric constant of 2.34plus-or-minus0.03 and dielectric loss of <0.005 at 10 kHz from MIMCAP structures. It is particularly unique compared to the other common parylene polymers. Namely,

  10. Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii (abstract)

    NASA Astrophysics Data System (ADS)

    Heyrovska, Raji; Narayan, Sara

    2009-04-01

    We have shown in recent years that interatomic and interionic distances are sums of the radii of the adjacent atoms or ions. Many examples are provided and it is shown how the experimental bond lengths agree with the radii sums. The examples include inorganic compounds such as alkali halides, metal hydrides, and graphene; organic compounds such as aliphatic and aromatic compounds; and biochemical compounds such as nucleic acids, amino acids, caffeine-related compounds, and vitamins.

  11. 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).

  12. Atomic structure of Fe thin-films on Cu(0 0 1) studied with stereoscopic photography

    Microsoft Academic Search

    Azusa N. Hattori; M. Fujikado; T. Uchida; S. Okamoto; K. Fukumoto; F. Z. Guo; F. Matsui; K. Nakatani; T. Matsushita; K. Hattori; H. Daimon

    2004-01-01

    The complex magnetic properties of Fe films epitaxially grown on Cu(001) have been discussed in relation to their atomic structure. We have studied the Fe films on Cu(001) by a new direct method for three-dimensional (3D) atomic structure analysis, so-called “stereoscopic photography”. The forward-focusing peaks in the photoelectron angular distribution pattern excited by the circularly polarized light rotate around the

  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. Isotope shift and hyperfine structure studies of the krypton ion and the thallium atom 

    E-print Network

    Li, Yingfeng

    1991-01-01

    ISOTOPE SHIFT AND HYPERFINE STRUCTURE STUDIES OF THE KRYPTON ION AND THE THALLIUM ATOM A Thesis by YINGFENG LI Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree...) Lewis A. Ford (Member) Christian P. Burger (Member) Richard L. Arnowitt (Head of Department) August 1991 777 ABSTRACT Isotope Shift and Hyperfine Structure Studies of the Krypton Ion and the Thallium Atom. tAugust 1991) Yingfeng Li, B. S...

  15. Quantum chemical 13Calpha chemical shift calculations for protein NMR structure determination, refinement, and validation

    Microsoft Academic Search

    Jorge A. Vila; James M. Aramini; Paolo Rossi; Alexandre Kuzin; Min Su; Jayaraman Seetharaman; Rong Xiao; Liang Tong; Gaetano T. Montelione; Harold A. Scheraga

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-alpha-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Calpha chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Calpha

  16. Atomic-scale nanowires: physical and electronic structure

    Microsoft Academic Search

    D R Bowler

    2004-01-01

    The technology to build and study nanowires with sizes ranging from individual atoms to tens of nanometres has been developing rapidly over the last few years. We survey the motivation behind these developments, and summarize the basics behind quantized conduction. Several of the different experimental techniques and materials systems used in the creation of nanowires are examined, and the range

  17. Atomic and Electronic Structure of Polar Oxide Interfaces

    SciTech Connect

    Gajdardziska-Josifovska, Marija [University of Wisconsin Milwaukee] [University of Wisconsin Milwaukee

    2014-01-17

    In this project we developed fundamental understanding of atomic and electronic mechanisms for stabilization of polar oxide interfaces. An integrated experimental and theoretical methodology was used to develop knowledge on this important new class of ionic materials with limited dimensionality, with implications for multiple branches of the basic and applied energy sciences.

  18. Adjoint design sensitivity analysis of reduced atomic systems using generalized Langevin equation for lattice structures

    SciTech Connect

    Kim, Min-Geun; Jang, Hong-Lae [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)] [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of); Cho, Seonho, E-mail: secho@snu.ac.kr [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)] [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)

    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.

  19. Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

    PubMed Central

    King, R D; Muggleton, S H; Srinivasan, A; Sternberg, M J

    1996-01-01

    We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity. PMID:8552655

  20. Nano structured carbon nitrides prepared by chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Karuppannan, Ramesh; Prashantha, M.

    2010-08-01

    Nanostructured carbon nitride films were prepared by pyrolysis assisted chemical vapour deposition(CVD). A two zone furnace with a temperature profile having a uniform temperature over a length of 20 cm length has been designed and developed. The precursor Azabenzimidazole was taken in a quartz tube and evaporated at 400 0C. The dense vapours enter the pyrolysis zone kept at a desired temperature and deposit on the quartz substrates. The FTIR spectrum of the prepared samples shows peaks at 1272 cm-1 (C.N stretching) and 1600 cm-1 (C=N) confirms the bonding of nitrogen with carbon. Raman D and G peaks, are observed at 1360 cm-1 and 1576 cm-1 respectively. XPS core level spectra of C 1s and N 1s show the formation of ? bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is ~100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

  1. Atomic structure of highly strained BiFeO3 thin films.

    PubMed

    Rossell, M D; Erni, R; Prange, M P; Idrobo, J-C; Luo, W; Zeches, R J; Pantelides, S T; Ramesh, R

    2012-01-27

    We determine the atomic structure of the pseudotetragonal T phase and the pseudorhombohedral R phase in highly strained multiferroic BiFeO(3) thin films by using a combination of atomic-resolution scanning transmission electron microscopy and electron energy-loss spectroscopy. The coordination of the Fe atoms and their displacement relative to the O and Bi positions are assessed by direct imaging. These observations allow us to interpret the electronic structure data derived from electron energy-loss spectroscopy and provide evidence for the giant spontaneous polarization in strained BiFeO(3) thin films. PMID:22400888

  2. Atomic Structure of Highly Strained BiFeO3 Thin Films

    SciTech Connect

    Rossell, M.D. [Lawrence Berkeley National Laboratory (LBNL); Erni, R. [Lawrence Berkeley National Laboratory (LBNL); Prange, Micah P [ORNL; Idrobo Tapia, Juan C [ORNL; Luo, Weidong [ORNL; Zeches, R J [University of California, Berkeley; Pantelides, Sokrates T [ORNL; Ramesh, R [Lawrence Berkeley National Laboratory (LBNL)

    2012-01-01

    We determine the atomic structure of the pseudotetragonal T phase and the pseudorhombohedral R phase in highly strained multiferroic BiFeO3 thin films by using a combination of atomic-resolution scanning transmission electron microscopy and electron energy-loss spectroscopy. The coordination of the Fe atoms and their displacement relative to the O and Bi positions are assessed by direct imaging. These observations allow us to interpret the electronic structure data derived from electron energy-loss spectroscopy and provide evidence for the giant spontaneous polarization in strained BiFeO3 thin films.

  3. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.(Columbia University) [Columbia University; Baik, Mu-Hyun (Columbia University) [Columbia University; Gherman, Benjamin F.(Columbia University) [Columbia University; Guallar, Victor (Washington University) [Washington University; Wirstam, Maria E.(1836) [1836; Murphy, Robert B.(Schrodinger Inc) [Schrodinger Inc; Lippard, Stephen J.(Massachusetts Institute of Technology) [Massachusetts Institute of Technology

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  4. The structural evolution and diffusion during the chemical transformation from cobalt to cobalt phosphide nanoparticles

    SciTech Connect

    Ha, Don-Hyung; Moreau, Liane M.; Bealing, Clive R.; Zhang, Haitao; Hennig, Richard G.; Robinson, Richard D.

    2011-01-01

    We report the structural evolution and the diffusion processes which occur during the phase transformation of nanoparticles (NPs), ?-Co to Co{sub 2}P to CoP, from a reaction with tri-n-octylphosphine (TOP). Extended X-ray absorption fine structure (EXAFS) investigations were used to elucidate the changes in the local structure of cobalt atoms which occur as the chemical transformation progresses. The lack of long-range order, spread in interatomic distances, and overall increase in mean-square disorder compared with bulk structure reveal the decrease in the NP’s structural order compared with bulk structure, which contributes to their deviation from bulk-like behavior. Results from EXAFS show both the Co{sub 2}P and CoP phases contain excess Co. Results from EXAFS, transmission electron microscopy, X-ray diffraction, and density functional theory calculations reveal that the inward diffusion of phosphorus is more favorable at the beginning of the transformation from ?-Co to Co{sub 2}P by forming an amorphous Co-P shell, while retaining a crystalline cobalt core. When the major phase of the sample turns to Co{sub 2}P, the diffusion processes reverse and cobalt atom out-diffusion is favored, leaving a hollow void, characteristic of the nanoscale Kirkendall effect. For the transformation from Co{sub 2}P to CoP theory predicts an outward diffusion of cobalt while the anion lattice remains intact. In real samples, however, the Co-rich nanoparticles continue Kirkendall hollowing. Knowledge about the transformation method and structural properties provides a means to tailor the synthesis and composition of the NPs to facilitate their use in applications.

  5. Nanoscale chemical and structural study of Co- based FEBID structures by STEM-EELS and HRTEM

    E-print Network

    Cordoba, Rosa; Fernandez-Pacheco, Rodrigo; Fernandez-Pacheco, Amalio; Gloter, Alexandre; Magen, Cesar; Stephan, Odile; Ricardo Ibarra, Manuel; De Teresa, Jose Maria

    2011-11-15

    NANO EXPRESS Open Access Nanoscale chemical and structural study of Co- based FEBID structures by STEM-EELS and HRTEM Rosa Córdoba1,2, Rodrigo Fernández-Pacheco1,3, Amalio Fernández-Pacheco1,2, Alexandre Gloter3, César Magén1,2,4, Odile Stéphan3... electron microscopy at the nanometric scale. The obtained results allow us to correlate the chemical and structural properties with the functionality of these magnetic nanostructures. Keywords: Co deposits, FEBID, EELS, HRTEM Background Despite its great...

  6. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    NASA Astrophysics Data System (ADS)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of ?-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the ?-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of ?-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in ?-oryzanol loaded systems were found at rather higher field than those in ?-oryzanol free systems, suggesting incorporation of ?-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of ?-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of ?-oryzanol and lipids (solid and liquid) inside the lipid nanoparticle systems are proposed.

  7. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  8. Functional Nano-Structures Using Atomic Layer Deposition

    E-print Network

    Salgård Cunha, Pedro

    2014-05-27

    and the fabrication of the active material to be optimised separately. Given the separation of the template fabrication and the replica- tion a range of different replication techniques can be used, including electrochemistry, sol-gel and atomic layer deposition. One... -state electrolyte cells will be described, together with the advantages and disadvantages of these device geometries. 2.1 Conventional photovoltaic devices The word photovoltaic stems from the Greek word photo meaning ‘light’ and voltaic designating ‘electricity...

  9. Electronic packing frustration in complex intermetallic structures: the role of chemical pressure in Ca2Ag7.

    PubMed

    Fredrickson, Daniel C

    2011-07-01

    The assignment of distinct roles to electronics and sterics has a long history in our rationalization of chemical phenomena. Exploratory synthesis in the field of intermetallic compounds challenges this dichotomy with a growing list of phases whose structural chemistry points to an interplay between atomic size effects and orbital interactions. In this paper, we begin with a simple model for how this interdependence may arise in the dense atomic packing of intermetallics: correlations between interatomic distances lead to the inability of a phase to optimize bonds without simultaneously shortening electronically under-supported contacts, a conflict we term electronic packing frustration (EPF). An anticipated consequence of this frustration is the emergence of chemical pressures (CPs) acting on the affected atoms. We develop a theoretical method based on DFT-calibrated ?(2)-Hückel calculations for probing these CP effects. Applying this method to the Ca(2)Ag(7) structure, a variant of the CaCu(5) type with defect planes, reveals its formation is EPF-driven. The defect planes resolve severe CPs surrounding the Ca atoms in a hypothetical CaCu(5)-type CaAg(5) phase. CP analysis also points to a rationale for these results in terms of a CP analogue of the pressure-distance paradox and predicts that the impetus for defect plane insertion is tunable via variations in the electron count. PMID:21619054

  10. Atomic-scale structural evolution from disorder to order in an amorphous metal

    NASA Astrophysics Data System (ADS)

    Li, F.; Liu, X. J.; Hou, H. Y.; Chen, G.; Chen, G. L.

    2011-12-01

    In this paper, we performed molecular dynamics simulations to study the atomic-scale structural evolution from disorder to order during the isothermal annealing of an amorphous Ni. Three plateaus in the time dependent potential energy and mean square displacement (MSD) curves were observed, indicating that the atomic ordering process from amorphous to nanocrystalline Ni undergoes three distinct stages. The structural analyses reveal that the atomic structural evolution is associated with these three stages: Disordered atoms adjust their relative positions to form a one-dimensional (1D) periodic structure at the first stage, then form a 2D periodic structure at the second stage, and finally form a 3D periodic nanocrystal. Further analyses of potential energy and MSD difference and dynamics demonstrate that the structural change from the 2D to 3D structure is more difficult than that from the 1D to 2D structure, because both the 1D and 2D quasi-ordered structures belong to transition states and have similar structural features in nature. Our findings may provide new insights into the nanocrystallization of amorphous alloys and implications for producing nanostructured materials.

  11. Shock-Induced Chemical Reactions in Structural Energetic Materials

    NASA Astrophysics Data System (ADS)

    Narayanan, V.; Lu, X.; Hanagud, S.

    2006-07-01

    Various powder mixtures like intermetallic mixtures and mixtures of metals and metal oxides have potential applications as structural energetic materials (SEMs). Technologies of varying the compositions and the powder sizes and their synthesis are being investigated to provide multiple desirable characteristics, like high strength and high energy content. In this paper, we formulate a model for SEMs for their application in shock conditions, in the framework of nonequilibrium thermodynamics and continuum mechanics. A mixture of Al and KClO4 is selected as the example for SEMs. A mixture, pore collapse and chemical reaction model are included. By adapting energy barriers for reaction as a function of temperature, particle size and pressure and introducing a relaxation mechanism in the reaction model, a shock-induced chemical reaction model is developed. The variation of the relaxation mechanism is also modeled. The initiation and propagation of chemical reactions are studied. The time and spatial dependency of chemical reaction on the shock wave conditions are investigated.

  12. Structural and Chemical Control of Supramolecular Coordination Self-Assembly Confined on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Shi, Ziliang

    This thesis is concerned with the structural and chemical control of two-dimensional (2D) supramolecular self-assemblies through judiciously manipulating bonding motifs at various intrinsic and external conditions. The self-selection and the self-recognition of the noncovalent interactions among organic and/or metallic building blocks govern the structural and chemical properties of the resultant self-assembled two-dimensional nanostructures, accompanying with the thermodynamic and kinetic process as well. In this thesis, we have investigated the supramolecular self-assembly achieved via coordination bonds assisted by transition metals and functional ligands on metal surfaces. The self-assembled nanostructures were studied by ultra-high vacuum scanning tunneling microscopy working at room temperatures. The structural transition processes were also inspected via the low energy electron diffraction. Further, artificial "quantum dots" represented by the cavities of the self-assembled networks were investigated. The modulation of surface electrons by these "quantum dots" was characterized by the local density of states detected by low-temperature scanning tunneling spectroscopy. The major contributions of this thesis are outlined as below: (1) Through modifying the chemical states of organic ligands, a unique coordination Kagome network structure was obtained for the first time by two distinct methods. TPyP (5, 10, 15, 20-tetra(4-pyridyl)porphyrin) species on Au(111) surfaces form the TPyP-Au coordination Kagome network achieved by a novel treatment that was suggested to modify the chemical state of the TPyP. In a condition that the TPyP coexists with Cu on a Au(111), Cu adatoms play two roles in the self-assembly---the coordination with pyridyl end-groups and the reaction with TPyP macrocycles, which control the chemical and structural phase of the self-assembly. Following a high temperature annealing, the same Kagome structure emerged from a precursor rhombus network structure. We proposed a new mechanism which provides a consistent explanation to both assembly methods. ZnTPyP (zinc 5, 10, 15, 20-tetra(4- pyridyl)porphyrin) molecules show chemical stability at high annealing temperature, which allows for preparing chemically pure ZnTPyP-Cu bimetallic networks. Furthermore, a reversible structural transformation between a hydrogen-bonded network and a coordination network was realized by either adding Cu atoms or annealing samples at certain temperatures. (2) The influence of the thermodynamic and kinetic effects on the selection of binding modes was studied by a combined STM and LEED investigation which offered spatial as well as temporal insights. The molecules of TPyB (1,3,5-trispyridylbenzene) coordinate with Cu or Fe respectively, forming two distinct polymorphism network structures. Two coordination binding modes show different binding energies. By the kinetic and thermodynamic control, either of binding modes was selected. LEED patterns revealed the dynamic process of structural transition from that of low binding-energy mode to that of high binding-energy mode. In the latter section the structural phase transition induced by two-dimensional compression is introduced. Pyridyl-Cu coordination bond is of certain liability, allowing for the alternation of bonds under various environments. Through increasing the coverage of molecules, distinctive polygraphic networks presented via different pyridyl-Cu binding modes. (3) The self-assembly of multiple components represent a much more complicated assembly system, where the elaborate balance of interactions among all components and substrates comprises greater challenging. To study such a system, the third part deals with the multiple-ligand self-assembly. Achieved by TPyP and PBTP 4',4"-(1,4- phenylene)bis(2,2':6',2"-terpyridine)) molecules and Fe, two types of network structure formed on Au(111) surfaces. Both networks coexisted due to similar bonding configurations and free energies. However, the entropy is presumably suggested to promote the

  13. Mechanism of pulse discharge production of iodine atoms from CF3I molecules for a chemical oxygen-iodine laser

    NASA Astrophysics Data System (ADS)

    Kochetov, I. V.; Napartovich, A. P.; Vagin, N. P.; Yuryshev, N. N.

    2009-03-01

    The pulsed chemical oxygen-iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and charged species, electric circuit equation, gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are found by solving the electron Boltzmann equation, which is re-calculated in a course of computations when plasma parameters changed. The processes accounted for in the Boltzmann equation include excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions, second-kind collisions and stepwise excitation of molecules. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. Results of numerical simulations are compared with experimental laser pulse waveforms. It is concluded that there is satisfactory agreement between theory and the experiment. The prevailing mechanism of iodine atom formation from the CF3I donor in a very complex kinetic system of the COIL medium under pulse discharge conditions, based on their detailed numerical modelling and by comparing these results both with experimental results of other authors and their own experiments, is established. The dominant iodine atom production mechanism for conditions under study is the electron-impact dissociation of CF3I molecules. It was proved that in the conditions of the experiment the secondary chemical reactions with O atoms play an insignificant role.

  14. Quantum chemical and solution phase evaluation of metallocenes as reducing agents for the prospective atomic layer deposition of copper.

