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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. Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution

    PubMed Central

    Nayak, Maheswar; Pradhan, P. C.; Lodha, G. S.

    2015-01-01

    We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field. PMID:25726866

  3. Quantitative Statistical Analysis of Atomic Scale Structural and Chemical Variations in Complex Oxides Interfaces

    NASA Astrophysics Data System (ADS)

    Yang, Hao

    Grain boundaries (GBs) are known to have far-reaching effects on the electrical and mechanical properties of materials. Understanding the atomic scale mechanisms behind these effects requires an accurate determination of the interplay between GB structure and composition. Based on the analysis of a range of grain boundaries using aberration corrected scanning transmission electron microscopy (STEM), a general structural units model has been derived for the structure of grain boundaries in various dense packing cubic materials including FCC metals, perovskites and fluorites. The similarities in the observed grain boundary structures of these materials originate from related space (and point) group symmetries of the parent structures. The presence of structural variations away from the general structural units model may be caused by frustrations of certain symmetry operations that result from the incorporation of point defects (vacancies and impurities). A clear understanding of the similarity and variation in grain boundary atomic structures will not only provide a means to infer the structure-property relationships in broad classes of materials, but also enables us eventually to effectively manipulate the GB structures to achieve better materials properties. To understand these chemical induced variations, and further quantify exactly how atomic scale variations at the boundary plane extend to the practical mesoscale operating length of the system, statistical analysis has been applied to the aberration corrected STEM Z-contrast images acquired from a series of undoped and doped SrTiO3 GBs. In order to understand the effects of oxygen vacancies incorporation, in-situ characterization of GB atomic structures were performed using the Environmental TEM under the reduced gas and heating environment. This analysis of GB similarity and variation provides insights into the structure-composition relationship in GBs to understand the influence of nonstoichiometry and dopant

  4. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-01-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule. PMID:26178193

  5. 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.

  6. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

    PubMed

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J; Le Thi Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Muñiz Olite, Jorge L; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel's Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  7. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    PubMed Central

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  8. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

    PubMed

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J; Le Thi Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Muñiz Olite, Jorge L; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M

    2016-05-27

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel's Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

  9. Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

    ERIC Educational Resources Information Center

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

    2015-01-01

    A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

  10. Correlating STM Contrast and Atomic-Scale Structure by Chemical Modification: Vacancy Dislocation Loops on FeO/Pt(111)

    SciTech Connect

    Merte, L. R.; Knudsen, Jan; Grabow, Lars C.; Vang, Ronnie T.; Laegsgaard, E.; Mavrikakis, Manos; Besenbacher, Fleming

    2008-11-28

    By chemically modifying the FeO(111) thin film on Pt(111), we show that it is possible to unambiguously correlate its STM morphology with its underlying structure without recourse to STM simulations. Partial reduction of the oxide surface leads to the formation of triangularly-shaped oxygen vacancy dislocation loops at specific sites in the moiré structure of the film. Their presence allows unambiguous identification of the high-symmetry domains of the moiré structure, whose differing chemical properties govern the templating effect on adsorbed metal atoms, clusters and molecules.

  11. Atomic and Molecular Structure in Chemical Education: A Critical Analysis from Various Perspectives of Science Education.

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

    Provides a critical analysis of the role that atomic theory plays in the science curriculum from elementary through secondary school. Examines structural concepts from the perspective of the theory of meaningful learning, information processing theory, and the alternative conceptions movement. Contains 54 references. (DDR)

  12. 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 BΙ-sites and Fe0.20Ti0.80 at BΙΙ-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

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

    DOE PAGES

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

    2014-09-25

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

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

    SciTech Connect

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

    2014-09-25

    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.

  15. Assembly of Complex Nano-Structure from Single Atoms
    Chemical Identification, Manipulation and Assembly by AFM—

    NASA Astrophysics Data System (ADS)

    Morita, Seizo; Sugimoto, Yoshiaki; Ooyabu, Noriaki; Custance, Óscar; Abe, Masayuki; Pou, Pablo; Jelinek, Pavel; Pérez, Rubén

    An atomic force microscope (AFM) under noncontact and nearcontact regions operated at room-temperature (RT) in ultrahigh vacuum, is used as a tool for topography-based atomic discrimination and atomic-interchange manipulations of two intermixed atomic species on semiconductor surfaces. Noncontact AFM topography based site-specific force curves provide the chemical covalent bonding forces between the tip apex and the atoms at the surface. Here, we introduced an example related to topography-based atomic discrimination using selected Sn and Si adatoms in Sn/Si(111)-(√3 ×√3 ) surface. Recently, under nearcontact region, we found a lateral atom-interchange manipulation phenomenon at RT in Sn/Ge(111)-c(2×8) intermixed sample. This phenomenon can interchange an embedded Sn atom with a neighbor Ge atom at RT. Using the vector scan method under nearcontact region, we constructed “Atom Inlay”, that is, atom letters “Sn” consisted of 19 Sn atoms embedded in Ge(111)-c(2×8) substrate. Using these methods, now we can assemble compound semiconductor nanostructures atom-by-atom.

  16. 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.

  17. The atomic structure and chemical composition of HfOx (x < 2) films prepared by ion-beam sputtering deposition

    NASA Astrophysics Data System (ADS)

    Aliev, V. S.; Gerasimova, A. K.; Kruchinin, V. N.; Gritsenko, V. A.; Prosvirin, I. P.; Badmaeva, I. A.

    2016-08-01

    Non-stoichiometric HfOx films of different chemical composition (x < 2) were fabricated by ion-beam sputtering deposition (IBSD) at room temperature. The ratio of O and Hf atoms in films x was varied by setting the O2 partial pressure in a chamber. An effect of chemical composition on the atomic structure of the films was studied by reflection high-energy electron diffraction, x-ray photoelectron spectroscopy and field emission scanning electron microscopy methods. The films were found to be amorphous, consisting only of three components: Hf-metal clusters, Hf4O7 suboxide and stoichiometric HfO2. The relative concentration of these components varies with changing x. The surface of the films contains the increased oxygen content compared to the bulk. It was found that the Hf4O7 suboxide concentration is maximal at x = 1.8. The concept of hafnium oxide film growth by the IBSD method is proposed to explain the lack of suboxides variety in the films and the instability of HfO2, when annealed at high temperature.