    PubMed

    Dey, Gangotri; Wrench, Jacqueline S; Hagen, Dirk J; Keeney, Lynette; Elliott, Simon D

    2015-05-27

    We propose and evaluate the use of metallocene compounds as reducing agents for the chemical vapour deposition (and specifically atomic layer deposition, ALD) of the transition metal Cu from metalorganic precursors. Ten different transition metal cyclopentadienyl compounds are screened for their utility in the reduction of Cu from five different Cu precursors by evaluating model reaction energies with density functional theory (DFT) and solution phase chemistry. PMID:25914999

  15. Laser-induced fluorescence measurements and kinetic analysis of Si atom formation in a rotating disk chemical vapor deposition reactor

    Microsoft Academic Search

    Pauline Ho; Michael E. Coltrin; William G. Breiland

    1994-01-01

    An extensive set of laser-induced fluorescence (LIF) measurements of Si atoms during the chemical vapor deposition (CVD) of silicon from silane and disilane in a research rotating disk reactor are presented. The experimental results are compared in detail with predictions from a numerical model of CVD from silane and disilane that treats the fluid flow coupled to gas-phase and gas-surface

  16. A framework for the evaluation of chemical structure databases.

    PubMed

    Cooke, F; Schofield, H

    2001-01-01

    Access to desk-top structure and reaction databases through applications such as Chemical Abstracts' SciFinder, MDL's Beilstein CrossFire, and ISIS Reaction Browser has led to changes in information seeking habits of research chemists, the impact of which has implications when database purchasing decisions are made. A semiquantitative assessment is proposed which takes into account key aspects of structure and reaction databases. Assessment criteria are identified which can be weighted according to an organization's information needs. Values are then assigned to criteria for each data source, after which a formula is applied which leads to an indication of the relative value of systems under consideration. The formula takes into account the cost of database products and also the incremental benefit of adding a new system to an existing collection. This work is presented as a generic approach to the evaluation of databases and is not limited in scope to only structure and reactions databases. PMID:11604014

  17. Atomic Force Microscopy of Physical and Chemical Processes at the Solid-Liquid Interface

    NASA Astrophysics Data System (ADS)

    Manne, Srinivas

    This thesis describes research using atomic force microscopy (AFM) to study dynamics of solid surfaces in contact with liquids. Specifically, three applications are described: electrochemistry (Chapters 1-3), crystal growth (Chapters 4 and 5), and biomineralization (Chapter 6). Chapter 1 shows the feasibility of using AFM to image metal atoms in liquid, which sets the stage for high -resolution electrochemistry. Chapter 2 describes methods to convert the standard AFM liquid cell into an electrochemical cell and shows images of a gold electrode during oxidation/reduction cycling. Chapter 3 follows an electroplating cycle, wherein copper is deposited from electrolyte onto a gold electrode and then stripped off. The surface lattice is shown to change from that of bulk gold to bulk copper during plating, and back to bulk gold after stripping. Moreover, the first monolayer of copper--which deposits at an "underpotential", before the bulk deposition--is shown to have a lattice which differs from the bulk and is electrolyte dependent. Like electrochemistry, the study of crystal growth is also perfectly suited to a surface technique such as AFM. AFM makes it possible to image "elemental steps" (i.e., steps one unit cell thick) on a single crystal and quantify their motion during growth and dissolution. This is illustrated for the inorganic crystal calcite (Chapter 4) and the more fragile organic crystal L-leucine (Chapter 5). In both cases it is shown that step speed is independent of spacing between steps, indicating that motion occurs by direct interaction of the step-site molecules with the solvent. Chapter 5 also describes techniques for growing and imaging organic crystals. Living organisms also use crystal growth, modified by inorganic and organic additives, to grow mineralized structures such as bones, teeth and seashells. In Chapter 6, AFM reveals the three-dimensional structure of the nacreous or pearly layer of mollusc shells by slowly etching away successive mineral layers (in weak acid) while imaging. Etch figures on the mineral (aragonite) are correlated with crystallographic directions, revealing overall crystalline order on large scans. In bivalves, this order is observed both laterally across the layer and vertically between layers, whereas gastropod nacre is observed to be ordered only vertically.

  18. Evolution of the electrical and structural properties during the growth of Al doped ZnO films by remote plasma-enhanced metalorganic chemical vapor deposition

    Microsoft Academic Search

    I. Volintiru; M. Creatore; B. J. Kniknie; C. I. M. A. Spee

    2007-01-01

    Al-doped zinc oxide (AZO) films were deposited by means of remote plasma-enhanced metalorganic chemical vapor deposition from oxygen\\/diethylzinc\\/trimethylaluminum mixtures. The electrical, structural (crystallinity and morphology), and chemical properties of the deposited films were investigated using Hall, four point probe, x-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), electron recoil detection (ERD), Rutherford backscattering (RBS), and time of

  19. Atomic-scale Structural Characterizations of Functional Epitaxial Thin Films

    E-print Network

    Zhu, Yuanyuan

    2013-06-03

    chemistry, interfacial defects and associated strain field. This dissertation reports in-depth microstructural characterization of the intrinsic chemical inhomogeneity in selected epitaxial thin films including superconducting Fe1+yTe1-xSex/SrTiO 3(STO...

  20. 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.

  1. Electrostatic Chemical Strain: An Approach to Electronic Structure Engineering in Layered Oxides

    NASA Astrophysics Data System (ADS)

    Rondinelli, James

    2015-03-01

    Traditional approaches to create and control functional electronic materials have focused on new phases in previously unknown bulk minerals. More recently, interlayer physics has spawned interest in known materials in unexplored atomic scale geometries, especially in complex transition metal oxides (TMO), where heterostructures and superlattices with abrupt interfaces can be created on demand. The interfaces between TMO overs a handle to direct the electrostatic field exerted on the transition metal centers via the coordinating oxygen ligands, which alter the M cation's d-orbital occupancies and spin state, thereby imparting desirable electronic functionality. In this talk, I describe an atomistic engineering approach that makes use of long-range electrostatic interactions between atomic metal-monoxide planes (AO and A'O) in naturally occurring superlattices, e.g., Ruddlesden-Popper (RP), phases, to tune interlayer atomic structure, orbital degeneracies, and magnetic properties. Using first-principles electronic structure calculations, I show how this electrostatic chemical strain (ECS) effect can be used to tune both crystal field energies and the frontier orbital structure in correlated (La, A)NiO4 RP phases at fixed stoichiometry. I describe how to enhance the Ni eg orbital polarization, resulting in NiO6 units that exhibit a single d (x2 -y2) band at the Fermi level--electronic features similar to the layered superconducting cuprates. This approach is generic in construction, making it applicable to any layered topology supporting heterovalent cation substitutions. I conclude by showing it is a realistic strategy to tailor the electronic properties of known materials, and discover yet-to-be realized novel functional oxides without resorting to complex assembly of multi-component heterostructures. Funding for this work is provided by the Defense Advanced Research Projects Agency (DARPA), Grant No. N66001-12-4224 and performed in collaboration with P. Balachandran and A. Cammarata.

  2. Study of light-induced vector changes in the local atomic structure of AsSe glasses by EXAFS

    E-print Network

    Drabold, David

    Study of light-induced vector changes in the local atomic structure of As­Se glasses by EXAFS G changes in the local structure of As­Se glasses using extended X-ray ab- sorption fine structure (EXAFS) by extended X-ray absorption fine structure (EXAFS) analysis around Se as well as As atoms in AsxSe1Àx films

  3. Impact of Atomic Layer Deposition to NanoPhotonic Structures and Devices: A Review

    NASA Astrophysics Data System (ADS)

    Saleem, Muhammad Rizwan; Ali, Rizwan; Khan, Mohammad Bilal; Turunen, Jari; Honkanen, Seppo

    2014-10-01

    We review the significance of optical thin films by Atomic Layer Deposition (ALD) method to fabricate nanophotonic devices and structures. ALD is a versatile technique to deposit functional coatings on reactive surfaces with conformal growth of compound materials, precise thickness control capable of angstrom resolution and coverage of high aspect ratio nanostructures using wide range of materials. ALD has explored great potential in the emerging fields of photonics, plasmonics, nano-biotechnology, and microelectronics. ALD technique uses sequential reactive chemical reactions to saturate a surface with a monolayer by pulsing of a first precursor (metal alkoxides or covalent halides), followed by reaction with second precursor molecules such as water to form the desired compound coatings. The targeted thickness of the desired compound material is controlled by the number of ALD cycles of precursor molecules that ensures the self limiting nature of reactions. The conformal growth and filling of TiO2 and Al2O3 optical material on nanostructures and their resulting optical properties have been described. The low temperature ALD-growth on various replicated sub-wavelength polymeric gratings is discussed.

  4. Atomic-scale structure and band-gap bowing in Cu(In,Ga)Se2

    NASA Astrophysics Data System (ADS)

    Schnohr, C. S.; Kämmer, H.; Stephan, C.; Schorr, S.; Steinbach, T.; Rensberg, J.

    2012-06-01

    Mixed systems such as the Cu(In,Ga)Se2 chalcopyrite semiconductor consist of different local atomic arrangements, that is, of different combinations of first-nearest-neighbor cations surrounding the Se anions. The anion position of Cu-III-VI2 compounds is predicted to strongly influence the material band gap. We therefore used extended x-ray absorption fine structure spectroscopy to study the atomic-scale structure of Cu(In,Ga)Se2 as a function of composition. Based on these results, the anion position was modeled for all first-nearest-neighbor configurations using a valence force-field approach. We show that the atomic-scale structure strongly depends on the kind of first-nearest-neighbor atoms. Structural relaxation of the anion occurs with respect to both (i) Cu and group III atoms and (ii) In and Ga atoms. In both cases, the average anion displacement exhibits a nonlinear behavior with changing composition and thus results in two separate but significant contributions to the band gap bowing observed in Cu(In,Ga)Se2.

  5. Virtual reality based approach to protein heavy-atom structure reconstruction

    E-print Network

    Xubiao Peng; Alireza Chenani; Shuangwei Hu; Yifan Zhou; Antti J. Niemi

    2014-12-26

    A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy over existing methods.

  6. ATOMIC AND MOLECULAR PHYSICS: Structures, stabilities and magnetic moment of small copper-nickel clusters

    NASA Astrophysics Data System (ADS)

    Feng, Cui-Ju; Xue, Yong-Hong; Zhang, Xiao-Yan; Zhang, Xiao-Chun

    2009-04-01

    This paper obtains the lowest-energy geometric structures and the electronic and magnetic properties of small CuNiN clusters by using all-electron density functional theory. The calculated results reveal that the Cu atom prefers to occupy the apical site when N <= 9 and for the clusters with N = 10, the Cu atom starts to encapsulate in the cage. The CuNi7 and CuNi9 are magic clusters. The magnetism correlates closely with the symmetry of the clusters. For these clusters, the charge tends to transfer from the nickel atoms to the copper atoms. It finds that the doping of Cu atom decreases the stability of pure NiN clusters.

  7. Atomic structure of nickel phthalocyanine probed by X-ray absorption spectroscopy and density functional simulations

    NASA Astrophysics Data System (ADS)

    Avakyan, L. A.; Manukyan, A. S.; Mirzakhanyan, A. A.; Sharoyan, E. G.; Zubavichus, Y. V.; Trigub, A. L.; Kolpacheva, N. A.; Bugaev, L. A.

    2013-03-01

    The local atomic structure of Ni in nickel phthalocyanine was studied by K-edge X-ray absorption fine structure spectroscopy. The obtained inter atomic nickel-nitrogen distance differs from the reference X-ray diffraction data so an additional study was performed within density functional theory framework. The justification of the used theoretical approach was provided by a comparison of theoretical free electron densities of states with experimental Ni K-edge X-ray absorption near edge spectra. The refined Ni local environment retain the reference structure of the molecule except for the length of Ni-N bond which increases to 1.90 Å.

  8. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T. [Zhejiang University; Wang, X. D. [Zhejiang University; Cao, Q. P. [Zhejiang University; Zhang, D. X. [Zhejiang University; Wang, S. Y. [Fudan University; Wang, Cai-Zhuang [Ames Laboratory; Jiang, J. Z. [Zhejiang University

    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.

  9. Atomic-resolution characterization of interface structure and chemistry in the STEM

    SciTech Connect

    Browning, N.D.; McGibbon, M.M.; McGibbon, A.J.; Chisholm, M.F.; Pennycook, S.J. [Oak Ridge National Lab., TN (United States); Ravikumar, V.; Dravid, V.P. [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering

    1994-03-01

    Combination of Z-contrast imaging and EELS (electron energy loss spectroscopy) allows the local structure and chemistry of interfaces to be determined on the atomic scale. In this paper, these two complementary techniques are used to analyze the structure and chemistry of a nominally 25 degree [100] symmetric tilt boundary in an electroceramic SrTiO{sub 3} bicrystal.

  10. Getting CAD in shape: the atomic structure of human dihydroorotase domain.

    PubMed

    Hermoso, Juan A

    2014-02-01

    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. PMID:24507779

  11. Gyration-radius dynamics in structural transitions of atomic clusters Tomohiro Yanao,a

    E-print Network

    Marsden, Jerrold

    Gyration-radius dynamics in structural transitions of atomic clusters Tomohiro Yanao,a Wang S. Koon Institute of Physics. DOI: 10.1063/1.2710272 I. INTRODUCTION Structural transition dynamics of molecules, and Jerrold E. Marsden Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena

  12. Correlation of diffusion coefficients with the electronic structure of interacting atoms

    Microsoft Academic Search

    G. V. Samsonov; I. S. Kiva; N. G. Kaidash; E. G. Borisenko

    1976-01-01

    spect to the electron-phonon structure of solids, the interaction between the diffusion parameters and the electronic structure of atoms interecting during the diffusion was followed. An analysis of diagrams constructed from experimental data on the activation energy A and the preexponential factor D o of elements diffusing into the matrix shows that both quantities are very sensitive to the electronic

  13. Energetics and structural properties of adsorbed atoms and molecules on silicon-doped carbon nanotubes

    SciTech Connect

    Fagan, Solange B.; Mota, R.; Baierle, R.J.; Silva, Antonio J.R. da; Fazzio, A

    2003-03-15

    The energetics and structural properties of atoms and molecules on a substitutional Si atom in single wall carbon nanotubes (SWCN) are investigated using first principle calculations based on density-functional theory. A detailed analysis is performed for the geometry and the electronic structures of a Si-doped semiconducting (10,0) carbon nanotube interacting with F, Cl, H, CH{sub 3}, and SiH{sub 3}. A common feature for the systems with these atoms or molecules is the presence of one half-filled level close to the top of the valence band. The specific position of this level in the gap depends on the chemisorbed species and the binding energy between this species and the Si atom.

  14. Atomic Physics

    NSDL National Science Digital Library

    Christopher Griffith

    This collection provides a basic introduction to Atomic Physics. It reviews the building blocks of atomic structure, explores atomic isotopes, explains Einstein's famous equation E = mc2, and introduces the various types of radiation.

  15. Multiple doping structures of the rare-earth atoms in ?-SiAlON:Ce phosphors and their effects on luminescence properties.

    PubMed

    Gan, Lin; Xu, Fang-Fang; Zeng, Xiong-Hui; Li, Zuo-Sheng; Mao, Zhi-Yong; Lu, Ping; Zhu, Ying-Chun; Liu, Xue-Jian; Zhang, Lin-Lin

    2015-06-25

    The critical doping structures of rare-earth atoms in the promising ?-SiAlON phosphors have long been argued owing to the lack of direct evidence. Here, the exact locations and coordination of the Ce rare-earth atoms in the ?-SiAlON structure have been examined using an atom-resolved Cs-corrected scanning transmission electron microscope. Three different occupation sites for the Ce atoms have been directly observed: two of them are in the structural channel coordinated with six and nine N(O) atoms, respectively; the other one is the unexpected substitution site for Si(Al). The chemical valences and stabilities of the doping Ce ions at the different occupation sites have been evaluated using density functional calculations. Correlation of the different doping structures with the luminescence properties has been investigated by the aid of cathodoluminescence (CL) microanalysis, which verifies the different contribution of the interstitial trivalent Ce ions to the light emission while no luminescence is observed for the substitutional doping of quadrivalent Ce. PMID:26073879

  16. Theoretical chemical kinetic study of the H-atom abstraction reactions from aldehydes and acids by ? atoms and ?H, H?2, and ?H3 radicals.

    PubMed

    Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

    2014-12-26

    We have performed a systematic, theoretical chemical kinetic investigation of H atom abstraction by ? atoms and ?H, H?2, and ?H3 radicals from aldehydes (methanal, ethanal, propanal, and isobutanal) and acids (methanoic acid, ethanoic acid, propanoic acid, and isobutanoic acid). The geometry optimizations and frequencies of all of the species in the reaction mechanisms of the title reactions were calculated using the MP2 method and the 6-311G(d,p) basis set. The one-dimensional hindered rotor treatment for reactants and transition states and the intrinsic reaction coordinate calculations were also determined at the MP2/6-311G(d,p) level of theory. For the reactions of methanal and methanoic acid with ? atoms and ?H, H?2, and ?H3 radicals, the calculated relative electronic energies were obtained with the CCSD(T)/cc-pVXZ (where X = D, T, and Q) method and were extrapolated to the complete basis set limit. The electronic energies obtained with the CCSD(T)/cc-pVTZ method were benchmarked against the CCSD(T)/CBS energies and were found to be within 1 kcal mol(-1) of one another. Thus, the energies calculated using the less expensive CCSD(T)/cc-pVTZ method were used in all of the reaction mechanisms and in calculating our high-pressure limit rate constants for the title reactions. Rate constants were calculated using conventional transition state theory with an asymmetric Eckart tunneling correction, as implemented in Variflex. Herein, we report the individual and average rate constants, on a per H atom basis, and total rate constants in the temperature range 500-2000 K. We have compared some of our rate constant results to available experimental and theoretical data, and our results are generally in good agreement. PMID:25387985

  17. Applications of the Quantum Theory of Atoms in Molecules to Chemical and Biochemical Problems

    Microsoft Academic Search

    Chérif F. Matta

    2002-01-01

    The quantum theory of atoms in molecules (QT-AIM) is a generalization of quantum mechanics to open subsystems. The theory enables one to study the properties of atoms or functional groups within a molecule, recovering the empirical observation that they exhibit characteristic and additive contributions to every molecular property. This thesis applies theory to explain and predict experiment. In this work,

  18. Chemical composition measurements of a nickel-base superalloy by atom probe field ion microscopy

    Microsoft Academic Search

    Nelia Wanderka; Uwe Glatzel

    1995-01-01

    Single crystals of the rhenium-containing nickel-base superalloy CMSX-4 were investigated using a time of flight atom probe. The distribution of the alloying elements in the two phases, matrix (? phase) and precipitate (?? phase), was studied. The high spatial resolution of the atom probe allows to analyse the ???? interface. The transition from matrix to ?? phase takes place within

  19. 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 [Vilnius University Research Institute of Theoretical Physics and Astronomy, A. Gostauto 12, LT-01108 Vilnius (Lithuania); European Commission, Joint Research Centre, Institute for Transuranium Elements, Postfach 2340, D-76125 Karlsruhe (Germany)

    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.

  20. Problem solving with pentagons: Tsai-type quasicrystal as a structural response to chemical pressure.

    PubMed

    Berns, Veronica M; Fredrickson, Daniel C

    2013-11-18

    Even after significant advances in the structural characterization of quasicrystals--phases whose diffraction patterns combine the sharp peaks normally associated with lattice periodicity and rotational symmetries antithetical to such periodicity--this new form of long-range order remains enigmatic. Here, we present DFT-chemical pressure calculations on the Tsai-type quasicrystal approximant CaCd6, which reveal how its icosahedral clusters can be traced to simple CaCu5-type (hP6) intermetallics. The results indicate that the Tsai-type clusters emerge from an atomic-size-driven transformation from planar arrangements to spherical clusters, recalling the relationship between graphene and C60. PMID:24161006

  1. 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.

  2. Virtual reality based approach to protein heavy-atom structure reconstruction

    E-print Network

    Peng, Xubiao; Hu, Shuangwei; Zhou, Yifan; Niemi, Antti J

    2014-01-01

    A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondar...

  3. Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates

    SciTech Connect

    Vedrinskii, R. V.; Lemeshko, M. P.; Novakovich, A. A. [Institute of Physics, Rostov State University, 194 Stachky Avenue, Rostov-on-Don 344090 (Russian Federation); Nazarenko, E. S. [Institute of Physics, Rostov State University, 194 Stachky Avenue, Rostov-on-Don 344090 (Russian Federation); Laboratoire de Cristallographie, CNRS, l'Universite Joseph Fourier, 166 Boite Postale, F-38042 Grenoble Cedex 9 (France); Nassif, V. [CEA/Grenoble, DRFMC/SP2M/NRS, F-38054 Grenoble Cedex 9 (France); BM30b CRG-FAME, European Synchrotron Radiation Facility, F-38043 Grenoble Cedex 9 (France); Proux, O. [Laboratoire de Geophysique Interne et Tectonophysique, UMR CNRS, Universite Joseph Fourier, F-38400 Saint-Martin-D'Heres (France); BM30b CRG-FAME, European Synchrotron Radiation Facility, F-38043 Grenoble Cedex 9 (France); Joly, Y. [Laboratoire de Cristallographie, CNRS, l'Universite Joseph Fourier, 166 Boite Postale, F-38042 Grenoble Cedex 9 (France)

    2006-04-01

    Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates PbZr{sub 0.515}Ti{sub 0.485}O{sub 3} (PZT), PbZrO{sub 3} (PZ), and BaZrO{sub 3} are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between {chi}(k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed.