  18. Structural and chemical characterization of novel NixZn1-xGa2O4 nanocatalysts at atomic resolution

    NASA Astrophysics Data System (ADS)

    Xu, Qian; Wu, Zhaochun; Hong, Jinhua; Chang, Xiaofeng; Li, Xueji; Yan, Shicheng; Wang, Peng

    2015-10-01

    NixZn1-xGa2O4 has already been demonstrated as a noteworthy example of potentially useful catalytic properties such as NOx reduction. In our previous work, it was interesting to find out that the operating temperature of NiGa2O4 catalyst in NOx reduction can be tuned by simple chemical substitution of Ni2+ by Zn2+. It is believed that the mechanism behind such stoichiometry-dependence on operating temperature should be strongly correlated with microstructure, surface morphology as well as the local composition of the nanocatalysts. In the present investigation, NixZn1-xGa2O4 solid solution was synthesized via a hydrothermal ion-exchange reaction, using NaGaO2 and the corresponding acetic salts as the starting materials. By means of a state-of-the-art aberration corrected STEM and high resolution TEM, the structural and chemical characterization at the atomic scale on the NixZn1-xGa2O4 nanocatalyst was carried out, including the crystal structure, size, morphology, surface structure and local composition. It is found that the catalyst was solid solution and most possible exposed facets may be (1 1 1).

  19. 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.

  20. Strain and structure heterogeneity in MoS2 atomic layers grown by chemical vapour deposition.

    PubMed

    Liu, Zheng; Amani, Matin; Najmaei, Sina; Xu, Quan; Zou, Xiaolong; Zhou, Wu; Yu, Ting; Qiu, Caiyu; Birdwell, A Glen; Crowne, Frank J; Vajtai, Robert; Yakobson, Boris I; Xia, Zhenhai; Dubey, Madan; Ajayan, Pulickel M; Lou, Jun

    2014-11-18

    Monolayer molybdenum disulfide (MoS2) has attracted tremendous attention due to its promising applications in high-performance field-effect transistors, phototransistors, spintronic devices and nonlinear optics. The enhanced photoluminescence effect in monolayer MoS2 was discovered and, as a strong tool, was employed for strain and defect analysis in MoS2. Recently, large-size monolayer MoS2 has been produced by chemical vapour deposition, but has not yet been fully explored. Here we systematically characterize chemical vapour deposition-grown MoS2 by photoluminescence spectroscopy and mapping and demonstrate non-uniform strain in single-crystalline monolayer MoS2 and strain-induced bandgap engineering. We also evaluate the effective strain transferred from polymer substrates to MoS2 by three-dimensional finite element analysis. Furthermore, our work demonstrates that photoluminescence mapping can be used as a non-contact approach for quick identification of grain boundaries in MoS2.

  1. Strain and structure heterogeneity in MoS2 atomic layers grown by chemical vapour deposition

    DOE PAGES

    Liu, Zheng; Amani, Matin; Najmaei, Sina; Xu, Quan; Zou, Xiaolong; Zhou, Wu; Yu, Ting; Qiu, Caiyu; Birdwell, A. Glen; Crowne, Frank J.; et al

    2014-11-18

    Monolayer molybdenum disulfide (MoS2) has attracted tremendous attention due to its promising applications in high-performance field-effect transistors, phototransistors, spintronic devices, and nonlinear optics. The enhanced photoluminescence effect in monolayer MoS2 was discovered and, as a strong tool, was employed for strain and defect analysis in MoS2. Recently, large-size monolayer MoS2 has been produced by chemical vapor deposition but has not yet been fully explored. Here we systematically characterize chemical vapor deposition grown MoS2 by PL spectroscopy and mapping, and demonstrate non-uniform strain in single-crystalline monolayer MoS2 and strain-induced band gap engineering. We also evaluate the effective strain transferred from polymermore » substrates to MoS2 by three-dimensional finite element analysis. In addition, our work demonstrates that PL mapping can be used as a non-contact approach for quick identification of grain boundaries in MoS2.« less

  2. 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

  3. Insights from atomic-resolution X-ray structures of chemically synthesized HIV-1 protease in complex with inhibitors.

    PubMed

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

    2007-10-26

    The human immunodeficiency virus 1 (HIV-1) protease (PR) is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 PR has one catalytic site formed by the homodimeric enzyme. We chemically synthesized fully active HIV-1 PR using modern ligation methods. When complexed with the classic substrate-derived inhibitors JG-365 and MVT-101, the synthetic HIV-1 PR formed crystals that diffracted to 1.04- and 1.2-A resolution, respectively. These atomic-resolution structures revealed additional structural details of the HIV-1 PR's 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.

  4. Influence of krypton atoms on the structure of hydrogenated amorphous carbon deposited by plasma enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Oliveira, M. H.; Viana, G. A.; de Lima, M. M.; Cros, A.; Cantarero, A.; Marques, F. C.

    2010-12-01

    Hydrogenated amorphous carbon (a-C:H) films were prepared by plasma enhanced chemical vapor deposition using methane (CH4) plus krypton (Kr) mixed atmosphere. The depositions were performed as function of the bias voltage and krypton partial pressure. The goal of this work was to study the influence of krypton gas on the physical properties of a-C:H films deposited on the cathode electrode. Krypton concentration up to 1.6 at. %, determined by Rutherford Back-Scattering, was obtained at high Kr partial pressure and bias of -120 V. The structure of the films was analyzed by means of optical transmission spectroscopy, multi-wavelength Raman scattering and Fourier Transform Infrared spectroscopy. It was verified that the structure of the films remains unchanged up to a concentration of Kr of about 1.0 at. %. A slight graphitization of the films occurs for higher concentration. The observed variation in the film structure, optical band gap, stress, and hydrogen concentration were associated mainly with the subplantation process of hydrocarbons radicals, rather than the krypton ion energy.

  5. Influence of krypton atoms on the structure of hydrogenated amorphous carbon deposited by plasma enhanced chemical vapor deposition

    SciTech Connect

    Oliveira, M. H. Jr.; Viana, G. A.; Marques, F. C.; Lima, M. M. Jr. de; Cros, A.; Cantarero, A.

    2010-12-15

    Hydrogenated amorphous carbon (a-C:H) films were prepared by plasma enhanced chemical vapor deposition using methane (CH{sub 4}) plus krypton (Kr) mixed atmosphere. The depositions were performed as function of the bias voltage and krypton partial pressure. The goal of this work was to study the influence of krypton gas on the physical properties of a-C:H films deposited on the cathode electrode. Krypton concentration up to 1.6 at. %, determined by Rutherford Back-Scattering, was obtained at high Kr partial pressure and bias of -120 V. The structure of the films was analyzed by means of optical transmission spectroscopy, multi-wavelength Raman scattering and Fourier Transform Infrared spectroscopy. It was verified that the structure of the films remains unchanged up to a concentration of Kr of about 1.0 at. %. A slight graphitization of the films occurs for higher concentration. The observed variation in the film structure, optical band gap, stress, and hydrogen concentration were associated mainly with the subplantation process of hydrocarbons radicals, rather than the krypton ion energy.

  6. Local atomic structure analysis of SiC interface with oxide using chemical-state-selective X-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Isomura, Noritake; Murai, Takaaki; Oji, Hiroshi; Nomoto, Toyokazu; Watanabe, Yukihiko; Kimoto, Yasuji

    2016-10-01

    A local atomic structure analysis of the interface between chemical vapor-deposited SiO2 and 4H-SiC was achieved via a combination of chemical-state-selective X-ray absorption spectroscopy and the use of a sample with a very thin oxide film. The Si K-edge spectrum, which monitors the SiC-assigned Auger peak, allows the SiC side of the SiO2/SiC interface to be selectively measured through the SiO2 film. We estimate the coordination number of the first nearest neighbor to be reduced by 17% with respect to the SiC bulk. This suggests that C vacancy defects exist at the SiC side of the interface.

  7. The atomic structure and chemical composition of HfOx (x < 2) films prepared by ion-beam sputtering deposition

    NASA Astrophysics Data System (ADS)

    Aliev, V. S.; Gerasimova, A. K.; Kruchinin, V. N.; Gritsenko, V. A.; Prosvirin, I. P.; Badmaeva, I. A.

    2016-08-01

    Non-stoichiometric HfOx films of different chemical composition (x < 2) were fabricated by ion-beam sputtering deposition (IBSD) at room temperature. The ratio of O and Hf atoms in films x was varied by setting the O2 partial pressure in a chamber. An effect of chemical composition on the atomic structure of the films was studied by reflection high-energy electron diffraction, x-ray photoelectron spectroscopy and field emission scanning electron microscopy methods. The films were found to be amorphous, consisting only of three components: Hf-metal clusters, Hf4O7 suboxide and stoichiometric HfO2. The relative concentration of these components varies with changing x. The surface of the films contains the increased oxygen content compared to the bulk. It was found that the Hf4O7 suboxide concentration is maximal at x = 1.8. The concept of hafnium oxide film growth by the IBSD method is proposed to explain the lack of suboxides variety in the films and the instability of HfO2, when annealed at high temperature.

  8. Quantitative chemical-structure evaluation using atom probe tomography: Short-range order analysis of Fe-Al.

    PubMed

    Marceau, R K W; Ceguerra, A V; Breen, A J; Raabe, D; Ringer, S P

    2015-10-01

    Short-range-order (SRO) has been quantitatively evaluated in an Fe-18Al (at%) alloy using atom probe tomography (APT) data and by calculation of the generalised multicomponent short-range order (GM-SRO) parameters, which have been determined by shell-based analysis of the three-dimensional atomic positions. The accuracy of this method with respect to limited detector efficiency and spatial resolution is tested against simulated D03 ordered data. Whilst there is minimal adverse effect from limited atom probe instrument detector efficiency, the combination of this with imperfect spatial resolution has the effect of making the data appear more randomised. The value of lattice rectification of the experimental APT data prior to GM-SRO analysis is demonstrated through improved information sensitivity.

  9. 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…

  10. 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.

  11. Strain and structure heterogeneity in MoS2 atomic layers grown by chemical vapour deposition

    SciTech Connect

    Liu, Zheng; Amani, Matin; Najmaei, Sina; Xu, Quan; Zou, Xiaolong; Zhou, Wu; Yu, Ting; Qiu, Caiyu; Birdwell, A. Glen; Crowne, Frank J.; Vajtai, Robert; Yakobson, Boris I.; Xia, Zhenhai; Dubey, Madan; Ajayan, Pulickel M.; Lou, Jun

    2014-11-18

    Monolayer molybdenum disulfide (MoS2) has attracted tremendous attention due to its promising applications in high-performance field-effect transistors, phototransistors, spintronic devices, and nonlinear optics. The enhanced photoluminescence effect in monolayer MoS2 was discovered and, as a strong tool, was employed for strain and defect analysis in MoS2. Recently, large-size monolayer MoS2 has been produced by chemical vapor deposition but has not yet been fully explored. Here we systematically characterize chemical vapor deposition grown MoS2 by PL spectroscopy and mapping, and demonstrate non-uniform strain in single-crystalline monolayer MoS2 and strain-induced band gap engineering. We also evaluate the effective strain transferred from polymer substrates to MoS2 by three-dimensional finite element analysis. In addition, our work demonstrates that PL mapping can be used as a non-contact approach for quick identification of grain boundaries in MoS2.

  12. RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.

    SciTech Connect

    HOLDEN, N.E.