  4. 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 levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

  5. Structures of ultra-thin atomic-layer-deposited TaNx films

    NASA Astrophysics Data System (ADS)

    Wu, Y. Y.; Kohn, A.; Eizenberg, M.

    2004-06-01

    Atomic layer deposition (ALD) is an attractive technique in fabrication of microelectronics presently and in the future, for its accurate thickness control in atomic scale, excellent conformality, and uniformity over large areas at low temperature. It has been adapted and used in deposition of ultrathin TaNx films as diffusion barriers for Cu metallization. In this study, composition, structure, and stability of ultra-thin (1.5-10 nm) atomic layer deposited films are characterized by a set of complementary analytical techniques. The results indicate that the N to Ta atomic concentration ratio in the ALD TaNx films is approximately 2, independent of the film thickness and annealing up to 750 °C. Hydrogen, oxygen, and carbon are detected as impurities within the as-deposited films. The as-deposited ALD TaNx films have an fcc NaCl-type nanocrystalline structure even when the film thickness is 1.5 nm. Following thermal anneal at 600 °C and higher, the films do not undergo a structural change except for an increase in grain size and a decrease in the lattice constant. X-ray photoelectron spectra results indicate that all the Ta atoms in the films are bonded ionically with the surrounding N atoms. An ex situ thermal treatment at 600 °C for 1 h removes the O, which penetrated the layers, by a reduction reaction with the residual H and results in densification of the ALD films. Our analysis of the experimental results indicates that the excess of N atoms of the ALD TaNx films is mainly due to Ta vacancies in the fcc NaCl-type structure. The structural and compositional characteristics of the films explain why the films serve as good diffusion barriers to Cu metallization.

  6. Structure and chemical properties of molybdenum oxide thin films

    SciTech Connect

    Ramana, C. V.; Atuchin, V. V.; Pokrovsky, L. D.; Becker, U.; Julien, C. M. [Nanoscience and Surface Chemistry Laboratory, Department of Geological Sciences, University of Michigan, Ann Arbor, Michigan 48109 (United States); Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Nanoscience and Surface Chemistry Laboratory, Department of Geological Sciences, University of Michigan, Ann Arbor, Michigan 48109 (United States); Institut des Nano-Sciences de Paris, CNRS-UMR 7588, Universite Pierre et Marie Curie Campus Boucicaut, 140 rue de Lourmel, 75015 Paris (France)

    2007-07-15

    Molybdenum oxide (MoO{sub 3}) exhibits interesting structural, chemical, electrical, and optical properties, which are dependent on the growth conditions and the fabrication technique. In the present work, MoO{sub 3} films were produced by pulsed-laser deposition and dc magnetron sputtering under varying conditions of growth temperature (T{sub s}) and oxygen pressure (pO{sub 2}). The effect of growth conditions on the structure and chemical properties of MoO{sub 3} films was examined using x-ray diffraction, reflection high-energy electron diffraction, x-ray photoelectron spectroscopy, and infrared spectroscopic measurements. The analyses indicate that the microstructure of Mo oxide films is sensitive to T{sub s} and pO{sub 2}. The growth conditions were optimized to produce stoichiometric and highly textured polycrystalline MoO{sub 3} films. A comparison of the microstructure of MoO{sub 3} films grown using pulsed-laser deposition and sputtering methods is also presented.

  7. Characterization of iron-phosphate-silicate chemical garden structures.

    PubMed

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. PMID:22035594

  8. Designing ionic liquids: the chemical structure role in the toxicity.

    PubMed

    Ventura, Sónia P M; Gonçalves, Ana M M; Sintra, Tânia; Pereira, Joana L; Gonçalves, Fernando; Coutinho, João A P

    2013-01-01

    Ionic liquids (ILs) are a novel class of solvents with interesting physicochemical properties. Many different applications have been reported for ILs as alternatives to organic solvents in chemical and bioprocesses. Despite the argued advantage of having low vapor pressure, even the most hydrophobic ILs show some degree of solubility in water, allowing their dispersion into aquatic systems and raising concerns on its pollutant potential. Moreover, nowadays most widespread notion concerning the ILs toxicity is that there is a direct relationship with their hydrophobicity/lipophilicity. This work aims at enlarging the currently limited knowledge on ILs toxicity by addressing negative impacts in aquatic ecosystems and investigating the possibility of designing hydrophobic ILs of low ecotoxicity, by the manipulation of their chemical structures. The impact of aromaticity on the toxicity of different cations (pyridinium, piperidinium, pyrrolidinium and imidazolium) and hydrophobic anions (bis(trifluoromethylsulfonyl)imide [NTf(2)] and hexafluorophosphate [PF(6)]) was analysed. Concomitantly, several imidazolium-based ILs of the type [C( n )C( m )C( j )im][NTf(2)] were also studied to evaluate the effects of the position of the alkyl chain on the ILs' toxicity. For that purpose, standard assays were performed using organisms of different trophic levels, Vibrio fischeri, Pseudokirchneriella subcapitata and Daphnia magna, allowing to evaluate the consistency of the structure-activity relationships across different biological targets. The results here reported suggest the possibility of designing ILs with an enhanced hydrophobic character and lower toxicity, by elimination of their aromatic nature. PMID:23010869

  9. Structure, chemical ordering and thermal stability of Pt-Ni alloy nanoclusters.

    PubMed

    Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

    2013-09-01

    Equilibrium structures, chemical ordering and thermal properties of Pt-Ni nanoalloys are investigated by using basin hopping-based global optimization, Monte Carlo (MC) and molecular dynamics (MD) methods, based on the second-moment approximation of the tight-binding potentials (TB-SMA). The TB-SMA potential parameters for Pt-Ni nanoalloys are fitted to reproduce the results of density functional theory calculations for small clusters. The chemical ordering in cuboctahedral (CO) Pt-Ni nanoalloys with 561 and 923 atoms is obtained from the so called semi-grand-canonical ensemble MC simulation at 100 K. Two ordered phases of L12 (PtNi3) and L10 (PtNi) are found for the CO561 and CO923 Pt-Ni nanoalloys, which is in good agreement with the experimental phase diagram of the Pt-Ni bulk alloy. In addition, the order-disorder transition and thermal properties of these nanoalloys are studied by using MC and MD methods, respectively. It is shown that the typical perfect L10 PtNi structure is relatively stable, showing high order-disorder transition temperature and melting point among these CO561 and CO923 Pt-Ni nanoalloys. PMID:23913101

  10. An Application of Interactive Graphics - The Nested Retrieval of Chemical Structures

    ERIC Educational Resources Information Center

    Feldman, Richard J.; Heller, Stephen R.

    1972-01-01

    A technique for structuring and searching a large file of chemical structures is presented. The technique involves generating a nested, structured tree based on the Wiswesser analysis of chemical structures. An important virtue of the tree is the rapid and inexpensive file updating. (9 references) (Author/NH)

  11. Measuring the atomic-scale structure of a Helmholtz `double layer'

    NASA Astrophysics Data System (ADS)

    Hayes, T. M.; Lurio, L. B.; Pant, J.; Wang, L.; Furtak, T. E.

    1997-03-01

    We propose a powerful new technique to measure the structure of the Helmholtz `double layer' formed in an aqueous electrolyte in contact with a metal electrode. The critical innovation is to couple a structural probe which is specific to the environment of a particular atom species with a `tag' layer of metal atoms electrodeposited in underpotential conditions on an unlike-metal electrode. The efficacy of our approach is illustrated through a measurement of the double layer in a dilute sulfuric acid electrolyte in contact with a Pt electrode decorated with Cu atoms, the surface structure of which we have studied extensively.( T E Furtak, L Wang, J Pant, K Pansewicz, and T M Hayes, J Electrochem Soc 141) 2369 (1994); L B Lurio, J Pant, T M Hayes, L Wang, and T E Furtak, Physica B 208 413 (1995)

  12. Modelling the atomic structure of Al92U8 metallic glass.

    PubMed

    Michalik, S; Bednarcik, J; Jóvári, P; Honkimäki, V; Webb, A; Franz, H; Fazakas, E; Varga, L K

    2010-10-13

    The local atomic structure of the glassy Al(92)U(8) alloy was modelled by the reverse Monte Carlo (RMC) method, fitting x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) signals. The final structural model was analysed by means of partial pair correlation functions, coordination number distributions and Voronoi tessellation. In our study we found that the most probable atomic separations between Al-Al and U-Al pairs in the glassy Al(92)U(8) alloy are 2.7 Å and 3.1 Å with coordination numbers 11.7 and 17.1, respectively. The Voronoi analysis did not support evidence of the existence of well-defined building blocks directly embedded in the amorphous matrix. The dense-random-packing model seems to be adequate for describing the connection between solvent and solute atoms. PMID:21386570

  13. Density functional study of ?-graphyne derivatives: Energetic stability, atomic and electronic structure

    NASA Astrophysics Data System (ADS)

    Sun, Chen; Liu, Yi; Xu, Jingcheng; Chi, Baoqian; Bai, Chenghao; Liu, Yifan; Li, Shengjuan; Zhao, Xinluo; Li, Xiaowu

    2015-06-01

    The energetic stability, atomic and electronic structures of ?-graphyne and its derivatives (?-GYs) with extended carbon chains were investigated by density functional (DF) calculations in this work. The studied ?-GYs consist of hexagon carbon rings sharing their edges with carbon atoms N=1-10. The structure and energy analyses show that ?-GYs with even-numbered carbon chains have alternating single and triple C-C bonds (polyyne), energetically more stable than those with odd-numbered carbon chains possessing continuous double C-C bonds (polycumulene). The calculated electronic structures indicate that ?-GYs can be either metallic (odd N) or semiconductive (even N) depending on the parity of number of atoms on hexagon edges despite the edge length. The semiconducting ?-graphyne derivatives are found to possess Dirac cones (DC) with small direct band gaps 2-40 meV and large electron velocities 0.554×106-0.671×106 m/s, 70-80% of that of graphene. Our DF studies suggest that introducing sp carbon atoms into the hexagon edges of graphene opens up an avenue to switch between metallic and DC electronic structures via tuning the parity of the number of hexagon edge atoms.

  14. CHEMICAL STRUCTURES IN COAL: GEOCHEMICAL EVIDENCE FOR THE PRESENCE OF MIXED STRUCTURAL COMPONENTS.

    USGS Publications Warehouse

    Hatcher, P.G.; Breger, I.A.; Maciel, G.E.; Szeverenyi, N.M.

    1983-01-01

    The purpose of this paper is to summarize work on the chemical structural components of coal, comparing them with their possible plant precursors in modern peat. Solid-state **1**3C nuclear magnetic resonance (NMR), infrared spectroscopy (IR), elemental analysis and, in some cases, individual compound analyses formed the bases for these comparisons.

  15. Chemical Structures at the Desktop: Integrating Drawing Tools with On-Line Registry Files.

    ERIC Educational Resources Information Center

    Baumgras, Jan L.; Rogers, Anne E.

    1995-01-01

    Examines and reviews the ability of various software packages and database systems to recognize and process chemical structures generated by chemical drawing packages, especially the ability of relational database management systems to recognize and process chemical structures from a variety of sources. The need for better standard representations…

  16. 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.

  17. 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.

  18. Unveiling the atomic and electronic structure of the VN/MgO interface

    SciTech Connect

    Zhang, Zaoli; Rashkova, B. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Leoben (Austria); Dehm, G. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Leoben (Austria); Department Materials Physics, University of Leoben, Leoben (Austria); Lazar, P.; Redinger, J. [Institute of Applied Physics, Vienna University of Technology, Vienna (Austria); Podloucky, R. [Department of Physical Chemistry, Vienna University, Vienna (Austria)

    2010-08-01

    We report a quantitative comparison of the interface structure of VN/MgO(001) using ab initio density-functional theory (DFT), aberration-corrected high-resolution transmission electron microscopy (HRTEM), and electron energy-loss spectroscopy (EELS). By HRTEM, we show an atomic resolution structure of epitaxially grown VN film on MgO with a clearly resolved oxygen and nitrogen sublattice across the interface. As revealed by DFT, the (002) interplanar spacing oscillates in the first several VN layers across the interface. Interfacial chemistry determined by EELS analysis shows the preponderance of O and V atom at the interface, resulting in a small detectable core-level shift.

  19. Role of N2 molecules in pulse discharge production of I atoms for a pulsed chemical oxygen-iodine laser

    NASA Astrophysics Data System (ADS)

    Kochetov, I. V.; Napartovich, A. P.; Vagin, N. P.; Yuryshev, N. N.

    2011-09-01

    A pulsed electric discharge is the most effective means to turn chemical oxygen-iodine laser (COIL) operation into the pulse mode by fast production of iodine atoms. Experimental studies and numerical simulations are performed on a pulsed COIL initiated by an electric discharge in a mixture CF3I : N2 : O2(3X) : O2(a 1?g) flowing out of a chemical singlet oxygen generator. A transverse pulsed discharge is realized at various iodide pressures. The model comprises a system of kinetic equations for neutral and charged species, the electric circuit equation, the gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are repeatedly re-calculated by the electron Boltzmann equation solver when the plasma parameters are changed. The processes accounted for in the Boltzmann equation include direct and stepwise excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions and second-kind collisions. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. A conclusion is drawn about satisfactory agreement between the theory and the experiment.

  20. Atomic structures and electronic properties of 2H-NbSe{sub 2}: The impact of Ti doping

    SciTech Connect

    Li, Hongping, E-mail: hpli@mail.ujs.edu.cn, E-mail: zcwang@wpi-aimr.tohoku.ac.jp; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng [Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); Liu, Xiaojuan; Meng, Jian [State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China); Wang, Zhongchang, E-mail: hpli@mail.ujs.edu.cn, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2014-09-14

    Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe{sub 2}. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe{sub 2} is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe{sub 2}, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe{sub 2}.

  1. Thermally Induced Changes in the Structure, Composition, and Chemical Properties of LiMn2O4 ± x Spinel Prepared by Sol-Gel Method

    Microsoft Academic Search

    Marcin Molenda; Roman Dziembaj; Wieslaw Lasocha; Czeslaw Rudowicz; Leonard M. Proniewicz; Edyta Podstawka; Hitoshi Ohta

    2006-01-01

    Sol-gel method followed by calcination at temperatures of 300-900 °C was used to obtain a series of LiMn2O4 samples with varying amounts of chemical and structural defects while preserving a constant Li:Mn atomic ratio. The physicochemical and structural properties of the samples were characterized by X-ray diffraction (XRD), thermal gravimetry analysis-mass spectrometry (TGA-MS), differential scanning calorimetry (DSC), and Raman spectroscopy

  2. Determination of atomic structure at surfaces and interfaces by high-resolution stem

    SciTech Connect

    Pennycook, S.J.; Chisholm, M.F. [Oak Ridge National Lab., TN (United States); Nellist, P.D. [Cambridge Univ. (United Kingdom). Cavendish Lab.; Browning, N.D. [Illinois Univ., Chicago, IL (United States). Dept. of Physics; Wallis, D.J. [Defence Research Agency, Malvern (United Kingdom); Dickey, E.C. [Northwestern Univ., Evanston, IL (United States)

    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.

  3. Structural stability and energy-gap modulation through atomic protrusion in freestanding bilayer silicene

    NASA Astrophysics Data System (ADS)

    Sakai, Yuki; Oshiyama, Atsushi

    2015-05-01

    We report on first-principles total-energy and phonon calculations that clarify structural stability and electronic properties of freestanding bilayer silicene. By extensive structural exploration, we reach all the stable structures reported before and find four additional dynamically stable structures, including the structure with the largest cohesive energy. We find that atomic protrusion from the layer is the principal relaxation pattern which stabilizes bilayer silicene and determines the lateral periodicity. The hybrid-functional calculation shows that the most stable bilayer silicene is a semiconductor with the energy gap of 1.3 eV.

  4. Evaluated Chemical Kinetic Data for the Reactions of Atomic Oxygen O(3P) with Sulfur Containing Compounds

    NASA Astrophysics Data System (ADS)

    Singleton, D. L.; Cvetanovi?, R. J.

    1988-10-01

    Chemical kinetic data for reactions of O(3P) atoms with sulfur containing compounds are compiled and critically evaluated. Specifically, the reactions considered include the interactions of the ground electronic state of oxygen atoms, O(3P), with S2, SF2, SF5, SOF, S2O, SO, SO2, SO3, SH, H2S, D2S, H2SO4, CS, CS2, COS, CH3SH, C2H5SH, C4H9SH, C5H11SH, CH3SCH3, cy-CH2SCH2, cy-CHCHSCHCH, CH3SSCH3, SCF2, SCCl2, and cy-CF2SCF2S. With one exception, the liquid phase reaction O(3P)+H2SO4?products, all the data considered were for gas phase reactions. Where possible, ``Recommended'' values of the rate parameters have been assessed and conservative uncertainty limits assigned to them.

  5. Low voltage electron diffractive imaging of atomic structure in single-wall carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Kamimura, Osamu; Maehara, Yosuke; Dobashi, Takashi; Kobayashi, Keita; Kitaura, Ryo; Shinohara, Hisanori; Shioya, Hiroyuki; Gohara, Kazutoshi

    2011-04-01

    The demand for atomic-scale analysis without serious damage to the specimen has been increasing due to the spread of applications with light-element three-dimensional (3D) materials. Low voltage electron diffractive imaging has the potential possibility to clarify the atomic-scale structure of 3D materials without causing serious damage to specimens. We demonstrate low-voltage (30 kV) electron diffractive imaging of single-wall carbon nanotube at a resolution of 0.12 nm. In the reconstructed pattern, the intensity difference between single carbon atom and two overlapping atoms can be clearly distinguished. The present method can generally be applied to other materials including biologically important ones.

  6. Systematic Study of Information Measures, Statistical Complexity and Atomic Structure Properties

    NASA Astrophysics Data System (ADS)

    Chatzisavvas, K. Ch.; Tserkis, S. T.; Panos, C. P.; Moustakidis, Ch. C.

    2015-05-01

    We present a comparative study of several information and statistical complexity measures in order to examine a possible correlation with certain experimental properties of atomic structure. Comparisons are also carried out quantitatively using Pearson correlation coefficient. In particular, it is shown that Fisher information in momentum space is very sensitive to shell effects. It is also seen that three measures expressed in momentum space that is Fisher information, Fisher-Shannon plane and LMC complexity are associated with atomic radius, ionization energy, electronegativity, and atomic dipole polarizability. Our results indicate that a momentum space treatment of atomic periodicity is superior to a position space one. Finally we present a relation that emerges between Fisher information and the second moment of the probability distribution in momentum space i.e. an energy functional of interest in (e,2e) experiments.

  7. Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation of cold molecular ions

    E-print Network

    Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation polarizability, of molecular ions composed of one alkali-metal atom and a Strontium ion are determined of molecular ions with laser-cooled atomic ions thus forming so-called ion crystals where individual ions

  8. 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

    2014-11-01

    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 ?-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 ?-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 ?-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to ?-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. PMID:25310276

  9. One-pot hydrazide-based native chemical ligation for efficient chemical synthesis and structure determination of toxin Mambalgin-1.

    PubMed

    Pan, Man; He, Yao; Wen, Ming; Wu, Fangming; Sun, Demeng; Li, Sijian; Zhang, Longhua; Li, Yiming; Tian, Changlin

    2014-06-01

    An efficient one-pot chemical synthesis of snake venom toxin Mambalgin-1 was achieved using an azide-switch strategy combined with hydrazide-based native chemical ligation. Synthetic Mambalgin-1 exhibited a well-defined structure after sequential folding in vitro. NMR spectroscopy revealed a three-finger toxin family structure, and the synthetic toxin inhibited human acid-sensing ion channel 1a. PMID:24619065

  10. A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  11. Chemical and structural analyses of titanium plates retrieved from patients.