    2005-08-13

    In the 1949 Report of the Atomic Weights Commission, a series of new elements were added to the Atomic Weights Table. Since these elements had been produced in the laboratory and were not discovered in nature, the atomic weight value of these artificial products would depend upon the production method. Since atomic weight is a property of an element as it occurs in nature, it would be incorrect to assign an atomic weight value to that element. As a result of that discussion, the Commission decided to provide only the mass number of the most stable (longest-lived) known isotope as the number to be associated with these entries in the Atomic Weights Table. As a function of time, the mass number associated with various elements has changed as longer-lived isotopes of a particular elements has been found in nature, or as improved half-life values of an element's isotopes might cause a shift in the longest-lived isotope from one mass number to another. In the 1957 Report of the Atomic Weights Commission, it was decided to discontinue the listing of the mass number in the Atomic Weights Table on the grounds that the kind of information supplied by the mass number is inconsistent with the primary purpose of the Table, i.e., to provide accurate values of ''these constants'' for use in chemical calculations. In addition to the Table of Atomic Weights, the Commission included an auxiliary Table of Radioactive Elements for the first time, where the entry would be the isotope of that element which was most stable, i.e., it had the longest known half-life. In their 1973 report, the Commission noted that the users of the Atomic Weights Table were dissatisfied with the omission of values in the Table for some elements and it was decided to reintroduce the mass number for elements. In their 1983 report, the Commission decided that radioactive elements were considered to lack a characteristic terrestrial isotopic composition, from which an atomic weight value could be calculated to

  13. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert.

  14. Direct Atom Imaging by Chemical-Sensitive Holography.

    PubMed

    Lühr, Tobias; Winkelmann, Aimo; Nolze, Gert; Krull, Dominique; Westphal, Carsten

    2016-05-11

    In order to understand the physical and chemical properties of advanced materials, functional molecular adsorbates, and protein structures, a detailed knowledge of the atomic arrangement is essential. Up to now, if subsurface structures are under investigation, only indirect methods revealed reliable results of the atoms' spatial arrangement. An alternative and direct method is three-dimensional imaging by means of holography. Holography was in fact proposed for electron waves, because of the electrons' short wavelength at easily accessible energies. Further, electron waves are ideal structure probes on an atomic length scale, because electrons have a high scattering probability even for light elements. However, holographic reconstructions of electron diffraction patterns have in the past contained severe image artifacts and were limited to at most a few tens of atoms. Here, we present a general reconstruction algorithm that leads to high-quality atomic images showing thousands of atoms. Additionally, we show that different elements can be identified by electron holography for the example of FeS2.

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

    ERIC Educational Resources Information Center

    Cipolla, Laura; Ferrari, Lia A.

    2016-01-01

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

  16. BOOK REVIEW: Computational Atomic Structure

    NASA Astrophysics Data System (ADS)

    Post, Douglass E.

    1998-02-01

    The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an

  17. Computational tests of quantum chemical models for structures, vibrational frequencies, and heats of formation of molecules with phosphorus and sulfur atoms.

    PubMed

    Hahn, David K; RaghuVeer, Krishans S; Ortiz, J V

    2010-08-12

    The Gaussian-n, complete basis set, and Weizmann-1 quantum chemical models for heats of formation are applied to a set of molecules with relevance to the combustion or pyrolysis of chemical warfare materials. Most of these models generate standard deviations from experiment that are less than 2 kcal/mol. The structures and vibrational frequencies that are generated in the course of these calculations are in good agreement with experimental data. Detailed comparisons with respect to structural types indicate that the present computational models are likely to generate useful data for complex models of combustion and pyrolysis of chemical warfare materials.

  18. Chemical domain of QSAR models from atom-centered fragments.

    PubMed

    Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2009-12-01

    A methodology to characterize the chemical domain of qualitative and quantitative structure-activity relationship (QSAR) models based on the atom-centered fragment (ACF) approach is introduced. ACFs decompose the molecule into structural pieces, with each non-hydrogen atom of the molecule acting as an ACF center. ACFs vary with respect to their size in terms of the path length covered in each bonding direction starting from a given central atom and how comprehensively the neighbor atoms (including hydrogen) are described in terms of element type and bonding environment. In addition to these different levels of ACF definitions, the ACF match mode as degree of strictness of the ACF comparison between a test compound and a given ACF pool (such as from a training set) has to be specified. Analyses of the prediction statistics of three QSAR models with their training sets as well as with external test sets and associated subsets demonstrate a clear relationship between the prediction performance and the levels of ACF definition and match mode. The findings suggest that second-order ACFs combined with a borderline match mode may serve as a generic and at the same time a mechanistically sound tool to define and evaluate the chemical domain of QSAR models. Moreover, four standard categories of the ACF-based membership to a given chemical domain (outside, borderline outside, borderline inside, inside) are introduced that provide more specific information about the expected QSAR prediction performance. As such, the ACF-based characterization of the chemical domain appears to be particularly useful for QSAR applications in the context of REACH and other regulatory schemes addressing the safety evaluation of chemical compounds.

  19. Noncontiguous atom matching structural similarity function.

    PubMed

    Teixeira, Ana L; Falcao, Andre O

    2013-10-28

    Measuring similarity between molecules is a fundamental problem in cheminformatics. Given that similar molecules tend to have similar physical, chemical, and biological properties, the notion of molecular similarity plays an important role in the exploration of molecular data sets, query-retrieval in molecular databases, and in structure-property/activity modeling. Various methods to define structural similarity between molecules are available in the literature, but so far none has been used with consistent and reliable results for all situations. We propose a new similarity method based on atom alignment for the analysis of structural similarity between molecules. This method is based on the comparison of the bonding profiles of atoms on comparable molecules, including features that are seldom found in other structural or graph matching approaches like chirality or double bond stereoisomerism. The similarity measure is then defined on the annotated molecular graph, based on an iterative directed graph similarity procedure and optimal atom alignment between atoms using a pairwise matching algorithm. With the proposed approach the similarities detected are more intuitively understood because similar atoms in the molecules are explicitly shown. This noncontiguous atom matching structural similarity method (NAMS) was tested and compared with one of the most widely used similarity methods (fingerprint-based similarity) using three difficult data sets with different characteristics. Despite having a higher computational cost, the method performed well being able to distinguish either different or very similar hydrocarbons that were indistinguishable using a fingerprint-based approach. NAMS also verified the similarity principle using a data set of structurally similar steroids with differences in the binding affinity to the corticosteroid binding globulin receptor by showing that pairs of steroids with a high degree of similarity (>80%) tend to have smaller differences

  20. Intermolecular atom-atom bonds in crystals - a chemical perspective.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-03-01

    Short atom-atom distances between molecules are almost always indicative of specific intermolecular bonding. These distances may be used to assess the significance of all hydrogen bonds, including the C-H⋯O and even weaker C-H⋯F varieties.