    PubMed

    Pinto, C M S A; Asprino, L; de Moraes, M

    2015-08-01

    The aim of this study was to evaluate the microscopic structure and chemical composition of titanium bone plates and screws retrieved from patients with a clinical indication and to relate the results to the clinical conditions associated with the removal of these devices. Osteosynthesis plates and screws retrieved from 30 patients between January 2010 and September 2013 were studied by metallographic, gas, and energy dispersive X-ray (EDX) analyses and the medical records of these patients were reviewed. Forty-eight plates and 238 screws were retrieved. The time elapsed between plate and screw insertion and removal ranged between 11 days and 10 years. Metallographic analysis revealed that all the plates were manufactured from commercially pure titanium (CP-Ti). The screw samples analyzed consisted of Ti-6Al-4V alloy, except four samples, which consisted of CP-Ti. Titanium plates studied by EDX analysis presented greater than 99.7% titanium by mass. On gas analysis of Ti-6Al-4V screws, three samples were outside the standard values. One CP-Ti screw sample and one plate sample also presented an oxygen analysis value above the standard. The results indicated that the physical properties and chemical compositions of the plates and screws did not correspond with the need to remove these devices or the time of retention. PMID:25735535

  12. Long range ordered magnetic and atomic structures of the quasicrystal approximant in the Tb-Au-Si system.

    PubMed

    Gebresenbut, Girma; Andersson, Mikael Svante; Beran, P?emysl; Manuel, Pascal; Nordblad, Per; Sahlberg, Martin; Gomez, Cesar Pay

    2014-08-13

    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. PMID:25055216

  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, P?emysl; 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. Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

    SciTech Connect

    Okada, H. [Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580 (Japan); Kato, M.; Ishimaru, T.; Sekiguchi, H.; Wakahara, A. [Department of Electrical- and Electronic Information Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580 (Japan); Furukawa, M. [Aries Research Group, 1-25-11 Fujizuka, Kohoku-ku, Yokohama 222-0012 (Japan)

    2014-02-20

    Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma is investigated. Feasibility of precursors of triethylsilane (TES) and bis(dimethylamino)dimethylsilane (BDMADMS) is discussed based on a calculation of bond energies by computer simulation. Refractive indices of 1.81 and 1.71 are obtained for deposited films with TES and BDMADMS, respectively. X-ray photoelectron spectroscopy (XPS) analysis of the deposited film revealed that TES-based film coincides with the stoichiometric thermal silicon nitride.

  15. Consensus methods for combining multiple clusterings of chemical structures.

    PubMed

    Saeed, Faisal; Salim, Naomie; Abdo, Ammar

    2013-05-24

    The goal of consensus clustering methods is to find a consensus partition that optimally summarizes an ensemble and improves the quality of clustering compared with single clustering algorithms. In this paper, an enhanced voting-based consensus method was introduced and compared with other consensus clustering methods, including co-association-based, graph-based, and voting-based consensus methods. The MDDR and MUV data sets were used for the experiments and were represented by three 2D fingerprints: ALOGP, ECFP_4, and ECFC_4. The results were evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster using four criteria: F-measure, Quality Partition Index (QPI), Rand Index (RI), and Fowlkes-Mallows Index (FMI). The experiments suggest that the consensus methods can deliver significant improvements for the effectiveness of chemical structures clustering. PMID:23581471

  16. Detuning-induced stimulated Raman adiabatic passage in atoms with hyperfine structure

    NASA Astrophysics Data System (ADS)

    Deng, Li; Nakajima, Takashi

    2014-02-01

    We theoretically study the generation of coherence in generalized two-level atoms with hyperfine structure by utilizing the detuning-induced stimulated Raman adiabatic passage (D-STIRAP). As expected, the degree of attainable coherence between the ground and excited states cannot be as large as that for the ideal two-level atoms without hyperfine structure. However, we find that the substantial degree of coherence can still be produced with small modulations, and the modulation period is essentially determined by the hyperfine splittings in the ground and excited states. The D-STIRAP scheme in generalized two-level atoms is sufficiently robust against the various parameters such as intensities of lasers, initial detuning, time delay between the laser pulses, and Doppler broadening. As a specific example, we show realistic results for the D1 transition of Na.

  17. Cobalt as chemical modifier to improve chromium sensitivity and minimize matrix effects in tungsten coil atomic emission spectrometry.

    PubMed

    Silva, Sidnei G; Donati, George L; Santos, Luana N; Jones, Bradley T; Nóbrega, Joaquim A

    2013-05-30

    Cobalt is used as chemical modifier to improve sensitivity and minimize matrix effects in Cr determinations by tungsten coil atomic emission spectrometry (WCAES). The atomizer is a tungsten filament extracted from microscope light bulbs. A solid-state power supply and a handheld CCD-based spectrometer are also used in the instrumental setup. In the presence of 1000 mg L(-1) Co, WCAES limit of detection for Cr (?=425.4 nm) is calculated as 0.070 mg L(-1); a 10-fold improvement compared to determinations without Co modifier. The mechanism involved in such signal enhancement is similar to the one observed in ICP OES and ICP-MS determinations of As and Se in the presence of C. Cobalt increases the population of Cr(+) by charge transfer reactions. In a second step, Cr(+)/e(-) recombination takes place, which results in a larger population of excited-state Cr atoms. This alternative excitation route is energetically more efficient than heat transfer from atomizer and gas phase to analyte atoms. A linear dynamic range of 0.25-10 mg L(-1) and repeatability of 3.8% (RSD, n=10) for a 2.0 mg L(-1) Cr solution are obtained with this strategy. The modifier high concentration also contributes to improving accuracy due to a matrix-matching effect. The method was applied to a certified reference material of Dogfish Muscle (DORM-2) and no statistically significant difference was observed between determined and certified Cr values at a 95% confidence level. Spike experiments with bottled water samples resulted in recoveries between 93% and 112%. PMID:23680545

  18. Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

    SciTech Connect

    Deckert, Katelyn; Budiardjo, S. Jimmy; Brunner, Luke C.; Lovell, Scott; Karanicolas, John (Kansas)

    2012-08-07

    Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a {beta}-glycosidase enzyme ({beta}-gly) and W492G in a {beta}-glucuronidase enzyme ({beta}-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of {beta}-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of {beta}-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate {beta}-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

  19. 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.

  20. Structure in multilayer films of zinc sulfide and copper sulfide via atomic layer deposition

    SciTech Connect

    Short, Andrew; Jewell, Leila; Bielecki, Anthony; Keiber, Trevor; Bridges, Frank; Carter, Sue; Alers, Glenn, E-mail: galers@ucsc.edu [Department of Physics, University of California at Santa Cruz, 1156 High Street, Santa Cruz, California 95064 (United States)

    2014-01-15

    Multilayer film stacks of ZnS and Cu{sub x}S (x???2) were made via atomic layer deposition. The precursors were bis(2,2,6,6-tetramethyl-3,5-heptanedionato)zinc, bis(2,2,6,6-tetramethyl-3,5-heptanedionato)copper, and H{sub 2}S generated in situ for sulfur. Samples were deposited at 200?°C, in layers ranging from approximately 2 to 20 nm thick, based on binary growth rates. The properties of the film stacks were studied with atomic force microscopy, ultraviolet–visible spectroscopy, and extended x-ray absorption fine structure. The results demonstrate that the structure of films with the thinnest layers is dominated by Cu{sub x}S, whereas in the thicker films, the structure is determined by whichever material is first deposited. This can be attributed to the crystal structure mismatch of ZnS and Cu{sub x}S.

  1. Effect of chemical pressure on the local structure of La1?xSmxFeAsO system

    NASA Astrophysics Data System (ADS)

    Iadecola, A.; Joseph, B.; Paris, E.; Provino, A.; Martinelli, A.; Manfrinetti, P.; Putti, M.; Saini, N. L.

    2015-02-01

    We have studied the effect of chemical pressure on the local structure of La1-xSmxFeAsO oxypnictides. The combination of arsenic K-edge and rare-earth (RE = La, Sm) L3-edge x-ray absorption spectra has permitted us to determine local bondlengths and unoccupied electronic states with varying chemical pressure controlled by the size difference of La and Sm. The Fe–As distance is hardly affected by the chemical pressure, and remains covalent as shown by As K-edge extended x-ray absorption fine structure (EXAFS) analysis. On the other hand, the As–RE and As–As distances show a gradual change. The changes indicate a larger effect of chemical pressure in the REO spacer layer and on the interlayer interactions, consistent with x-ray absorption near edge structure (XANES) data. The results suggest that interlayer atomic correlations are likely to have an important role in the physical properties of the La1-xSmxFeAsO parent phases of the superconducting oxypnictides.

  2. Most probable distance between the nucleus and HOMO electron: the latent meaning of atomic radius from the product of chemical hardness and polarizability.

    PubMed

    Szarek, Pawe?; Grochala, Wojciech

    2014-11-01

    The simple relationship between size of an atom, the Pearson hardness, and electronic polarizability is described. The estimated atomic radius correlates well with experimental as well as theoretical covalent radii reported in the literature. Furthermore, the direct connection of atomic radius to HOMO electron density and important notions of conceptual DFT (such as frontier molecular orbitals and Fukui function) has been shown and interpreted. The radial maximum of HOMO density distribution at (??)(1/2) minimizes the system energy. Eventually, the knowledge of the Fukui function of an atom is sufficient to estimate its electronic polarizability, chemical potential, and hardness. PMID:25286065

  3. Imaging the atomic surface structures of CeO2 nanoparticles

    SciTech Connect

    Lin, Yuyuan [Northwestern University, Evanston] [Northwestern University, Evanston; Wu, Zili [ORNL] [ORNL; Wen, Jianguo [Argonne National Laboratory (ANL)] [Argonne National Laboratory (ANL); Poeppelmeier, Kenneth R [Northwestern University, Evanston] [Northwestern University, Evanston; Marks, Laurence D [Northwestern University, Evanston] [Northwestern University, Evanston

    2014-01-01

    Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear experimental determination of the positions of the surface oxygen atoms. Particularly controversial is the (100) surface structure of this material. In this study, with oxygen atoms clearly observed using aberration corrected high resolution electron microscopy, we determined the atomic structures of the (100), (110) and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has a mixture of Ce, O, and reduced CeO terminations, underscoring the complex structures of this polar surface that previously was often oversimplified. The (110) surface shows saw-like (111) nanofacets and flat CeO2-x terminations with oxygen vacancies. The (111) surface has an O termination. As these three low index surfaces are the most often exposed facets in the majority of CeO2 nanoparticles, these findings can be extended to the surfaces of differently shaped CeO2 nanoparticles as well as provide insight about face-selective catalysis.

  4. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS An all-atom knowledge-based energy function

    E-print Network

    Zhou, Yaoqi

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS An all-atom knowledge-based energy function Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana. Interaction between DNA and proteins could be described by various types of energy functions. Existing energy

  5. 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…

  6. Atomic and electronic structures of surface kinks on GaAs(001) surfaces

    Microsoft Academic Search

    Kenji Shiraishi; Tomonori Ito

    1997-01-01

    We investigate the atomic and electronic structures of surface dimer kinks using the ab initio calculations. We investigated the (2 × 4) and the c(2 × 8) dimer kink models. The calculated results show that weak As dimers are formed at (2 × 4) dimer kinks by the de-stabilization of occupied As dangling bond states and that (2 × 4)

  7. Photodissociation of HI and DI: Testing models for electronic structure via polarization of atomic photofragments

    E-print Network

    Brown, Alex

    Photodissociation of HI and DI: Testing models for electronic structure via polarization of atomic The photodissociation dynamics of HI and DI are examined using time-dependent wave-packet techniques. The orientation would be able to distinguish between the available models for the HI potential-energy curves

  8. Three-dimensional imaging of local atomic and magnetic structure in compound epitaxial films

    E-print Network

    Korecki, Pawe³

    Three-dimensional imaging of local atomic and magnetic structure in compound epitaxial films with c in compound epitaxial films and in low-dimensional systems is investigated using realistic simulations performed for magnetite Fe3O4. Ó 2002 Elsevier Science B.V. All rights reserved. Keywords: X-ray scattering

  9. Dynamic Load Balancing of Atomic Structure Programs on a PVM Cluster

    E-print Network

    Stathopoulos, Andreas

    Dynamic Load Balancing of Atomic Structure Programs on a PVM Cluster Andreas Stathopoulos \\Lambda, modifications of two well­known dynamic load balancing schemes are implemented and tested. The resulting codes­ tational demands, the package has previously been implemented in PVM. The codes have been used

  10. Atomic structure of carbon nanotubes from scanning tunneling microscopy L. C. Venema

    E-print Network

    electronic2 and mechanical3 properties. They can be considered as graphene sheets that are rolled upAtomic structure of carbon nanotubes from scanning tunneling microscopy L. C. Venema Department of a carbon nanotube can be described by its chiral angle and diameter and can be specified by a pair

  11. Effect of the porous structure of graphite on atomic hydrogen diffusion and inventory

    E-print Network

    Nordlund, Kai

    : Nuclear Fusion 1. Introduction Graphites and carbon fiber composites (CFCs) are used as plasma facing is an illustration of the composition of a granule. It consists of 50-100 °A sized crystallites of graphiteEffect of the porous structure of graphite on atomic hydrogen diffusion and inventory M.Warrier1

  12. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates

    PubMed Central

    Radisky, Evette S.; Lee, Justin M.; Lu, Chia-Jung Karen; Koshland, Daniel E.

    2006-01-01

    Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction. PMID:16636277

  13. Protein structure prediction by all-atom free-energy refinement

    Microsoft Academic Search

    Abhinav Verma; Wolfgang Wenzel

    2007-01-01

    BACKGROUND: The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure

  14. The atomic and electronic structure of the Sigma=3 (211) twin boundary in Si

    Microsoft Academic Search

    M. Kohyama; R. Yamamoto; Y. Watanabe; Y. Ebata; M. Kinoshita

    1988-01-01

    The atomic and electronic structures of the Sigma =3 (211) twin boundary in Si have been calculated using a supercell method based on a semi-empirical tight-binding model. Energy-minimisation calculations have shown that the system described by the reconstructed model given by Bourret and Bacmann (1986) can exist stably in Si. For this boundary structure, no deep states or band tails

  15. From Favorable Atomic Configurations to Supershell Structures: A New Interpretation of Conductance Histograms

    SciTech Connect

    Hasmy, A.; Medina, E.; Serena, P. A.

    2001-06-11

    Simulated minimum cross-section histograms of breaking Al nanocontacts are produced using molecular dynamics. The results allow a new interpretation of the controverted conductance histogram peaks based on preferential geometrical arrangements of nanocontact necks. As temperature increases, lower conductance peaks decrease in favor of broader and higher conductance structures. This reveals the existence of shell and supershell structures favored by the increased mobility of Al atoms.

  16. Ellipsoid-like structures formed by atomic force microscopy in Langmuir-Blodgett films of PMMA

    Microsoft Academic Search

    J. B. Peng; G. T. Barnes

    1996-01-01

    The surface structure of Langmuir-Blodgett (LB) and cast films of poly(methyl methacrylate) (PMMA) in isotactic, syndiotactic and atactic conformations were probed by atomic force microscopy. The LB films exhibited smooth surfaces during the first scan, but as scanning continued ellipsoid-like structures developed with the long axes oriented parallel to the scanning direction of the tip. The average size of the

  17. NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

    PubMed Central

    Dunn, Michael F.

    2013-01-01

    Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the ?-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

  18. Crystal structure, spectroscopic investigations and quantum chemical calculational studies of N-diphenylphosphino-4-methylpiperidine sulfide

    NASA Astrophysics Data System (ADS)

    Saraço?lu, Hanife; Sariöz, Özlem; Öznergiz, Sena

    2014-04-01

    The title molecule, N-diphenylphosphino-4-methylpiperidine sulfide (I), has been synthesized and characterized by elemental analysis, 1H NMR, 31P NMR, IR and X-ray single-crystal determination. The molecular geometry from X-ray determination, vibrational frequencies and gauge, including atomic orbital (GIAO) 1H NMR and 31P NMR chemical shift values of the title compound (I) in the ground state have been calculated using the density functional theory with the 6-31G(d), 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results show that the optimized geometry can well reproduce the crystal structure, and theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. The predicted nonlinear optical properties of the title compound are greater than those of urea. In addition, DFT calculations of the molecular electrostatic potentials, frontier molecular orbitals of the title compound were carried out at the B3LYP/6-31G(d) level of theory.

  19. Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations.

    PubMed

    Nagabalasubramanian, P B; Periandy, S; Karabacak, Mehmet; Govindarajan, M

    2015-06-15

    The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100cm(-1). The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated. PMID:25795608

  20. Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Nagabalasubramanian, P. B.; Periandy, S.; Karabacak, Mehmet; Govindarajan, M.

    2015-06-01

    The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100 cm-1. The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.

  1. The Distortion of the Hexagonal Close Packing of Oxygen Atoms in Co(OH) 2 Compared to Isotypic Brucite-Type Structures

    Microsoft Academic Search

    Franz Pertlik

    1999-01-01

    Summary.  ?A refinement of the crystal structure of Co(OH)2 (structure type brucite; a=3.186(1), c=4.653(1) Å; space group P;m1) is the basis for crystal chemical considerations about distortions of the MeO6 octahedra and deviations of the lattice parameters ratio c\\/a from the ideal value of (8\\/3)1\\/2?1.633 for the theoretical model of a hexagonal close packing of oxygen atoms. The MeO6 octahedra in

  2. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  3. Computer Prediction of Possible Toxic Action from Chemical Structure; The DEREK System

    Microsoft Academic Search

    D. M. Sanderson; C. G. Earnshaw

    1991-01-01

    1 The development of DEREK, a computer-based expert system (derived from the LHASA chemical synthesis design program) for the qualitative prediction of possible toxic action of compounds on the basis of their chemical structure is described.2 The system is able to perceive chemical sub-structures within molecules and relate these to a rulebase linking the sub-structures with likely types of toxicity.3

  4. Query Chem: a Google-powered web search combining text and chemical structures

    Microsoft Academic Search

    Justin Klekota; Frederick P. Roth; Stuart L. Schreiber

    2006-01-01

    Summary: Query Chem (www.QueryChem.com) is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program Interface (API). Query Chem makes it possible to search the Web for information about chemical structures without knowing their common names or identifiers. Furthermore, a structure can be com- bined with textual query terms to

  5. Atomic-scale dynamical structures of fatty acid bilayers observed by ultrafast electron crystallography.

    PubMed

    Chen, Songye; Seidel, Marco T; Zewail, Ahmed H

    2005-06-21

    The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the two chains containing 40 carbon atoms (approximately = 50 angstroms), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a0 = 4.7 angstroms, b0 = 8.0 angstroms, and c0 = 2.54 angstroms. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump. The observed motions, with sub-angstroms resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times. This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast electron crystallography. PMID:15956181

  6. An x ray scatter approach for non-destructive chemical analysis of low atomic numbered elements

    NASA Technical Reports Server (NTRS)

    Ross, H. Richard

    1993-01-01

    A non-destructive x-ray scatter (XRS) approach has been developed, along with a rapid atomic scatter algorithm for the detection and analysis of low atomic-numbered elements in solids, powders, and liquids. The present method of energy dispersive x-ray fluorescence spectroscopy (EDXRF) makes the analysis of light elements (i.e., less than sodium; less than 11) extremely difficult. Detection and measurement become progressively worse as atomic numbers become smaller, due to a competing process called 'Auger Emission', which reduces fluorescent intensity, coupled with the high mass absorption coefficients exhibited by low energy x-rays, the detection and determination of low atomic-numbered elements by x-ray spectrometry is limited. However, an indirect approach based on the intensity ratio of Compton and Rayleigh scattered has been used to define light element components in alloys, plastics and other materials. This XRS technique provides qualitative and quantitative information about the overall constituents of a variety of samples.

  7. Single-molecule chemical reactions tracked at the atomic-bond level.

    PubMed

    Lu, Jiong; Loh, Kian Ping

    2013-12-16

    On the right track: Recent advances in noncontact atomic force microscopy (nc-AFM) have enabled the bond-resolved imaging of reaction pathways. In particular, unprecedented insights into complex enediyne cyclization cascades on silver surfaces were gained by single-molecule imaging. PMID:24155108

  8. Measuring Atomic Emission from Beacons for Long-Distance Chemical Signaling

    E-print Network

    Weitz, David

    by a combustion reaction. Our system uses the thermal excitation of alkali metals to transmit an encoded signal for nearly 10 min. The signal is isotropic, is self-powered, and has a low background. A potential distances. The beacon is fueled by the combustion of methanol. Our atomic emission beacon is prepared

  9. A novel cleaning method of gold-coated atomic force microscope tips for their chemical modification

    Microsoft Academic Search

    Masamichi Fujihira; Yoh Okabe; Yuki Tani; Manabu Furugori; Uichi Akiba

    2000-01-01

    For chemical modification of gold-coated AFM tips with thiol or sulfide compounds, a new two-step precleaning procedure was studied. The two-step cleaning procedure involves (i) oxidation of organic contaminants on the AFM tips with ozone treatment and (ii) reduction of the oxidized gold surface by immersing the oxidized tip into pure hot ethanol at ca. 65°C. The chemically modified tips

  10. Determination of bismuth in environmental samples by slurry sampling graphite furnace atomic absorption spectrometry using combined chemical modifiers.

    PubMed

    Dobrowolski, Ryszard; Dobrzy?ska, Joanna; Gawro?ska, Barbara

    2015-01-01

    Slurry sampling graphite furnace atomic absorption spectrometry technique was applied for the determination of Bi in environmental samples. The study focused on the effect of Zr, Ti, Nb and W carbides, as permanent modifiers, on the Bi signal. Because of its highest thermal and chemical stability and ability to substantially increase Bi signal, NbC was chosen as the most effective modifier. The temperature programme applied for Bi determination was optimized based on the pyrolysis and atomization curves obtained for slurries prepared from certified reference materials (CRMs) of the soil and sediments. To overcome interferences caused by sulfur compounds, Ba(NO?)? was used as a chemical modifier. Calibration was performed using the aqueous standard solutions. The analysis of the CRMs confirmed the reliability of the proposed analytical method. The characteristic mass for Bi was determined to be 16 pg with the detection limit of 50 ng/g for the optimized procedure at the 5% (w/v) slurry concentration. PMID:25384374

  11. Development of Constraint Algorithm for the Number of Electrons in Molecular Orbitals Consisting Mainly 4 f Atomic Orbitals of Rare-Earth Elements and Its Introduction to Tight-Binding Quantum Chemical Molecular Dynamics Method

    NASA Astrophysics Data System (ADS)

    Endou, Akira; Onuma, Hiroaki; Jung, Sun-ho; Ishimoto, Ryota; Tsuboi, Hideyuki; Koyama, Michihisa; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A.; Miyamoto, Akira

    2007-04-01

    Our original tight-binding quantum chemical molecular dynamics code, “Colors”, has been successfully applied to the theoretical investigation of complex materials including rare-earth elements, e.g., metal catalysts supported on a CeO2 surface. To expand our code so as to obtain a good convergence for the electronic structure of a calculation system including a rare-earth element, we developed a novel algorithm to provide a constraint condition for the number of electrons occupying the selected molecular orbitals that mainly consist of 4 f atomic orbitals of the rare-earth element. This novel algorithm was introduced in Colors. Using Colors, we succeeded in obtaining the classified electronic configurations of the 4 f atomic orbitals of Ce4+ and reduced Ce ions in a CeO2 bulk model with one oxygen defect, which makes it difficult to obtain a good convergence using a conventional first-principles quantum chemical calculation code.

  12. Electronic structure and chemical bonding in PuO2

    NASA Astrophysics Data System (ADS)

    Teterin, Yu. A.; Maslakov, K. I.; Teterin, A. Yu.; Ivanov, K. E.; Ryzhkov, M. V.; Petrov, V. G.; Enina, D. A.; Kalmykov, St. N.

    2013-06-01

    Quantitative analysis of the x-ray photoelectron spectra structure in the binding energy (BE) range of 0 eV-˜35 eV for plutonium dioxide (PuO2) valence electrons was done. The BEs and structure of the core electronic shells (35 eV-1250 eV BE), as well as the relativistic discrete variation calculation results for the finite fragments of the PuO2 lattice and the data of other authors, were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the outer (0 eV-˜15 eV) and the inner (˜15 eV-˜35 eV) valence molecular orbitals (OVMO and IVMO, respectively). The filled Pu 5f electronic states were shown to form in the PuO2 valence band. The Pu 6p electrons participate in the formation of both the IVMO and the OVMO (bands). The filled Pu 6p3/2 and the O 2s electronic shells were found to take maximum part in the IVMO formation. The MO composition and the sequence order in the BE range of 0 eV-˜35 eV in PuO2 were established. The experimental and theoretical data allowed a quantitative MO scheme for PuO2, which is fundamental for understanding both the chemical bond nature in plutonium dioxide and the interpretation of other x-ray spectra of PuO2.

  13. Atomic scale identification of the terminating structure of compound materials by CAICISS (coaxial impact collision ion scattering spectroscopy)

    Microsoft Academic Search

    O. Ishiyama; T. Nishihara; S. Hayashi; M. Shinohara; M. Yoshimoto; T. Ohnishi; H. Koinuma; S. Nishino; J. Saraie

    1997-01-01

    Quantitative surface analysis includes the determination of the elemental composition and the structure of the sample under investigation. Although LEED, XPS, and SPM etc. have been used to investigate the surface structure of the materials, ambiguity remains in determining quantitatively the topmost atomic species and its alignment on an atomic scale. Therefore, we adopted coaxial impact collision ion scattering spectroscopy

  14. Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR.

    PubMed

    Franks, W Trent; Wylie, Benjamin J; Schmidt, Heather L Frericks; Nieuwkoop, Andrew J; Mayrhofer, Rebecca-Maria; Shah, Gautam J; Graesser, Daniel T; Rienstra, Chad M

    2008-03-25

    Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography. PMID:18344321

  15. On the chemical and structural evolution of the galactic disk

    SciTech Connect

    Toyouchi, Daisuke; Chiba, Masashi [Astronomical Institute, Tohoku University, Aoba-ku, Sendai 980-8578 (Japan)

    2014-06-10

    We study the detailed properties of the radial metallicity gradient in the stellar disk of our Galaxy to constrain its chemical and structural evolution. For this purpose we select and analyze ?18,500 disk stars taken from two data sets, the Sloan Digital Sky Survey (SDSS) and the High-Accuracy Radial velocity Planetary Searcher (HARPS). On these surveys we examine the metallicity gradient, ?[Fe/H]/?R {sub g}, along the guiding center radii, R {sub g}, of stars and its dependence on the [?/Fe] ratios to infer the original metallicity distribution of the gas disk from which those stars formed and its time evolution. In both sample sources, the thick-disk candidate stars characterized by high [?/Fe] ratios ([?/Fe] > 0.3 in SDSS, [?/Fe] > 0.2 in HARPS) are found to show a positive ?[Fe/H]/?R {sub g}, whereas the thin-disk candidate stars characterized by lower [?/Fe] ratios show a negative one. Furthermore, we find that the relatively young thin-disk population characterized by much lower [?/Fe] ratios ([?/Fe] < 0.2 in SDSS, [?/Fe] < 0.1 in HARPS) notably shows a flattening ?[Fe/H]/?R {sub g} with decreasing [?/Fe], in contrast to the old one with higher [?/Fe] ratios ([?/Fe] ? 0.2 in SDSS, [?/Fe] ? 0.1 in HARPS). The possible implication for early disk evolution is discussed in the context of galaxy formation accompanying the rapid infall of primordial gas on the inner disk region, which can generate a positive metallicity gradient, and the subsequent chemical evolution of the disk, which results in a flattening effect of a metallicity gradient at later epochs.

  16. Competition between surface modification and abrasive polishing: a method of controlling the surface atomic structure of 4H-SiC (0001)

    PubMed Central

    Deng, Hui; Endo, Katsuyoshi; Yamamura, Kazuya

    2015-01-01

    The surface atomic step-terrace structure of 4H-SiC greatly affects its performance in power device applications. On the basis of the crystal structure of 4H-SiC, we propose the generation mechanism of the a-b-a*-b* type, a-b type and a-a type step-terrace structures. We demonstrate that the step-terrace structure of SiC can be controlled by adjusting the balance between chemical modification and physical removal in CeO2 slurry polishing. When chemical modification plays the main role in the polishing of SiC, the a-b-a*-b* type step-terrace structure can be generated. When the roles of physical removal and chemical modification have similar importance, the a-b-a*-b* type step-terrace structure changes to the a-b type. When physical removal is dominant, the uniform a-a type step-terrace structure can be generated. PMID:25752524

  17. Competition between surface modification and abrasive polishing: a method of controlling the surface atomic structure of 4H-SiC (0001)

    NASA Astrophysics Data System (ADS)

    Deng, Hui; Endo, Katsuyoshi; Yamamura, Kazuya

    2015-03-01

    The surface atomic step-terrace structure of 4H-SiC greatly affects its performance in power device applications. On the basis of the crystal structure of 4H-SiC, we propose the generation mechanism of the a-b-a*-b* type, a-b type and a-a type step-terrace structures. We demonstrate that the step-terrace structure of SiC can be controlled by adjusting the balance between chemical modification and physical removal in CeO2 slurry polishing. When chemical modification plays the main role in the polishing of SiC, the a-b-a*-b* type step-terrace structure can be generated. When the roles of physical removal and chemical modification have similar importance, the a-b-a*-b* type step-terrace structure changes to the a-b type. When physical removal is dominant, the uniform a-a type step-terrace structure can be generated.

  18. Competition between surface modification and abrasive polishing: a method of controlling the surface atomic structure of 4H-SiC (0001).

    PubMed

    Deng, Hui; Endo, Katsuyoshi; Yamamura, Kazuya

    2015-01-01

    The surface atomic step-terrace structure of 4H-SiC greatly affects its performance in power device applications. On the basis of the crystal structure of 4H-SiC, we propose the generation mechanism of the a-b-a*-b* type, a-b type and a-a type step-terrace structures. We demonstrate that the step-terrace structure of SiC can be controlled by adjusting the balance between chemical modification and physical removal in CeO2 slurry polishing. When chemical modification plays the main role in the polishing of SiC, the a-b-a*-b* type step-terrace structure can be generated. When the roles of physical removal and chemical modification have similar importance, the a-b-a*-b* type step-terrace structure changes to the a-b type. When physical removal is dominant, the uniform a-a type step-terrace structure can be generated. PMID:25752524

  19. Atomic-scale structure of single-layer MoS2 nanoclusters

    PubMed

    Helveg; Lauritsen; Laegsgaard; Stensgaard; Norskov; Clausen; Topsoe; Besenbacher

    2000-01-31

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide ( MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2 nanoparticles synthesized on Au(111), and establishes a new picture of the active edge sites of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in general. PMID:11017413

  20. The atomic structure of {101¯0} inversion domain boundaries in GaN/sapphire layers

    NASA Astrophysics Data System (ADS)

    Potin, V.; Ruterana, P.; Nouet, G.

    1997-09-01

    Using high resolution electron microscopy and extensive image simulation, the atomic structure of the inversion boundaries has been determined in GaN layers grown on sapphire by electron cyclotron resonance assisted molecular beam epitaxy. They form nanometric domains (5-20 nm) limited by {101¯0} planes crossing the whole epitaxial layer. These small dimensions excluded the use of more conventional microscopy methods such as convergent beam diffraction for their characterization. For image simulations, up to 10 models including the well known Austerman-Gehman and Holt ones were considered for the boundary atomic structure. The overall agreement with the observed contrast was reached for a Holt type model of structure in which the boundary plane contains two wrong bonds per atom. Although the overall atomic configuration is neutral in {101¯0} boundary planes, it is expected to be highly energetic in ionic materials like GaN due to the difference in Ga-Ga and N-N bond length and local charge difference. This may probably explain the small size of the domains observed in the present samples.

  1. Microscopic Structure of Mn Atom Chains on the Si(001) Surface Investigated by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Fuhrer, A.; Rueß, F. J.; Moll, N.; Curioni, A.; Widmer, D.

    2013-03-01

    The Si(001) 2x1 reconstructed surface has the interesting property that many metal atom species form nearly perfect 1D atomic wires oriented perpendicular to the Si dimer rows during deposition at room temperature. These wires are thought to consist of metal dimers located between the dimer rows linking up to form atomic chains. More recent experiments indicated that similar wire formation occurs for Mn which, with its half filled d-shell, has interesting magnetic properties e.g. when used as a dopant in dilute magnetic semiconductors. In our experiments we use scanning tunneling microscopy to study the atomic structure of these Mn-wires in detail and find that it is different from that of the other known metal wires. We show that two distinct types of Mn wires occur, with an asymmetric appearance relative to the underlying Si lattice. While one type of asymmetry can be linked to the buckling of the Si dimers near the Mn-wires the other is found to be intrinsic to the microscopic structure of the Mn-wires. We further compare high-resolution bias-dependent constant current images with images simulated for a Mn trimer wire structure using density functional calculations employing the CPMD code.

  2. New icosahedral nanoclusters in crystal structures of intermetallic compounds: Topological types of 50-atom deltahedra D50 in samson phases ?-Mg2Al3 and ?-Mg23Al30

    NASA Astrophysics Data System (ADS)

    Blatov, V. A.; Ilyushin, G. D.

    2012-12-01

    A database of intermetallic compounds has been compiled using the TOPOS program package. This database includes 514 topological types, containing 12- and 13-atom icosahedral i clusters. An isolated group of 1649 i clusters is described by 14 point groups and their maximum symmetry D 3 d (bar 3 m) and T h ( m bar 3) is established, respectively, in 47 and 25 types of crystal structures. A structural analysis of the outer quasispherical shells showed that local 63-atom i configurations 1@12@50, which contain 50 atoms in the second layer, are implemented in 8 out of 19 cases. Examples of new topologically different types of 50-atom D50 deltahedra in the Samson phases ?-Mg23Al30 and ?-Mg2Al3 are presented. Four topologically different sites with coordination numbers of 5, 6, 6, or 7 are established in the ? shell and seven sites with coordination numbers of 5, 5, 6, 6, 6, 6, or 7 are found in the ? shell. The inner i clusters for the ?-Mg2Al3 structure (with the symmetry bar 3 m) and the ?-Mg23Al30 structure (with the symmetry bar 3) have a similar chemical composition, i.e., Mg7Al6 and Mg6Al7, and their 50-atom shells are chemically identical to 18Mg + 32Al. The configurations found supplement the series of known two-layer icosahedral Bergman and Mackay clusters in the form of deltahedra with 32- and 42-atom shells.

  3. Prediction of Harmful Human Health Effects of Chemicals from Structure

    Microsoft Academic Search

    Mark T. D. Cronin

    2010-01-01

    There is a great need to assess the harmful effects of chemicals to which man is exposed. Various in silico techniques including chemical grouping and category formation, as well as the use of (Q)SARs can be applied to predict the toxicity of chemicals for a number of toxicological effects. This chapter provides an overview of the state of the art

  4. Charge transfer driven surface segregation of gold atoms in 13-atom Au–Ag nanoalloys and its relevance to their structural, optical and electronic properties

    Microsoft Academic Search

    Fuyi Chen; Roy L. Johnston

    2008-01-01

    The structural, optical and electronic properties of 13-atom Ag–Au nanoalloys are determined by a combination of global optimization using semi-empirical potentials and density functional theory calculations. A family of Au surface-segregated structures are found for core–shell AgnAu13?n (n=1,2,3,5,7,8,9,12) and hollow AgnAu13?n (n=4,6,10,11) clusters, whose stability is enhanced by directional charge transfer. The atomic ordering in core–shell structures is related to

  5. 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. PMID:25470462

  6. Atomic structure and electronic properties of the In/Si(111)2×2 surface

    NASA Astrophysics Data System (ADS)

    Chou, J. P.; Wei, C. M.; Wang, Y. L.; Gruznev, D. V.; Bondarenko, L. V.; Matetskiy, A. V.; Tupchaya, A. Y.; Zotov, A. V.; Saranin, A. A.

    2014-04-01

    The Si(111)2×2-In reconstruction can be considered as a precursor phase for the formation of the metallic ?7 ×?3 phases of In overlayers on a Si(111) surface. Using the ab initio random structure searching method, comparison of simulated and experimental scanning tunneling microscopy images, and resemblance of the calculated band structure to the experimental angle-resolved photoelectron spectra, we examined various 2×2 structure models with 0.5, 0.75, 1.0, and 1.25 monolayer In coverage. The only model which fits well all the requirements is the one-monolayer model, where three In atoms in the T4 sites form a trimer centered in the H3 site and the fourth In atom occupies the on-top (T1) site.

  7. ATOMIC AND MOLECULAR PHYSICS: Structures and Electronic Properties of CuN (N <= 13) Clusters

    NASA Astrophysics Data System (ADS)

    Feng, Cui-Ju; Zhang, Xiao-Yan

    2009-10-01

    A systematic study on the structures and electronic properties of copper clusters has been performed using the density functional theory. In the calculation, there are many isomers near the ground state for small copper clusters. Our results show that the three-dimensional isomers of copper clusters start from Cu7 cluster and then show a tendency to form more compact structures. The results of the formation energy and the second derivative of binding energy with cluster size show that besides N = 8, N = 11 is also a magic number. Furthermore, it is the first time to find that the ground state of 11-atom clusters is a biplanar structure as same as the 13-atom cluster. The clear odd-even alternation as cluster size for the formation energy indicates the stability of electronic close shell existed in the range studied.

  8. Light-Assisted Cold Chemical Reactions of Barium Ions with Rubidium Atoms

    E-print Network

    Hall, Felix H J; Raoult, Maurice; Dulieu, Olivier; Willitsch, Stefan

    2013-01-01

    Light-assisted reactive collisions between laser-cooled Ba+ ions and Rb atoms were studied in an ion-atom hybrid trap. The reaction rate was found to strongly depend on the electronic state of the reaction partners with the largest rate constant (7(2) x 10^-11 cm^3 s^-1) obtained for the excited Ba+(6s)+Rb(5p) reaction channel. Similar to the previously studied Ca+ + Rb system, charge transfer and radiative association were found to be the dominant reactive processes. The generation of molecular ions by radiative association could directly be observed by their sympathetic cooling into a Coulomb crystal. Potential energy curves up to the Ba+(6s)+Rb(5p) asymptote and reactive-scattering cross sections for the radiative processes were calculated. The theoretical rate constant obtained for the lowest reaction channel Ba+(6s)+Rb(5s) is compatible with the experimental estimates obtained thus far.

  9. Chemical reaction of atomic oxygen with evaporated films of copper, part 4

    NASA Technical Reports Server (NTRS)

    Fromhold, A. T.; Williams, J. R.