  1. Chemical control of electrical contact to sp2 carbon atoms

    PubMed Central

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

    2014-01-01

    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. PMID:24736561

  2. Chemical structure of interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.

    1985-01-01

    The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

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

    PubMed

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

    2011-06-30

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

  4. Atomic structures and compositions of internal interfaces

    SciTech Connect

    Seidman, D.N. . Dept. of Materials Science and Engineering); Merkle, K.L. )

    1992-03-01

    This research program addresses fundamental questions concerning the relationships between atomic structures and chemical compositions of metal/ceramic heterophase interfaces. The chemical composition profile across a Cu/MgO {l brace}111{r brace}-type heterophase interface, produced by the internal oxidation of a Cu(Mg) single phase alloy, is measured via atom-probe field-ion microscopy with a spatial resolution of 0.121 nm; this resolution is equal to the interplanar space of the {l brace}222{r brace} MgO planes. In particular, we demonstrate for the first time that the bonding across a Cu/MgO {l brace}111{r brace}-type heterophase interface, along a <111> direction common to both the Cu matrix and an MgO precipitate, has the sequence Cu{vert bar}O{vert bar}Mg{hor ellipsis} and not Cu{vert bar}Mg{vert bar}O{hor ellipsis}; this result is achieved without any deconvolution of the experimental data. Before determining this chemical sequence it was established, via high resolution electron microscopy, that the morphology of an MgO precipitate in a Cu matrix is an octahedron faceted on {l brace}111{r brace} planes with a cube-on-cube relationship between a precipitate and the matrix. First results are also presented for the Ni/Cr{sub 2}O{sub 4} interface; for this system selected area atom probe microscopy was used to analyze this interface; Cr{sub 2}O{sub 4} precipitates are located in a field-ion microscope tip and a precipitate is brought into the tip region via a highly controlled electropolishing technique.

  5. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

    This dissertation consists of topics in two related areas of research that together provide quantum mechanical descriptions of atomic and molecular interactions and reactions. The first is the ab initio electronic structure calculation that provides the atomic and molecular interaction potential, including the long-range potential. The second is the quantum theory of interactions that uses such potentials to understand scattering, long-range molecules, and reactions. In ab initio electronic structure calculations, we present results of dynamic polarizabilities for a variety of atoms and molecules, and the long-range dispersion coefficients for a number of atom-atom and atom-molecule cases. We also present results of a potential energy surface for the triatomic lithium-ytterbium-lithium system, aimed at understanding the related chemical reactions. In the quantum theory of interactions, we present a multichannel quantum-defect theory (MQDT) for atomic interactions in a magnetic field. This subject, which is complex especially for atoms with hyperfine structure, is essential for the understanding and the realization of control and tuning of atomic interactions by a magnetic field: a key feature that has popularized cold atom physics in its investigations of few-body and many-body quantum systems. Through the example of LiK, we show how MQDT provides a systematic and an efficient understanding of atomic interaction in a magnetic field, especially magnetic Feshbach resonances in nonzero partial waves.

  6. Electronic structure interpolation via atomic orbitals.

    PubMed

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

    2011-08-17

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

  7. 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; Jakubec, I

    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)

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

    SciTech Connect

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

    1996-09-01

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

  9. 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.

  10. 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)

  11. 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.

  12. Evolution of atomic structure during nanoparticle formation.

    PubMed

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

    2014-05-01

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

  13. Evolution of atomic structure during nanoparticle formation

    PubMed Central

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

    2014-01-01

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

  14. Electrochemical Potential Derived from Atomic Cluster Structures.

    PubMed

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

    2016-02-01

    Based on the atomic cluster structures and free electron approximation model, it is revealed that the electrochemical potential (ECP) for the system of interest is proportional to the reciprocal of atomic cluster radius squared, i.e., φ = k·(1/r(2)). Applied to elemental crystals, the correlation between atomic cluster radii and the ECP that we have predicted agrees well with the previously reported results. In addition, some other physicochemical properties associated with the ECP have also been found relevant to the atomic cluster radii of materials. Thus, the atomic cluster radii can be perceived as an effective characteristic parameter to measure the ECP and related properties of materials. Our results provide a better understanding of ECP directly from the atomic structures perspective. PMID:26801811

  15. Electrochemical Potential Derived from Atomic Cluster Structures.

    PubMed

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

    2016-02-01

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

  16. Some Experiments in Atomic Structure

    ERIC Educational Resources Information Center

    Logan, Kent R.

    1974-01-01

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

  17. 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)

  18. About the atomic structures of icosahedral quasicrystals

    NASA Astrophysics Data System (ADS)

    Quiquandon, Marianne; Gratias, Denis

    2014-01-01

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

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

    PubMed

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

    2013-08-27

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

  20. Chemical Analysis of Impurity Boron Atoms in Diamond Using Soft X-ray Emission Spectroscopy

    SciTech Connect

    Muramatsu, Yasuji; Iihara, Junji; Takebe, Toshihiko; Denlinger, Jonathan D.

    2008-03-29

    To analyze the local structure and/or chemical states of boron atoms in boron-doped diamond, which can be synthesized by the microwave plasma-assisted chemical vapor deposition method (CVD-B-diamond) and the temperature gradient method at high pressure and high temperature (HPT-B-diamond), we measured the soft X-ray emission spectra in the CK and BK regions of B-diamonds using synchrotron radiation at the Advanced Light Source (ALS). X-ray spectral analyses using the fingerprint method and molecular orbital calculations confirm that boron atoms in CVD-B-diamond substitute for carbon atoms in the diamond lattice to form covalent B-C bonds, while boron atoms in HPT-B-diamond react with the impurity nitrogen atoms to form hexagonal boron nitride. This suggests that the high purity diamond without nitrogen impurities is necessary to synthesize p-type B-diamond semiconductors.

  1. Effects of rapid thermal annealing on structural, chemical, and electrical characteristics of atomic-layer deposited lanthanum doped zirconium dioxide thin film on 4H-SiC substrate

    NASA Astrophysics Data System (ADS)

    Lim, Way Foong; Quah, Hock Jin; Lu, Qifeng; Mu, Yifei; Ismail, Wan Azli Wan; Rahim, Bazura Abdul; Esa, Siti Rahmah; Kee, Yeh Yee; Zhao, Ce Zhou; Hassan, Zainuriah; Cheong, Kuan Yew

    2016-03-01

    Effects of rapid thermal annealing at different temperatures (700-900 °C) on structural, chemical, and electrical characteristics of lanthanum (La) doped zirconium oxide (ZrO2) atomic layer deposited on 4H-SiC substrates have been investigated. Chemical composition depth profiling analysis using X-ray photoelectron spectroscopy (XPS) and cross-sectional studies using high resolution transmission electron microscopy equipped with energy dispersive X-ray spectroscopy line scan analysis were insufficient to justify the presence of La in the investigated samples. The minute amount of La present in the bulk oxide was confirmed by chemical depth profiles of time-of-flight secondary ion mass spectrometry. The presence of La in the ZrO2 lattice led to the formation of oxygen vacancies, which was revealed through binding energy shift for XPS O 1s core level spectra of Zrsbnd O. The highest amount of oxygen vacancies in the sample annealed at 700 °C has yielded the acquisition of the highest electric breakdown field (∼ 6.3 MV/cm) and dielectric constant value (k = 23) as well as the highest current-time (I-t) sensor response towards oxygen gas. The attainment of both the insulating and catalytic properties in the La doped ZrO2 signified the potential of the doped ZrO2 as a metal reactive oxide on 4H-SiC substrate.

  2. Chemical Principles Revisited: Updating the Atomic Theory in General Chemistry.

    ERIC Educational Resources Information Center

    Whitman, Mark

    1984-01-01

    Presents a descriptive overview of recent achievements in atomic structure to provide instructors with the background necessary to enhance their classroom presentations. Topics considered include hadrons, quarks, leptons, forces, and the unified fields theory. (JN)

  3. Atomic structures of 13-atom clusters by density functional theory

    NASA Astrophysics Data System (ADS)

    Chen, Hsin-Yi; Wei, Ching-Ming

    2007-03-01

    The 13-atom cluster structures of the alkaline metals, alkaline earth metals, boron group, 3d, 4d, and 5d transition metals in the periodic table, and Pb are investigated by density functional theory with three kinds of exchange correlation approximation: i) LDA (Local Density Approximation), ii) GGA (Generalized Gradient Approximation) [1], and iii) PBE (Perdew-Burke-Ernzerhof) [2]. The results mainly focus on five 3-D structures: icosahedral, cuboctahedral, hexagonal-closed packed, body-center cubic, decahedral, and the other two layer structures: buckled biplanar (bbp) and garrison-cap biplanar (gbp) structures. Limited by accuracy of exchange correlation approximation, two interesting results are found. The ground states of Ca13, Sr13, Ba13, Sc13, Y13, La13, Ti13, Zr13, and Hf13 are icosahedral structures. The clusters of Ir13, Pt13, Cu13, Ag13, and Au13 are more favorable for layer structures (i.e. bbp and gbp) than the other five 3-D structures. [1] J. P. Perdew et al., Phys. Rev. B 46, 6671 (1992). [2] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).

  4. Atomic vapor spectroscopy in integrated photonic structures

    SciTech Connect

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

    2015-07-27

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

  5. Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

    DOE R&D Accomplishments Database

    Continetti, R. E.; Balko, B. A.; Lee, Y. T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

  6. 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.

  7. Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds.

    PubMed

    Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

    2015-05-01

    The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

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

    SciTech Connect

    Barzegar Vishlaghi, M.; Farzalipour Tabriz, M.; Mohammad Moradi, O.

    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.

  9. Structural materials: understanding atomic scale microstructures

    SciTech Connect

    Marquis, E A; Miller, Michael K; Blavette, D; Ringer, S. P.; Sudbrack, C; Smith, G.D.W.

    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.

  10. 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.

  11. Energetics of atomic scale structure changes in graphene.

    PubMed

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

    2015-05-21

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

  12. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    SciTech Connect

    Schwarz, Udo

    2014-12-10

    The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3D-AFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

  13. Imaging DNA Structure by Atomic Force Microscopy.

    PubMed

    Pyne, Alice L B; Hoogenboom, Bart W

    2016-01-01

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

  14. Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations.

    PubMed

    Lu, Ping; Yuan, Ren Liang; Ihlefeld, Jon F; Spoerke, Erik David; Pan, Wei; Zuo, Jian Min

    2016-04-13

    Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena.