    1990-01-01

    Evaporated copper films were exposed to an atomic oxygen flux of 1.4 x 10(exp 17) atoms/sq cm per sec at temperatures in the range 285 to 375 F (140 to 191 C) for time intervals between 2 and 50 minutes. Rutherford backscattering spectroscopy (RBS) was used to determine the thickness of the oxide layers formed and the ratio of the number of copper to oxygen atoms in the layers. Oxide film thicknesses ranged from 50 to 3000 A (0.005 to 0.3 microns, or equivalently, 5 x 10(exp -9) to 3 x 10(exp -7); it was determined that the primary oxide phase was Cu2O. The growth law was found to be parabolic (L(t) varies as t(exp 1/2)), in which the oxide thickness L(t) increases as the square root of the exposure time t. The analysis of the data is consistent with either of the two parabolic growth laws. (The thin-film parabolic growth law is based on the assumption that the process is diffusion controlled, with the space charge within the growing oxide layer being negligible. The thick-film parabolic growth law is also based on a diffusion controlled process, but space-charge neutrality prevails locally within very thick oxides.) In the absence of a voltage measurement across the growing oxide, a distinction between the two mechanisms cannot be made, nor can growth by the diffusion of neutral atomic oxygen be entirely ruled out. The activation energy for the reaction is on the order of 1.1 eV (1.76 x 10(exp -19) joule, or equivalently, 25.3 kcal/mole).

  10. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

    Microsoft Academic Search

    Xueming Yang

    2005-01-01

    In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The

  11. Reactions of dimethyl ether with atomic oxygen: A matrix isolation and a quantum chemical study

    Microsoft Academic Search

    Roman Wrobel; Wolfram Sander; Elfi Kraka; Dieter Cremer

    1999-01-01

    The reaction of dimethyl ether (1) with atomic oxygen generated by photolysis of ozone or NâO was examined in low-temperature matrices. The major reaction products are two conformers of methoxymethanol (5). IR absorptions of the products were assigned by isotopic labeling (¹⁸O and D) and DFT calculations at the B3LYP\\/6-311++G(d,p) level of theory. The mechanism of the formation of 5,

  12. Annealing temperature dependence of local atomic and electronic structure of polycrystalline La0.5Sr0.5MnO3

    NASA Astrophysics Data System (ADS)

    Zhang, Hong-Guang; Li, Yong-Tao; Xie, Liang; Dong, Xue-Guang; Li, Qi

    2015-10-01

    The local atomic and electronic structure of La0.5Sr0.5MnO3 was investigated at different annealing temperatures (TA) by X-ray absorption spectroscopy (XAS) and photoemission spectroscopy (XPS). The extended X-ray absorption fine structure indicates that the MnO6 octahedral distortion is reduced by increasing TA. The chemical shift for the sample with TA = 1350°C measured by XPS of Mn 2p core level demonstrates the increasing of Mn3+ ions content. From the deconvolution of valence band photoemission spectra, the number of eg electron is also proved to increase with increasing TA. It is also demonstrated that there is a strongest hybridization between O 2p and surrounding atomic orbital states in sample with TA = 1350°C, which is consistent with valence band photoemission.

  13. ATOMIC AND MOLECULAR PHYSICS: Electronic Structure Analysis of USiO

    NASA Astrophysics Data System (ADS)

    Murat Özkendir, Osman

    2010-05-01

    Uranium is a member of Actinides and plays important role in nuclear science and technology. Electronic and structural investigations of actinide compounds attract major interest in science. The electronic structure and chemical bonding of coffinite USiO4 are investigated by X-ray Absorption Fine Structure spectroscopy (XAFS). U L3- edge absorption spectrum in USiO4 is compared with U L3-edge spectra in UO2 and UTe due to their different electronic and chemical structures. The study presents XANES (x-ray Absorption Near-Edge Structure) and Extended XAFS (EXAFS) calculations of USiO4 thin films. The full multiple scattering approach has been applied to the calculation of U L3 edge XANES spectra of USiO4, UO2 and UTe, based on different choices of one electron potentials according to Uranium coordinations by using the real space multiple scattering method FEFF 8.2 code.

  14. Atomic data for Zn II - Improving Spectral Diagnostics of Chemical Evolution in High-redshift Galaxies

    E-print Network

    Kisielius, Romas; Ferland, Gary J; Bogdanovich, Pavel; Som, Debopam; Lykins, Matt L

    2015-01-01

    Damped Lyman-alpha (DLA) and sub-DLA absorbers in quasar spectra provide the most sensitive tools for measuring element abundances of distant galaxies. 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/UV spectral lines using state-of-the-art computer codes employing very broad configuration interaction basis. Here we report our results for Zn II, an ion used widely in studies of the interstellar medium (ISM) as well as DLA/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 configuration interaction approach within a numerical Hartree-Fock framework. We use both non-relativistic 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 a...

  15. Atomic structure and polarity compensation of BaTiO3 (1?1?1) surface.

    PubMed

    Li, Yueliang; Yu, Rong; Shi, Tao; Liao, Zhenyu; Song, Dongsheng; Zhou, Huihua; Cheng, Zhiying; Zhu, Jing

    2015-03-11

    Surfaces of perovskite-type oxides have been attracting increasing interest for their primary importance in various potential applications such as multiferroic thin films, interface electronics and catalysis. However, the (1?1?1) surface of BaTiO3, the most typical ferroelectric, is far from well understood. In this work, the atomic structure and polarity compensation of BaTiO3 (1?1?1) surface have been investigated combining aberration-corrected transmission electron microscopy and first-principle calculations. Depending on the density of oxygen vacancies, the surface shows different degrees of atomic relaxation and electronic charge transfer, which compensates the surface polarity together with the ionic charges associated with the oxygen vacancies. The atomic relaxation and charge transfer would have a direct impact on the ferroelectric and catalytic properties of low-dimensional BaTiO3. PMID:25671525

  16. 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.

  17. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

    EPA Science Inventory

    Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors ...

  18. STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSII. MODELLING OF REACTIONS

    E-print Network

    Meyers, Marc A.

    STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSÐII. MODELLING OF REACTIONS IN SHEAR BAND V 1997; accepted in revised form 26 April 1998) AbstractÐThe problem on strain-induced chemical reaction is connected with the additional heating due to RIP. A kinetic criterion of chemical reaction is formulated

  19. Atomic-resolution 3D structure of amyloid ? fibrils: The Osaka mutation

    DOE PAGESBeta

    Schutz, Anne K.; Wall, Joseph; Vagt, Toni; Huber, Matthias; Ovchinnikova, Oxana Y.; Cadalbert, Riccardo; Guntert, Peter; Bockmann, Anja; Glockshuber, Rudi; Meier, Beat H.

    2015-01-02

    Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid ?-peptide (A?) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the A? 1-40 peptide with the Osaka mutation (E22?), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

  20. Dynamic structure elucidation of chemical reactivity by laser pulses and X-ray probes.

    PubMed

    Bartlett, Stuart A; Hamilton, Michelle L; Evans, John

    2015-04-14

    Visualising chemical reactions by X-ray methods is a tantalising prospect. New light sources provide the prospect for studying atomic, electronic and energy transfers accompanying chemical change by X-ray spectroscopy and inelastic scattering. Here we assess how this adventure can illuminate inorganic and catalytic chemistry. In particular X-ray inelastic scattering provides a means of exploiting X-ray free electron lasers, as a parallel to laser Raman spectroscopy. PMID:25741902

  1. 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

    2015-03-01

    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. PMID:25671351

  2. Atomic and electronic structure of Mo6S9-xIx nanowires

    NASA Astrophysics Data System (ADS)

    Meden, A.; Kodre, A.; Padeznik Gomilsek, J.; Arcon, I.; Vilfan, I.; Vrbanic, D.; Mrzel, A.; Mihailovic, D.

    2005-09-01

    Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse, and they exhibit a variety of functional properties in which they are superior to other one-dimensional materials. However, further progress in the understanding of physical properties and the development of new and specific applications have so far been impeded by the fact that their structure was not accurately known. Here we report on a combination of systematic x-ray diffraction and extended x-ray absorption fine structure experiments, and first-principles theoretical structure calculations, which are used to determine the atomic skeletal structure of individual Mo6S9-xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure. From this work we conclude that the variations in functional properties appear to arise from different stoichiometry, not skeletal structure. A supplementary data file is available from http://stacks.iop.org/0957-4484/16/1578

  3. Chemical structural changes in the early stages of coalification

    SciTech Connect

    Given, P.H.; Ryan, M.J.; Spackman, W.; Stout, S.A.

    1985-01-01

    The Brandon lignite in Vermont (20-30 M. years old) consists mostly of gelified coal but contains also much material to be described as woody material or coalified logs. Faces on lumps of woody material have been polished and examined with a hand lens. Various zones could be distinguished: thus one zone (IV) contained well preserved vessel cells, while another associated zone (III) did not. There was a darker zone (II) with no cells visible, and a dark rim (I) around the margin (oxidation.). Fourier Transform infrared spectra of the corresponding zones III and IV from two different specimens of woody material were almost identical with each other; zone II was quite similar in showing a large number of sharp, well-defined, bands quite closely resembling those in the spectrum of dicotyledon lignin. The authors conclude that (i) chemical differences in zones of woody material are considerably smaller than visible differences in degree of preservation of wood indicate, (ii) there are processes in the earliest stages of coalification that usually, but not invariably, destroy both cellular anatomy and lignin structure, (iii) the effect of these processes begins to be evident in the outer zones of coalified logs and is fully seen in the gelified matrix. Woody material from the Morwell lignite, Victoria, Australia gave spectra having some lignin character, but much less marked that in those of the Brandon samples.

  4. Unique structure/properties of chemical vapor deposited parylene E

    NASA Astrophysics Data System (ADS)

    Senkevich, Jay J.; Mitchell, Christopher J.; Vijayaraghavan, Aravind; Barnat, Edward V.; McDonald, John F.; Lu, Toh-Ming

    2002-07-01

    Parylene E, a low kappa polymer thin film, with the approximate composition 69% diethylated and 25% monoethylated poly(p-xylylene), has been chemical vapor deposited via a cyclophane precursor at room temperature. It has a dielectric constant of 2.34plus-or-minus0.03 and dielectric loss of <0.005 at 10 kHz from MIMCAP structures. It is particularly unique compared to the other common parylene polymers. Namely, it is nearly optically isotropic and it is soluble in common laboratory solvents such as methylene chloride, chloroform, and toluene. It is shown to have an optical birefringence of -0.0112 at 634.1 nm and a correspondingly low degree of crystallization after a 150 degC postdeposition anneal. The low degree of crystallization results in a smooth film (10 A rms surface roughness for a 2060 A thin film) with no optical loss (in reflection mode), i.e., an extinction coefficient of zero. These properties for parylene E make it appropriate for use as an optical waveguide and for archival conservation or other applications where low optical loss or film removal might be necessary. copyright 2002 American Vacuum Society.

  5. Shock tube study of the fuel structure effects on the chemical kinetic mechanisms responsible for soot formation, part 2

    NASA Technical Reports Server (NTRS)

    Frenklach, M.; Clary, D. W.; Ramachandra, M. K.

    1985-01-01

    Soot formation in oxidation of allene, 1,3-butadiene, vinylacetylene and chlorobenzene and in pyrolysis of ethylene, vinylacetylene, 1-butene, chlorobenzene, acetylen-hydrogen, benzene-acetylene, benzene-butadiene and chlorobenzene-acetylene argon-diluted mixtures was studied behind reflected shock waves. The results are rationalized within the framework of the conceptual models. It is shown that vinylacetylene is much less sooty than allene, which indicates that conjugation by itself is not a sufficient factor for determining the sooting tendency of a molecule. Structural reactivity in the context of the chemical kinetics is the dominant factor in soot formation. Detailed chemical kinetic modeling of soot formation in pyrolysis of acetylene is reported. The main mass growth was found to proceed through a single dominant route composed of conventional radical reactions. The practically irreversible formation reactions of the fused polycyclic aromatics and the overshoot by hydrogen atom over its equilibrium concentration are the g-driving kinetic forces for soot formation.

  6. Prediction of the rodent carcinogenicity of organic compounds from their chemical structures using the FALS method.

    PubMed Central

    Moriguchi, I; Hirano, H; Hirono, S

    1996-01-01

    Fuzzy adaptive least-squares (FALS), a pattern recognition method recently developed in our laboratory for correlating structure with activity rating, was used to generate quantitative structure-activity relationship (QSAR) models on the carcinogenicity of organic compounds of several chemical classes. Using the predictive models obtained from the chemical class-based FALS QSAR approach, the rodent carcinogenicity or noncarcinogenicity of a group of organic chemicals currently being tested by the U.S. National Toxicology Program was estimated from their chemical structures. PMID:8933054

  7. Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations.

    PubMed

    Debnath, Ananya; Schäfer, Lars V

    2015-06-11

    We investigated structural and dynamical properties of nanodiscs comprising dimyristoylphosphatidylcholine (DMPC) lipids and major scaffold protein MSP1?(1-22) from human apolipoprotein A-1 using combined all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. The computational efficiency of the Martini-CG force field enables the spontaneous self-assembly of lipids and scaffold proteins into stable nanodisc structures on time scales up to tens of microseconds. Subsequent all-atom and CG-MD simulations reveal that the lipids in the nanodisc have lower configurational entropy and higher acyl tail order than in a lamellar bilayer phase. These altered average properties arise from rather differential behavior of lipids, depending on their location in the nanodisc. Since the scaffold proteins exert constrictive forces from the outer rim of the disc toward its center, lipids at the center of the nanodisc are highly ordered, whereas annular lipids that are in contact with the MSP proteins are remarkably disordered due to perturbed packing. Although specific differences between all-atom and CG simulations are also evident, the results obtained at both levels of resolution are in overall good agreement with each other and provide atomic level interpretations of recent experiments. Thus, the present study highlights the applicability of multiscale simulation approaches for nanodisc systems and opens the way for future applications, including the study of nanodisc-embedded membrane proteins. PMID:25978497

  8. Atomic-scale X-ray structural analysis of self-assembled monolayers on Silicon

    NASA Astrophysics Data System (ADS)

    Lin, J.-C.; Kellar, J. A.; Kim, J.-H.; Yoder, N. L.; Bevan, K. H.; Nguyen, S. T.; Hersam, M. C.; Bedzyk, M. J.

    2009-02-01

    Two related self-assembled monolayers (SAMs), 4-bromostyrene (BrSty) and 4-bromophenylacetylene (BPA), are photochemically grown from solution on to the monohydride-terminated Si(111) surface. The atomic-scale structures of the resulting SAMs are examined by X-ray standing waves (XSW), X-ray reflectivity (XRR), X-ray fluorescence, atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). The coverage is 0.5 ML. The results show that in each case the molecule covalently bonds to a single Si T1 site and stands up-right with a slight molecular tilt of 17? that leaves the Br terminal end over a neighboring T4 site. The Br height is 8.5 Å (BrSty) and 8.6 Å (BPA) above the top surface Si atom. The combined XSW and XRR results rule-out two alternative bonding models predicted by DFT that have the root of the molecule bonded to two neighboring top Si surface atoms. Based on the XSW 111 and 333 coherent fractions, the BPA/Si(111) has a reduced vertical Br distribution width in comparison to BrSty. This greater rigidity in the molecular structure is correlated to a C=C bond at the root.

  9. Atomic-scale X-ray structural analysis of self-assembled monolayers on Silicon

    SciTech Connect

    Lin, J.-C.; Kellar, J.A.; Kim, J.-H.; Yoder, N.L.; Bevan, K.H.; Nguyen, S.T.; Hersam, M.C.; Bedzyk, M.J.; (NWU); (Purdue)

    2009-04-02

    Two related self-assembled monolayers (SAMs), 4-bromostyrene (BrSty) and 4-bromophenylacetylene (BPA), are photochemically grown from solution on to the monohydride-terminated Si(111) surface. The atomic-scale structures of the resulting SAMs are examined by X-ray standing waves (XSW), X-ray reflectivity (XRR), X-ray fluorescence, atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). The coverage is 0.5 ML. The results show that in each case the molecule covalently bonds to a single Si T{sub 1} site and stands up-right with a slight molecular tilt of 17{sup o} that leaves the Br terminal end over a neighboring T{sub 4} site. The Br height is 8.5 {angstrom} (BrSty) and 8.6 {angstrom} (BPA) above the top surface Si atom. The combined XSW and XRR results rule-out two alternative bonding models predicted by DFT that have the root of the molecule bonded to two neighboring top Si surface atoms. Based on the XSW 111 and 333 coherent fractions, the BPA/Si(111) has a reduced vertical Br distribution width in comparison to BrSty. This greater rigidity in the molecular structure is correlated to a C=C bond at the root.

  10. Correlations between dynamics and atomic structures in Cu64.5Zr35.5 metallic glass

    NASA Astrophysics Data System (ADS)

    Wang, C. Z.; Zhang, Y.; Zhang, F.; Mendelev, M. I.; Kramer, M. J.; Ho, K. M.

    2015-03-01

    The atomic structure of Cu-Zr metallic glasses (MGs) has been widely accepted to be heterogeneous and dominated by icosahedral short range order (ISRO). However, the correlations between dynamics and atomic structures in Cu-Zr MGs remain an enigma. Using molecular dynamics (MD) simulations, we investigated the correlations between dynamics and atomic structures in Cu64.5Zr35.5 MG. The atomic structures are characterized using ISRO and the Bergman-type medium range order (BMRO). The simulation and analysis results show that the majority of the mobile atoms are not involved in ISRO or BMRO, indicating that the dynamical heterogeneity has a strong correlation to structural heterogeneity. Moreover, we found that the localized soft vibration modes below 1.0 THz are mostly concentrated on the mobile atoms. The diffusion was studied using the atomic trajectory collected in an extended time interval of 1.2 ?s at 700 K in MD simulations. It was found that the long range diffusion in MGs is highly heterogeneous, which is confined to the liquid-like regions and strongly avoids the ISRO and the Bergman-type MRO. All These results clearly demonstrate strong correlations between dynamics (in terms of dynamical heterogeneity and diffusion) and atomic structures in Cu64.5Zr35.5 MGs. This work was supported by the U.S. Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering under the Contract No. DE-AC02-07CH11358.

  11. STRUCTURE-ACTIVITY RELATIONSHIPS FOR SCREENING ORGANIC CHEMICALS FOR POTENTIAL ECOTOXICITY EFFECTS

    EPA Science Inventory

    The paper presents structure-activity relationships (QSAR) for estimating the bioconcentration factor and acute toxicity of some classes of industrial chemicals using only the n-octanol/water partition coefficient (Log P) which is derived from chemical structure. The bioconcentra...

  12. Reduction of protein adsorption on well-characterized polymer brush layers with varying chemical structures

    Microsoft Academic Search

    Yuuki Inoue; Kazuhiko Ishihara

    2010-01-01

    To clarify protein adsorption behavior on polymer brush layers, surface characteristics and protein adsorption repellency on polymer brush layers should be precisely determined. Here, we clearly delineated the chemical structure of the polymer brush layers containing various hydrophilic groups, namely, phosphorylcholine, sulfoxybetaine, carboxybetaine (zwitterionic), and hydroxyl group (nonionic) and examined the effects of the chemical structure on initial protein adsorption

  13. Prediction of Harmful Human Health Effects of Chemicals from Structure

    Microsoft Academic Search

    Mark T. D. Cronin

    \\u000a There is a great need to assess the harmful effects of chemicals to which man is exposed. Various in silico techniques including\\u000a chemical grouping and category formation, as well as the use of (Q)SARs can be applied to predict the toxicity of chemicals\\u000a for a number of toxicological effects. This chapter provides an overview of the state of the art

  14. Chemical durability and structure of zinc–iron phosphate glasses

    Microsoft Academic Search

    S. T Reis; M Karabulut; D. E Day

    2001-01-01

    The chemical durability of zinc–iron phosphate glasses with the general composition (40?x)ZnO–xFe2O3–60P2O5 has been measured. The chemical durability and density of these glasses increase with increasing Fe2O3 content. Glasses containing more than 30 mol% Fe2O3 had an excellent chemical durability. The dissolution rate (DR), calculated from the weight loss in distilled water at 90 °C for up to 32 days,

  15. Structure of self-interstitial atom clusters in iron and copper

    SciTech Connect

    Takahashi, Akiyuki [Department of Mechanical Engineering, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510 (Japan); Ghoniem, Nasr M. [Department of Mechanical and Aerospace Engineering, University of California-Los Angeles, Los Angeles, California 90095 (United States)

    2009-11-01

    The dislocation core structure of self-interstitial atom (SIA) clusters in bcc iron and fcc copper is determined using the hybrid ab initio continuum method of Banerjee et al. [Philos. Mag. 87, 4131 (2007)]. To reduce reliance on empirical potentials and to facilitate predictions of the effects of local chemistry and stress on the structure of defects, we present here a hybrid extension of the Peierls-Nabarro continuum model, with lattice resistance to slip determined separately from ab initio calculations. A method is developed to reconstruct atomic arrangements and geometry of SIA clusters from the hybrid model. The results are shown to compare well with molecular-dynamics simulations. In iron, the core structure does not show dependence on the size of the self-interstitial cluster, and is nearly identical to that of a straight edge dislocation. However, the core structure of SIA clusters in Cu is shown to depend strongly on the cluster size. Small SIA clusters are found to have nondissociated compact dislocation cores, with a strong merging of Shockley partial dislocations and a relatively narrow stacking fault (SF) region. The compact nature of the SIA core in copper is attributed to the strong dependence of the self-energy on the cluster size. As the number of atoms in the SIA cluster increases, Shockley partial dislocations separate and the SF region widens, rendering the SIA core structure to that of an edge dislocation. The separation distance between the two partials widens as the cluster size increases, and tends to the value of a straight edge dislocation for cluster sizes above 400 atoms. The local stress is found to have a significant effect on the atomic arrangements within SIA clusters in copper and the width of the stacking faults. An applied external shear can delocalize the core of an SIA cluster in copper, with positive shear defined to be on the (111) plane along the [112] direction. For an SIA cluster containing 1600 atoms, a positive 1 GPa shear stress delocalizes the cluster and expands the SF to 30b, while a negative shear stress of 2 GPa contracts the core to less than 5b, where b is the Burgers vector magnitude.

  16. Structure of self-interstitial atom clusters in iron and copper

    NASA Astrophysics Data System (ADS)

    Takahashi, Akiyuki; Ghoniem, Nasr M.

    2009-11-01

    The dislocation core structure of self-interstitial atom (SIA) clusters in bcc iron and fcc copper is determined using the hybrid ab initio continuum method of Banerjee [Philos. Mag. 87, 4131 (2007)]. To reduce reliance on empirical potentials and to facilitate predictions of the effects of local chemistry and stress on the structure of defects, we present here a hybrid extension of the Peierls-Nabarro continuum model, with lattice resistance to slip determined separately from ab initio calculations. A method is developed to reconstruct atomic arrangements and geometry of SIA clusters from the hybrid model. The results are shown to compare well with molecular-dynamics simulations. In iron, the core structure does not show dependence on the size of the self-interstitial cluster, and is nearly identical to that of a straight edge dislocation. However, the core structure of SIA clusters in Cu is shown to depend strongly on the cluster size. Small SIA clusters are found to have nondissociated compact dislocation cores, with a strong merging of Shockley partial dislocations and a relatively narrow stacking fault (SF) region. The compact nature of the SIA core in copper is attributed to the strong dependence of the self-energy on the cluster size. As the number of atoms in the SIA cluster increases, Shockley partial dislocations separate and the SF region widens, rendering the SIA core structure to that of an edge dislocation. The separation distance between the two partials widens as the cluster size increases, and tends to the value of a straight edge dislocation for cluster sizes above 400 atoms. The local stress is found to have a significant effect on the atomic arrangements within SIA clusters in copper and the width of the stacking faults. An applied external shear can delocalize the core of an SIA cluster in copper, with positive shear defined to be on the (111) plane along the [1¯1¯2] direction. For an SIA cluster containing 1600 atoms, a positive 1 GPa shear stress delocalizes the cluster and expands the SF to 30b , while a negative shear stress of 2 GPa contracts the core to less than 5b , where b is the Burgers vector magnitude.

  17. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    SciTech Connect

    Sadtler, Bryce F

    2009-05-20

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or Ag2S lattices were used to calculate interface formation energies. The formation energies indicate the favorability for interface nucleation at different facets of the nanorod and the stability of the interfaces during growth of the secondary material (Cu2S or Ag2S) within the CdS nanocrystal. The physical properties of the CdS-Ag2S and CdS-Cu2S binary nanorods are discussed in terms of the electronic structure of their components and the heterostructure morphology.

  18. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work Supported by the NSF MRI Program.

  19. Atomic structure and phonons of a Pb ultrathin film on the Al(100) surface

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    The atomic and phonon structures of a Pb ultrathin film on the Al(100) surface have been theoretically studied. Surface relaxation, local density of vibrational states, and polarization of the phonon modes of adatoms and atoms of a substrate have been discussed. It has been shown that the adsorption of Pb results in the oscillating relaxation of the surface of the substrate and warping of the structure in subsurface layers. Comparative analysis of the vibrational characteristics of the pure surface of the substrate and the surface with adatoms has shown that the adsorptive interaction in the system and its dynamic stability are governed by new vibrational modes that are not inherent in pure Al and Pb surfaces.

  20. Formation of conductive structures in insulate layers by selective removal of atoms technique

    NASA Astrophysics Data System (ADS)

    Gurovich, B.; Prikhodko, K.; Domantovsky, A.; Kuleshova, E.; Olshansky, E.; Maslakov, K.; Lunin, Y.

    2006-05-01

    The structure and electric properties of initial oxides and metals (Bi, Ag, Cu, Ni, Co, Mo and W) produced by Selective Removal of oxygen Atoms technique (SRA) were studied. It was found a correspondence of electrical conductivity of SRA metals and pure sputtered metals films. At the same time, low resistance of some oxides, for instance CuO, will initiate big leakage currents inside the layer. Among the investigated materials special attention will be paid to SRA Bi, Mo and W because of the high values of contact resistance and puncture potential with initial oxides. It is shown the adaptability of Selective Removal of Atoms technique for formation of conductive insulated structures in layers for new micro and nano-electronic devices.

  1. Structure and Function of Voltage-Gated Sodium Channels at Atomic Resolution

    PubMed Central

    Catterall, William A.

    2013-01-01

    Voltage-gated sodium channels initiate action potentials in nerve, muscle, and other excitable cells. Early physiological studies described sodium selectivity, voltage-dependent activation, and fast inactivation, and developed conceptual models for sodium channel function. This review article follows the topics of my 2013 Sharpey-Schafer Prize Lecture and gives an overview of research using a combination of biochemical, molecular biological, physiological, and structural biological approaches that has elucidated the structure and function of sodium channels at the atomic level. Structural models for voltage-dependent activation, sodium selectivity and conductance, drug block, and both fast and slow inactivation are discussed. A perspective for the future envisions new advances in understanding the structural basis for sodium channel function and the opportunity for structure-based discovery of novel therapeutics. PMID:24097157

  2. Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

    PubMed

    Sun, Yongfu; Gao, Shan; Xie, Yi

    2014-01-21

    Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices. PMID:24122032

  3. Spectral fitting for signal assignment and structural analysis of uniformly 13 C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

    Microsoft Academic Search

    Yoh Matsuki; Hideo Akutsu; Toshimichi Fujiwara

    2007-01-01

    We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional 13C–13C magic-angle-spinning solid-state NMR spectra of uniformly 13C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained\\u000a molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent\\u000a chemical

  4. Atomic and electronic structures of superconducting BaFe2As2/SrTiO3 superlattices

    NASA Astrophysics Data System (ADS)

    Gao, P.; Zhang, Y.; Zhang, S. Y.; Lee, S.; Weiss, J.; Jokisaari, J. R.; Hellstrom, E. E.; Larbalestier, D. C.; Eom, C. B.; Pan, X. Q.

    2015-03-01

    The nanoscale structural, chemical, and electronic properties of artificial engineered superlattice thin films consisting of superconducting Co-doped BaF e2A s2(Ba - 122 ) and nonsuperconducting SrTi O3(STO ) layers are determined by using atomically resolved scanning transmission electron microscopy and electron energy loss spectroscopy. The bonding of Ba - 122 /STO occurring between As (Ba) and SrO (Ti O2) terminated layers has been identified. The thin STO (3 unit cell) insertion layers are a mixture of cations (Ba, Sr, Fe, and Ti) and rich in oxygen vacancies and the Ba-122 layers (10 unit cell) are free of vertical second phases. Our results explain why these superlattices show anisotropic transport response to an external magnetic field, i.e., strong a b -axis pinning (enhancing critical current density) and no c -axis pinning, which is opposite to single layer Ba-122 thin films. These findings reveal physical and chemical properties of superconducting/nonsuperconducting heterostructures and provide important insights into engineering of superconducting devices.

  5. Direct atomic resolution imaging of dislocation core structures in a 300 kV stem

    SciTech Connect

    McGibbon, A.J. [Univ. of Glasgow (United Kingdom). Dept. of Physics and Astronomy; Pennycook, S.J. [Oak Ridge National Lab., TN (United States). Solid State Div.

    1995-05-01

    By employing the incoherent imaging technique of Z-contrast imaging in a 300kV STEM, the authors show that it is possible to provide directly interpretable, atomic resolution images of the sublattice in compound semiconductors. Using this approach, analysis of dislocations at an interface in the CdTe(001)/GaAs(001) system reveals unexpected core structures at Lomer dislocations.

  6. Interrelations between atomic and electronic structures-Liquid and amorphous metals as model systems

    Microsoft Academic Search

    P. Häussler

    1992-01-01

    In this paper we review an intimate interrelationship between atomic and electronic structures. Charge- and spin-density oscillations in the electron system, giving rise to so-called Friedel and RKKY oscillations in the effective pair potential or the effective magnetic interaction, cause indirect ion-ion and spin-spin interactions mediated by the conduction electrons. These interactions prefer positions of neighbouring ions and local moments

  7. The atomic structure of growth interfaces in Y-Ba-Cu-O thin films

    Microsoft Academic Search

    R. Ramesh; A. Inam; D. M. Hwang; T. S. Ravi; T. Sands; X. X. Xi; X. D. Wu; Q. Li; T. Venkatesan; R. Kilaas

    1991-01-01

    We have examined the atomic structure of growth interfaces in thin films of Y--Ba--Cu--O grown on (001) perovskite or cubic substrates. At substrate heater temperatures in the range of 780--820 °C c-axis oriented growth is observed on these substrates. On SrTiOâ, the first layer appears to be either a BaO or a CuOâ plane while on LaAlOâ the first layer

  8. Investigating the Effectiveness of Computer Simulations in the Teaching of “Atomic Structure and Bonding”

    Microsoft Academic Search

    S. Abdoolatiff; F. B. Narod

    The purpose of this study was to investigate the effectiveness of using computer simulations on students’ understanding of\\u000a “Atomic Structure and Bonding” over the traditionally designed instruction. The impact of computer simulations on students’\\u000a attitude and motivation was also studied during the research. The study was carried out in a girls’ State Secondary School\\u000a in Mauritius. The sample consisted of

  9. Observation of banded spherulites and lamellar structures by atomic force microscopy

    Microsoft Academic Search

    Jiang Yong; Luo Yanhong; Fan Zefu; Wang Xiayu; Xu Jun; Guo Baohua; Li Lin

    2003-01-01

    Lamellar structures of banded spherulites of poly(?-caprolactone)\\/poly(vinyl chloride) (PCL\\/PVC) blends are observed using\\u000a tapping mode atomic force microscopy (AFM). The surface of the PCL\\/PVC banded spherulites presents to be concentric periodic\\u000a ups and downs. The period of the bands corresponds to the extinction rings under the polarized optical microscopy observation.\\u000a The lamellae with edge-on orientation in the ridges and the

  10. Al4Mn quasicrystal atomic structure, diffraction data and Penrose tiling

    Microsoft Academic Search

    M. Audier; P. Guyot

    1986-01-01

    The modelling of the Al4Mn quasicrystal, recently proposed by Guyot and Audier (1985) on the basis of icosahedral atomic units characteristic of the crystalline phase ?(AlFeSi) or ?(AlMnSi), is analysed more deeply. After building the quasicrystal by connecting the basic structural units-double Al and Mn icosahedra with vacant centresm?according to the rules previously described, it is found that the Mn

  11. Selective area atomic layer deposition of rhodium and effective work function characterization in capacitor structures

    Microsoft Academic Search

    K. J. Park; G. N. Parsons

    2006-01-01

    Atomic layer deposition (ALD) of rhodium was investigated using rhodium(III) acetylacetonate and oxygen, and capacitance versus voltage is used to extract the effective work function in metal\\/insulator\\/semiconductor structures. Self-limiting growth was observed, and the resistivity of Rh deposited at 300 °C is ?10 ?? cm, approximately a factor of 2 larger than the Rh bulk resistivity (4.3 ?? cm). Selective

  12. Selective area atomic layer deposition of rhodium and effective work function characterization in capacitor structures

    Microsoft Academic Search

    K. J. Park; G. N. Parsons

    2006-01-01

    Atomic layer deposition (ALD) of rhodium was investigated using rhodium(III) acetylacetonate and oxygen, and capacitance versus voltage is used to extract the effective work function in metal\\/insulator\\/semiconductor structures. Self-limiting growth was observed, and the resistivity of Rh deposited at 300 °C is ~10 muOmega cm, approximately a factor of 2 larger than the Rh bulk resistivity (4.3 muOmega cm). Selective

  13. Local Atomic Structure and Superconductivity of NEODYMIUM(2-X) Cerium(x) COPPEROXIDE(4-Y): a Pair-Distribution Study

    NASA Astrophysics Data System (ADS)

    Billinge, Simon John Laird

    1992-01-01

    We have carried out a detailed Pair Distribution Function Analysis of powder diffraction data from samples of Nd_{2-x}Ce _{x}CuO _{4-y} with x = 0.165 and x = 0.2. The former is superconducting with an almost full Meissner fraction, and T_{c} = 22K. The latter is isostructural, but exhibits no superconductivity. A "real space refinement" of the PDF has been carried out to extract quantitative information about the local atomic structure of the material. Two main observations were made. The local structure is significantly different from the average crystal structure (T ^' structure) of this material. The differences are explained by displacements of oxygen. The second result was that the local structure changes with the appearance of superconductivity. This was the first observation of such a change in this material. These changes are explained by an increase in the degree of local order of the above mentioned oxygen displacements. The displacements are inhomogeneously distributed throughout the sample and interspersed with regions of undistorted crystal. We argue that this is best explained as the direct observation of the presence of polarons, or bipolarons in the structure. We speculate that the driving force that could give rise to these polarons is a strong coupling of the lattice with the O p_{z} states which lie just below the Fermi surface in the undistorted material. The effective mass of the (bi)polarons, calculated using values estimated from the experiment, was such as to give the bipolarons a condensation temperature of 17K. This is the same order of magnitude as the observed T _{c}. Thus it is plausible that the superconductivity is due to a bipolaronic condensation. The density of polarons is too small to account for all of the chemically doped carriers. Thus it appears that they form the minority of carriers. They coexist with a majority of high mobility, wide band, electronic states, of sigma character.

  14. Self-assembly of carbon atoms on transition metal surfaces--chemical vapor deposition growth mechanism of graphene.

    PubMed

    Zhang, Xiuyun; Li, Hui; Ding, Feng

    2014-08-20

    As the most promising method for high quality, large area graphene synthesis, chemical vapor decomposition (CVD) has drawn enormous attention. Understanding of the growth mechanism is crucial for optimizing the experimental design to synthesize the desired graphene for various applications. Recently, many theoretical efforts have been devoted to explore the decomposition of feedstock, nucleation of small graphene islands, and the expansion of graphene islands to a large graphene sheet on various catalyst surfaces. Here we summarize the key progresses on the three aspects in order to provide a complete scenery of graphene CVD growth at the atomic level and to guide the experimental design for the synthesis of desired graphene, e.g., high quality graphene sheets with large single crystalline domains or controlled doping. PMID:24633927

  15. Flow-injection chemical vapor-generating procedure for the determination of Au by atomic absorption spectrometry.

    PubMed

    Du, X; Xu, S

    2001-08-01

    Volatile Au species in an acidified medium were generated at room temperature by reduction with NaBH4 in acidified aqueous medium using a flow-injection chemical vapor-generation atomic absorption spectrometric (FI-CVG-AAS) system in the presence of micro amounts of sodium diethyldithiocarbamate (DDTC). Precision of 2.0% RSD (n = 11, 2.0 mg L(-1) level) was obtained at a sample throughput of 180 h(-1). A detection limit of 24 ng mL(-1) (3sigma) was obtained with 300 microL sample solution. The method was used for the determination of gold in ore sample digests, and the results obtained agreed well with those obtained by flame AAS. PMID:11583088

  16. Role of extrinsic atoms on the morphology and field emission properties of carbon nanotubes

    Microsoft Academic Search

    L. H. Chan; K. H. Hong; D. Q. Xiao; W. J. Hsieh; S. H. Lai; H. C. Shih; T. C. Lin; F. S. Shieu; K. J. Chen; H. C. Cheng

    2003-01-01

    Extrinsic atoms were doped into multiwalled carbon nanotubes (MWCNTs) using microwave plasma-enhanced chemical vapor deposition. Doped nitrogen atoms alter the original parallel graphenes into highly curved ones including some fullerene-like structures. Doped nitrogen atoms could replace carbon atoms in MWCNTs and therefore increase the electronic density that enhances the electron field emission properties. On the other hand, the incorporation of

  17. On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.

    PubMed

    Müller-Herold, Ulrich

    2006-01-01

    The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure. PMID:16409022

  18. Atomic Structures of a Cu(111) Surface Under Electrochemical Conditions:. AN In-Situ STM Study

    NASA Astrophysics Data System (ADS)

    Broekmann, P.; Wilms, M.; Wandelt, K.

    The atomic structures of a Cu(111) electrode in dilute sulfuric electrolyte have been studied using in-situ STM. At anodic potentials near the copper dissolution the adsorbed sulfate anions form a characteristic anisotropic Moiré pattern. The appearance of the long range Moiré modulation is explained by a sulfate-induced reconstruction (expansion) of the topmost copper layer and the resulting misfit between the first and the second copper layer. For the first time it was possible to image not only the sulfate adsorbate but also the underlying reconstructed copper substrate at the same anodic working potential by a systematical variation of the tunneling parameters. On an atomic scale the observed sulfate structure on Cu(111) is very similar to those found for other fcc(111) surfaces (Au, Pt and Rh). On these electrodes sulfate anions form a regular (? 3× ? 7) superstructure. For the Cu(111) surface a (? 3× ? 7)-like unit cell is found which is slightly distorted. Also for the first time it was possible to image the atomic structure of an electrode during a massive hydrogen evolution current at cathodic potentials. Even under such extreme electrochemical conditions far from the thermodynamic equilibrium an ordered superstructure of hydronium cations is found. At the anodic end of the cyclic voltammogram a pit-etching mechanism is induced by a fast copper corrosion.

  19. Extraction of chemical structures and reactions from the literature

    E-print Network

    Lowe, Daniel Mark

    2012-10-09

    Entities of Biological Interest CIP = Cahn-Ingold-Prelog CML = Chemical Markup Language DTD = Document Type Definition EPO = European Patent Office InChI = IUPAC International Chemical Identifier IPC = International Patent Classification IUPAC... ................................................................................................ 121 3.2.16 Output formats ...................................................................................................... 124 3.2.16.1 CML...