  15. Atomic Force Tomography of a Nonplanar Molecule: Role of Lateral and Chemical Sample-Tip Interactions

    NASA Astrophysics Data System (ADS)

    Kong, Xianghua; Ji, Wei; Physics department, McGill Team; Physics department, Renmin University of China Team

    Atomically identification of the molecular geometric structures is an important prerequisite to understand their chemical and electrical properties. TiOPc, a steric structure, gives rise to two adsorption configurations of TiOPc on Cu(111), namely O-dn and O-up. The roles of chemical specific interactions of different intramolecular atoms with the AFM tips were discussed at the submolecular level. For O-up, the molecular backbone of TiOPc is only visible out of a certain range from the center of the molecule, accompanied with significant dissipation signal. Theoretical calculation identifies such dissipation signal as the chemical attraction between the out-of-plane O in TiOPc and the Cu atoms behind the CO of a tip at a certain range of lateral distance between them. When they approach closer, the sample O repulses another O in the CO tip making it tilting strongly, which softens the tip and thus leads to even stronger O (sample) - Cu (tip) attraction. A direct demonstration of sample-tip electronic hybridization was manifested in the simpler O-dn case where an explicit wavefunction overlap between the tip O atom and the sample Ti atom. Given these results presented here, we anticipate that this method might be developed further generally useful in single-molecule chemistry and physics. X.K. thanks the Chinese Scholarship Council for support.

  16. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

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

    2016-05-11

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

  17. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

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

    2016-05-11

    Understanding of the atomic structure and stability of nanowires (NWs) is critical for their applications in nanotechnology, especially when the diameter of NWs reduces to ultrathin scale (1-2 nm). Here, using aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM), we report a detailed atomic structure study of the ultrathin Au NWs, which are synthesized using a silane-mediated approach. The NWs contain large amounts of generalized stacking fault defects. These defects evolve upon sustained electron exposure, and simultaneously the NWs undergo necking and breaking. Quantitative strain analysis reveals the key role of strain in the breakdown process. Besides, ligand-like morphology is observed at the surface of the NWs, indicating the possibility of using AC-HRTEM for surface ligand imaging. Moreover, the coalescence dynamic of ultrathin Au NWs is demonstrated by in situ observations. This work provides a comprehensive understanding of the structure of ultrathin metal NWs at atomic-scale and could have important implications for their applications. PMID:27071038

  18. 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.

  19. GRASP: General-purpose Relativistic Atomic Structure Package

    NASA Astrophysics Data System (ADS)

    Grant, I. P.; McKenzie, B. J.; Norrington, P. H.; Mayers, D. F.; Pyper, N. C.

    2016-09-01

    GRASP (General-purpose Relativistic Atomic Structure Package) calculates atomic structure, including energy levels, radiative rates (A-values) and lifetimes; it is a fully relativistic code based on the jj coupling scheme.

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

    PubMed

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

    2015-06-01

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

  1. Chemical erosion of atomically dispersed doped hydrocarbon layers by deuterium

    NASA Astrophysics Data System (ADS)

    Balden, M.; Roth, J.; Pardo, E. de Juan; Wiltner, A.

    2003-03-01

    The chemical erosion of atomically dispersed Ti-doped (˜10 at.%) amorphous hydrocarbon layers (a-C:H:Ti) was investigated in the temperature range of 300-800 K for 30 eV deuterium impact. Compared to pyrolytic graphite, the methane production yield is strongly reduced at elevated temperatures. This reduction starts from temperatures just above room temperature and is even larger than for B-doped graphite. The reduction of the activation energy for hydrogen release may be the dominant interpretation for the decreased hydrocarbon formation. The ratio of emitted CD 3 to CD 4 increases with temperature for pyrolytic graphite and even stronger for the doped layers. The fluence dependence of the chemical erosion yield was determined, which is explained by enrichment of the dopant due to the preferential erosion of C.

  2. The heavy atom microwave structure of 2-methyltetrahydrofuran

    NASA Astrophysics Data System (ADS)

    Van, Vinh; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2016-11-01

    The rotational spectra of 2-methyltetrahydrofuran have been observed using a pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Conformational analysis using quantum chemical calculations yields two stable conformers; both of them possess an envelope structure. The conformational transformation can occur via two different transition states. The Cremer-Pople notation for five-membered rings is chosen for describing the conformations. Only one conformer with equatorial position of the methyl group is assigned in the experimental spectrum. The fits of its parent species, 13C- and 18O-isotopologues result in highly accurate molecular parameters, and enable the determination of a heavy atom rs structure using Kraitchman's equations. This experimentally determined structure is in excellent agreement with the structure calculated by anharmonic frequency calculations.

  3. Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Urban, Knut W.

    2008-07-01

    Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.

  4. Studying atomic structures by aberration-corrected transmission electron microscopy.

    PubMed

    Urban, Knut W

    2008-07-25

    Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli-electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations. PMID:18653874

  5. Structure and stability of semiconductor tip apexes for atomic force microscopy.

    PubMed

    Pou, P; Ghasemi, S A; Jelinek, P; Lenosky, T; Goedecker, S; Perez, R

    2009-07-01

    The short range force between the tip and the surface atoms, that is responsible for atomic-scale contrast in atomic force microscopy (AFM), is mainly controlled by the tip apex. Thus, the ability to image, manipulate and chemically identify single atoms in semiconductor surfaces is ultimately determined by the apex structure and its composition. Here we present a detailed and systematic study of the most common structures that can be expected at the apex of the Si tips used in experiments. We tackle the determination of the structure and stability of Si tips with three different approaches: (i) first principles simulations of small tip apexes; (ii) simulated annealing of a Si cluster; and (iii) a minima hopping study of large Si tips. We have probed the tip apexes by making atomic contacts between the tips and then compared force-distance curves with the experimental short range forces obtained with dynamic force spectroscopy. The main conclusion is that although there are multiple stable solutions for the atomically sharp tip apexes, they can be grouped into a few types with characteristic atomic structures and properties. We also show that the structure of the last atomic layers in a tip apex can be both crystalline and amorphous. We corroborate that the atomically sharp tips are thermodynamically stable and that the tip-surface interaction helps to produce the atomic protrusion needed to get atomic resolution.

  6. Tangent Sphere Model. An Analog to Chemical Structure.

    ERIC Educational Resources Information Center

    Schultz, Ethel L.