  20. Structural analysis of a (Pt/Co){sub 3}/IrMn multilayer: Investigation of sub-nanometric layers by tomographic atom probe

    SciTech Connect

    Larde, R.; Lechevallier, L.; Zarefy, A.; Bostel, A.; Juraszek, J; Le Breton, J. M. [Groupe de Physique des Materiaux, UMR CNRS 6634, Universite de Rouen, Avenue de l'Universite, BP 12, 76801 Saint Etienne du Rouvray (France); Rodmacq, B.; Dieny, B. [SPINTEC (URA 2512 CNRS/CEA), INAC, CEA/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble (France)

    2009-04-15

    The structure of a Ta{sub 3nm}/[(Pt{sub 2nm}/Co{sub 0.4nm}){sub 3}/IrMn{sub 7nm}]{sub 7}/Pt{sub 10nm} multilayer exhibiting perpendicular exchange bias has been investigated by x-ray reflectometry and laser-assisted tomographic atom probe (LATAP). A strong intermixing at the Co/IrMn interface is pointed out by x-ray reflectometry, this interface being more diffuse than the IrMn/Pt interface. A direct observation of this intermixing at the atomic scale is obtained thanks to the LATAP in real space. The three-dimensional reconstructions reveal the atomic planes in the Pt layers and the Pt-Co intermixing in the (Pt/Co){sub 3} multilayer. The analysis of the concentration profiles allows to determine the chemical composition of the Co subnanometric layers; thus providing for the first time an accurate structural characterization of such layers leading to an estimation of their thickness, roughness, atomic concentration and width of their interfaces.

  1. [Chemical structure and immunomodulating activities of peptidoglycan from Actinobacillus actinomycetemcomitans].

    PubMed

    Kinoshita, F

    1989-12-01

    The chemical structure and immunomodulating activities of the cell wall peptidoglycans isolated from Actinobacillus actinomycetemcomitans were investigated. Peptidoglycans were isolated from A. actinomycetemcomitans strains Y4 and ATCC 29522 by boiling in 4% sodium dodecyl sulfate and by digestion with pronase, trypsin and alpha-amylase. Analysis of amino acids and amino sugars of the peptidoglycans revealed that glucosamine, muramic acid, D-glutamic acid, D-alanine, and meso-2, 6-diaminopimelic acid (A2pm) were the principal components. Serine and glycine were not found. Dinitrophenylation method revealed that about half of A2pm residue had a free aminogroup, and analysis by hydrazinolysis showed that a small part of alanine and A2pm located at the C-terminal. The above results indicate that one of the amino groups of A2pm residue at one strand of the stem peptide subunit crosslinked to the carboxyl group of alanine of the neighboring strand. It was thus revealed that the peptidoglycans of A. actinomycetemcomitans belonged to the Al gamma type of the classification by Schleifer and Kandler. Peptidoglycans isolated from A. actinomycetemcmitans strain Y4 and ATCC 29522 were found to be definitely adjuvant-active in induction of delayed type hypersensitivity against ovalbumin when administered to guinea pigs as water-in oil emulsion and stimulation of increase serum antibody levels was found in both peptidoglycans. Regarding mitogenicity on splenocytes of BALB/c and BALB/c nu/nu mice, peptidoglycans from two strains of A. actinomycetemcomitans were markedly enhanced the uptake [3H] thymidine in dose of 10 micrograms/10(5) cells, however thymocytes were not reactive. Stimulation effects on peritoneal macrophages from a guinea pig to incorporation of 14C-glucosamin were not exhibited on addition of 100 micrograms of both peptidoglycans. These findings indicate that peptidoglycan of A. actinomycetemcomitans might eventually be responsible for destruction of periodontal tissue by host mediated activities. PMID:2489665

  2. Determination of interface structure and bonding at atomic resolution in the stem

    SciTech Connect

    Pennycook, S.J.; McGibbon, A.J.; McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.; Jesson, D.E.

    1994-03-01

    The scanning transmission electron microscope now routinely produces probes of atomic dimensions, 2.2{Angstrom} at 100 kV and 1.3{Angstrom} at 300 kV. This capability opens up a new strategy for determining the structure and bonding of materials at the atomic scale, which is particularly advantageous for complex interfaces such as grain boundaries. The Z-contrast image allows the high-Z column locations to be determined by direct inspection, and quantified through maximum entropy methods to a positional accuracy of currently {approximately}0.2{Angstrom}. With the same electron probe, located to sub-Angstrom precision with reference to the Z-contrast image, parallel detection EELS can determine light element coordination from core edge fine structure, in principle around a single atomic column. There are several attractive features to combining Z-contrast imaging with EELS. First, the incoherent nature of Z-contrast imaging provides higher resolution, compared with 0.66 for phase contrast imaging, freedom from contrast reversals and a highly local image. This allows a greatly extended regieme of intuitive image interpretation. For example, the presence of dumbbells, with a spacing of 1.36{Angstrom}, in a Si<110> image is seen directly at 2.2{Angstrom} resolution from the elongation of the image features. For microanalysis, the Z-contrast image facilitates the accurate placement of the probe over selected atomic columns, either a single atomic column or using a line scan to reduce the effects of beam damage. Column-by-column analysis by EELS is possible, without beam broadening, through the columnar channeling effect that occurs when a highly convergent coherent probe is incident along a low order crystal zone axis.

  3. The clumpy structure of the chemically active L1157 outflow

    E-print Network

    Milena Benedettini; Serena Viti; Claudio Codella; Rafael Bachiller; Frederic Gueth; Maria T. Beltràn; Anne Dutrey; Stephane Guilloteau

    2007-08-01

    We present high spatial resolution maps, obtained with the Plateau de Bure Interferometer, of the blue lobe of the L1157 outflow. We observed four lines at 3 mm, namely CH3OH (2_K-1_K), HC3N (11-10), HCN (1-0) and OCS (7-6). Moreover, the bright B1 clump has also been observed at better spatial resolution in CS (2-1), CH3OH (2_1-1_1)A-, and 34SO (3_2-2_1). These high spatial resolution observations show a very rich structure in all the tracers, revealing a clumpy structure of the gas superimposed to an extended emission. In fact, the three clumps detected by previous IRAM-30m single dish observations have been resolved into several sub-clumps and new clumps have been detected in the outflow. The clumps are associated with the two cavities created by two shock episodes driven by the precessing jet. In particular, the clumps nearest the protostar are located at the walls of the younger cavity with a clear arch-shape form while the farthest clumps have slightly different observational characteristics indicating that they are associated to the older shock episode. The emission of the observed species peaks in different part of the lobe: the east clumps are brighter in HC3N (11-10), HCN (1-0) and CS (2-1) while the west clumps are brighter in CH3OH(2_K-1_K), OCS (7-6) and 34SO (3_2-2_1). This peak displacement in the line emission suggests a variation of the physical conditions and/or the chemical composition along the lobe of the outflow at small scale, likely related to the shock activity and the precession of the outflow. In particular, we observe the decoupling of the silicon monoxide and methanol emission, common shock tracers, in the B1 clump located at the apex of the bow shock produced by the second shock episode.

  4. Chemical reactivity of hydrogen, nitrogen, and oxygen atoms at temperatures below 100 k

    NASA Technical Reports Server (NTRS)

    Mcgee, H. A., Jr.

    1973-01-01

    The synthesis of unusual compounds by techniques employing cryogenic cooling to retard their very extreme reactivity was investigated. Examples of such species that were studied are diimide (N2H2), cyclobutadiene (C4H4), cyclopropanone (C3H4O), oxirene (C2H2O), and many others. Special purpose cryogenically cooled inlet arrangements were designed such that the analyses incurred no warm-up of the cold, and frequently explosively unstable, compounds. Controlled energy electron impact techniques were used to measure critical potentials and to develop the molecular energetics and thermodynamics of these molecules and to gain some insight into their kinetic characteristics as well. Three and four carbon strained ring molecules were studied. Several reactions of oxygen and hydrogen atoms with simple molecules of H, N, C, and O in hard quench configurations were studied. And the quench stabilization of BH3 was explored as a model system in cryochemistry.

  5. Three-dimensional chemical imaging of embedded nanoparticles using atom probe tomography.

    PubMed

    Kuchibhatla, Satyanarayana V N T; Shutthanandan, V; Prosa, T J; Adusumilli, P; Arey, B; Buxbaum, A; Wang, Y C; Tessner, T; Ulfig, R; Wang, C M; Thevuthasan, S

    2012-06-01

    Analysis of nanoparticles is often challenging especially when they are embedded in a matrix. Hence, we have used laser-assisted atom probe tomography (APT) to analyze the Au nanoclusters synthesized in situ using ion-beam implantation in a single crystal MgO matrix. APT analysis along with scanning transmission electron microscopy and energy dispersive spectroscopy (STEM-EDX) indicated that the nanoparticles have an average size ~8-12 nm. While it is difficult to analyze the composition of individual nanoparticles using STEM, APT analysis can give three-dimensional compositions of the same. It was shown that the maximum Au concentration in the nanoparticles increases with increasing particle size, with a maximum Au concentration of up to 50%. PMID:22551877

  6. Surface structure analysis of atomically smooth BaBiO3 Films

    NASA Astrophysics Data System (ADS)

    Gozar, A.; Logvenov, G.; Butko, V. Y.; Bozovic, I.

    2007-05-01

    Using low-energy time-of-flight scattering and recoil spectroscopy (TOFSARS) and mass spectroscopy of recoiled ions (MSRI) we analyze the surface structure of an atomically smooth BaBiO3 film grown by molecular beam epitaxy. We demonstrate high sensitivity of the TOFSARS and MSRI spectra to slight changes in the orientation of the ion scattering plane with respect to the crystallographic axes. The observed angle dependence allows us to clearly identify the termination layer as BiO2 . Our data also indicate that angle-resolved MSRI data can be used for high-resolution studies of the surface structure of complex oxide thin films.

  7. Structural and Magnetic Evolution of Bimetallic MnAu Clusters Driven by Asymmetric Atomic Migration

    SciTech Connect

    Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

    2014-03-12

    The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L10 structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

  8. Spin-flip induction of Fano resonance upon electron tunneling through atomic-scale spin structures

    NASA Astrophysics Data System (ADS)

    Val'kov, V. V.; Aksenov, S. V.; Ulanov, E. A.

    2013-05-01

    The inclusion of inelastic spin-dependent electron scatterings by the potential profiles of a single magnetic impurity and a spin dimer is shown to induce resonance features due to the Fano effect in the transport characteristics of such atomic-scale spin structures. The spin-flip processes leading to a configuration interaction of the system's states play a fundamental role for the realization of Fano resonance and antiresonance. It has been established that applying an external magnetic field and a gate electric field allows the conductive properties of spin structures to be changed radically through the Fano resonance mechanism.

  9. Correlation between atomic structure and localized gap states in silicon grain boundaries

    SciTech Connect

    Cleri, F. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States); [Divisione Materiali Avanzati, ENEA, Centro Ricerche Casaccia, Casella Postale, 2400, 00100Roma (Italy); Keblinski, P. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States); Colombo, L. [Dipartimento di Scienza dei Materiali, Universita di Milano, and Istituto Nazionale per la Fisica della Materia, via Emanueli 15, 20126Milano (Italy)] [Dipartimento di Scienza dei Materiali, Universita di Milano, and Istituto Nazionale per la Fisica della Materia, via Emanueli 15, 20126Milano (Italy); Phillpot, S.R.; Wolf, D. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)

    1998-03-01

    Tight-binding molecular-dynamics simulations of a typical high-energy grain boundary in silicon show that its equilibrium atomic structure is similar to that of bulk amorphous silicon and contains coordination defects. The corresponding electronic structure is also amorphouslike, displaying gap states mainly localized around the coordination defects, where large changes in the bond-hybridization character are observed. It is proposed that such coordination defects in disordered high-energy grain boundaries are responsible for the experimentally observed gap states in polycrystalline Si. {copyright} {ital 1998} {ital The American Physical Society}

  10. Refined MCHF evaluations of field isotope shift and hyperfine structure in the calcium atom

    NASA Astrophysics Data System (ADS)

    Fonseca, A. L. A.; Bauche, J.

    1984-08-01

    In the calcium atom, the MCHF method has been applied for evaluating the field-shift electronic parts of both 4 s 2-4 s4 p lines, and the hyperfine-structure electronic effective parameters of the 4 s4 p 3 P 2 and1 P 1 levels. For the hyperfine structures, the far-configuration mixing corrections have been computed with the assumption that the lower state is itself a two-component sp+dp state in close-configuration mixing.

  11. Inelastic collisions between selectively excited rubidium 6/sup 2/D-state atoms and noble-gas atoms: Fine-structure-state mixing

    SciTech Connect

    Zollars, B.G.; Schuessler, H.A.; Parker, J.W.; Hill, R.H. Jr.

    1983-09-01

    Inelastic collisional processes in fine-structure-state mixing have been studied by selective stepwise excitation and observation of the resulting fluorescence during collisions of excited rubidium 6/sup 2/D/sub 5/2/ state atoms with various noble-gas atoms. It is shown that for intermediately excited rubidium atoms the fine-structure-state mixing cross sections are generally p increasing from helium to xenon. The cross sections for the process Rb(6/sup 2/D/sub 5/2/)+A(n /sup 1/S/sub 0/)..-->..Rb(6/sup 2/D/sub 3/2/)+ A(n /sup 1/S/sub 0/)+..delta..E /sup 1/S/sub 0/)+..delta..E have the values sigma/sub fs/( = 2.4 +- 0.9, 3.1 +- 1.2, 2.6 +- 1.0, 5.8 +- 2.2, and 9.3 +- 5.6 in units of 10/sup -14/ cm/sup 2/, where A denotes in sequence any one of the noble gas atoms He, Ne, Ar, Kr, and Xe, respectively. Transfer cross sections for the transfer of excited Rb6 /sup 2/D-state atoms out of the doublet were also determined and are about an order of magnitude smaller than the fine-structure-mixing cross sections.

  12. Atomic structure of misfit dislocations in nonpolar ZnO/Al2O3 heterostructures

    SciTech Connect

    Zhou, Honghui [ORNL; Chisholm, Matthew F [ORNL; Pant, Punam [North Carolina State University; Chang, Hye Jung [ORNL; Gazquez Alabart, Jaume [ORNL; Pennycook, Stephen J [ORNL; Narayan, Jagdish [North Carolina State University

    2010-01-01

    Understanding dislocation core structure at the atomic level is of significant theoretical and technological importance because of the role dislocations play in the electronic/optical properties of materials. In this letter, we report our aberration-corrected scanning transmission electron microscopy study on misfit dislocation core structures at the ( ) ZnO/( ) Al2O3 (a-ZnO/r-Al2O3) interface, a nonpolar system that has recently drawn intensive research interest. The dislocations are found to be perfect edge dislocations with a Burgers vector of b = 1/3 Al2O3. The atomic configuration of the core structure is closely related to the preferred interfacial bonding configuration. A significant number of these misfit dislocations have undergone a core structure modification involving the incorporation of Zn in the Al2O3 side of the dislocation (under compression). This core structure modification appears to be effective in reducing the strain in the ZnO in the vicinity of the core.

  13. Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin / mitomycin C resistance in other bacteria

    E-print Network

    Yu, Shen; Vit, Allegra; Devenish, Sean; Mahanty, H Khris; Itzen, Aymelt; Goody, Roger S; Blankenfeldt, Wulf

    2011-08-17

    RESEARCH ARTICLE Open Access Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria Shen Yu1,2, Allegra Vit3, Sean Devenish4,5, H Khris... of bacteria-produced antibio- tics that has gained increasing attention in recent years [3]. They comprise a group of over 100 compounds iso- lated from natural sources and several thousand deriva- tives that have been synthesized by chemical methods [4...

  14. Substrate Effects for Atomic Chain Electronics

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige; Saini, Subhash (Technical Monitor)

    1998-01-01

    A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. For excellent structural stability, we demand chemical bonding between the adatoms and substrate atoms, but then good electronic isolation may not be guaranteed. Conditions are clarified for good isolation. Because of the chemical bonding, fundamental adatom properties are strongly influenced: a chain with group IV adatoms having two chemical bonds, or a chain with group III adatoms having one chemical bond is semiconducting. Charge transfer from or to the substrate atoms brings about unintentional doping, and the electronic properties have to be considered for the entire combination of the adatom and substrate systems even if the adatom modes are well localized at the surface.

  15. Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture

    Microsoft Academic Search

    Jianmin Yuan

    2002-01-01

    An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density

  16. The virtual-photon effects in spontaneous emission from an atom embedded in a photonic band gap structure

    Microsoft Academic Search

    Zhengdong Liu; Y. Lin; Shiyao Zhu; K. Shang; Liang Zeng

    1999-01-01

    In a three-level atom embedded in a photonic band gap structure, the spontaneous emission is studied both with and without rotating-wave approximation. The virtual-photon-localized field is found, which causes a greater population of the atom trapped in its upper states.

  17. Surface structures and surface-atom vibrations determined using photoelectron diffraction

    SciTech Connect

    Wang, L.Q. (California Univ., Berkeley, CA (United States). Dept. of Chemistry Lawrence Berkeley Lab., CA (United States))

    1991-07-01

    Surface structures of {radical}3 {times} {radical}3 R30{degrees} Cl/Ni(111) and c(2 {times} 2)Cl/Cu(001) were determined using low- temperature angle-resolved photoemission extended fine structure (ARPEFS), which yields both more accurate surface and near-surface structural information for deeper substrate layers. A study of surface-atom vibrations for {radical}3 {times} {radical}3 R30{degrees} Cl/Ni(111) and c(2 {times} 2)Cl/Cu(001) was made using temperature-dependent ARPEFS. A model for predicting the adsorbate vibrational anisotropy from surface structures was proposed and also successfully applied to several adsorbate systems. This model offered a simple and straightforward physical picture for understanding different types of vibrational anisotropy.

  18. Protein structure evaluation using an all-atom energy based empirical scoring function.

    PubMed

    Narang, Pooja; Bhushan, Kukum; Bose, Surojit; Jayaram, B

    2006-02-01

    Arriving at the native conformation of a polypeptide chain characterized by minimum most free energy is a problem of long standing interest in protein structure prediction endeavors. Owing to the computational requirements in developing free energy estimates, scoring functions--energy based or statistical--have received considerable renewed attention in recent years for distinguishing native structures of proteins from non-native like structures. Several cleverly designed decoy sets, CASP (Critical Assessment of Techniques for Protein Structure Prediction) structures and homology based internet accessible three dimensional model builders are now available for validating the scoring functions. We describe here an all-atom energy based empirical scoring function and examine its performance on a wide series of publicly available decoys. Barring two protein sequences where native structure is ranked second and seventh, native is identified as the lowest energy structure in 67 protein sequences from among 61,659 decoys belonging to 12 different decoy sets. We further illustrate a potential application of the scoring function in bracketing native-like structures of two small mixed alpha/beta globular proteins starting from sequence and secondary structural information. The scoring function has been web enabled at www.scfbio-iitd.res.in/utility/proteomics/energy.jsp. PMID:16363875

  19. Characterization of lead zirconate titanate--lanthanum ruthenate thin film structures prepared by chemical solution deposition.

    PubMed

    Bencan, Andreja; Malic, Barbara; Drazic, Goran; Vukadinovi?, Miso; Kosec, Marija

    2007-01-01

    In this work, the results of compositional and microstructural analysis of lead zirconate titanate--lanthanum ruthenate thin film structures prepared by chemical solution deposition are discussed. The cross-section transmission electron microscope (TEM) micrographs of the La-Ru-O film deposited on a SiO2/Si substrate and annealed at 700 degrees C revealed RuO2 crystals embedded in a glassy silicate matrix. When the La-Ru-O film was deposited on a Pt/TiO2/SiO2/Si substrate, RuO2 and La4Ru6O19 crystallized after annealing at 700 degrees C. After firing at 550 degrees C randomly oriented lead zirconate titanate (PZT) thin films crystallized on the La-Ru-O/SiO2/Si substrate, while on La-Ru-O/Pt/TiO2/SiO2/Si substrates PZT thin films with (111) preferred orientation were obtained. No diffusion of the Ru atoms in the PZT film was found. Ferroelectric response of PZT thin films on these substrates is shown in comparison with the PZT film deposited directly on the Pt/TiO2/SiO2/Si substrate without a La-Ru-O layer. PMID:18076056

  20. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol

    NASA Astrophysics Data System (ADS)

    Moorthi, P. P.; Gunasekaran, S.; Swaminathan, S.; Ramkumaar, G. R.

    2015-02-01

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (?0) of this novel molecular system and related properties (?, ?0 and ??) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.