    1986-01-01

    Discusses the use of the Tangent Sphere Model (TSM) in introducing chemical structure to beginning chemistry students at both the secondary school and college levels. Describes various applications of the use of such models, including instruction of the atom's kernel and valence electrons. (TW)

  7. Progress in Visualizing Atomic Size Effects with DFT-Chemical Pressure Analysis: From Isolated Atoms to Trends in AB5 Intermetallics.

    PubMed

    Berns, Veronica M; Engelkemier, Joshua; Guo, Yiming; Kilduff, Brandon J; Fredrickson, Daniel C

    2014-08-12

    The notion of atomic size poses an important challenge to chemical theory: empirical evidence has long established that atoms have spatial requirements, which are summarized in tables of covalent, ionic, metallic, and van der Waals radii. Considerations based on these radii play a central role in the design and interpretation of experiments, but few methods are available to directly support arguments based on atomic size using electronic structure methods. Recently, we described an approach to elucidating atomic size effects using theoretical calculations: the DFT-Chemical Pressure analysis, which visualizes the local pressures arising in crystal structures from the interactions of atomic size and electronic effects. Using this approach, a variety of structural phenomena in intermetallic phases have already been understood in terms that provide guidance to new synthetic experiments. However, the applicability of the DFT-CP method to the broad range of the structures encountered in the solid state is limited by two issues: (1) the difficulty of interpreting the intense pressure features that appear in atomic core regions and (2) the need to divide space among pairs of interacting atoms in a meaningful way. In this article, we describe general solutions to these issues. In addressing the first issue, we explore the CP analysis of a test case in which no core pressures would be expected to arise: isolated atoms in large boxes. Our calculations reveal that intense core pressures do indeed arise in these virtually pressure-less model systems and allow us to trace the issue to the shifts in the voxel positions relative to atomic centers upon expanding and contracting the unit cell. A compensatory grid unwarping procedure is introduced to remedy this artifact. The second issue revolves around the difficulty of interpreting the pressure map in terms of interatomic interactions in a way that respects the size differences of the atoms and avoids artificial geometrical

  8. High-resolution electron spin resonance spectroscopy of XeF* in solid argon. The hyperfine structure constants as a probe of relativistic effects in the chemical bonding properties of a heavy noble gas atom.

    PubMed

    Misochko, Eugenii Ya; Akimov, Alexander V; Goldschleger, Ilya U; Tyurin, Danil A; Laikov, Dimitri N

    2005-01-15

    Xenon fluoride radicals were generated by solid-state chemical reactions of mobile fluorine atoms with xenon atoms trapped in Ar matrix. Highly resolved electron spin resonance spectra of XeF* were obtained in the temperature range of 5-25 K and the anisotropic hyperfine parameters were determined for magnetic nuclei 19F, 129Xe, and 131Xe using naturally occurring and isotopically enriched xenon. Signs of parallel and perpendicular hyperfine components were established from analysis of temperature changes in the spectra and from numerical solutions of the spin Hamiltonian for two nonequivalent magnetic nuclei. Thus, the complete set of components of hyperfine- and g-factor tensors of XeF* were obtained: 19F (Aiso=435, Adip=1249 MHz) and 129Xe (Aiso=-1340, Adip=-485 MHz); g(parallel)=1.9822 and g(perpendicular)=2.0570. Comparison of the measured hyperfine parameters with those predicted by density-functional theory (DFT) calculations indicates, that relativistic DFT gives true electron spin distribution in the 2Sigma+ ground-state, whereas nonrelativistic theory underestimates dramatically the electron-nuclear contact Fermi interaction (Aiso) on the Xe atom. Analysis of the obtained magnetic-dipole interaction constants (Adip) shows that fluorine 2p and xenon 5p atomic orbitals make a major contribution to the spin density distribution in XeF*. Both relativistic and nonrelativistic calculations give close magnetic-dipole interaction constants, which are in agreement with the measured values. The other relativistic feature is considerable anisotropy of g-tensor, which results from spin-orbit interaction. The orbital contribution appears due to mixing of the ionic 2Pi states with the 2Sigma+ ground state, and the spin-orbit interaction plays a significant role in the chemical bonding of XeF*.

  9. Structurally uniform and atomically precise carbon nanostructures

    NASA Astrophysics Data System (ADS)

    Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro

    2016-01-01

    Nanometre-sized carbon materials consisting of benzene units oriented in unique geometric patterns, hereafter named nanocarbons, conduct electricity, absorb and emit light, and exhibit interesting magnetic properties. Spherical fullerene C60, cylindrical carbon nanotubes and sheet-like graphene are representative forms of nanocarbons, and theoretical simulations have predicted several exotic 3D nanocarbon structures. At present, synthetic routes to nanocarbons mainly lead to mixtures of molecules with a range of different structures and properties, which cannot be easily separated or refined into pure forms. Some researchers believe that it is impossible to synthesize these materials in a precise manner. Obtaining ‘pure’ nanocarbons is a great challenge in the field of nanocarbon science, and the construction of structurally uniform nanocarbons, ideally as single molecules, is crucial for the development of functional materials in nanotechnology, electronics, optics and biomedical applications. This Review highlights the organic chemistry approach — more specifically, bottom-up construction with atomic precision — that is currently the most promising strategy towards this end.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  12. 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.

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

    PubMed

    Murshudov, G N

    2016-01-01

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

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

    PubMed

    Murshudov, G N

    2016-01-01

    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models. PMID:27572731

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

    SciTech Connect

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

    2014-12-02

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

  16. 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.

  17. Chemical control of electrical contact to sp² carbon atoms.

    PubMed

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

    2014-01-01

    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 sp(2) carbon structures.

  18. Single molecule and single atom sensors for atomic resolution imaging of chemically complex surfaces.

    PubMed

    Kichin, Georgy; Weiss, Christian; Wagner, Christian; Tautz, F Stefan; Temirov, Ruslan

    2011-10-26

    Individual Xe atoms as well as single CO and CH(4) molecules adsorbed at the tip apex of a scanning tunneling microscope (STM) function as microscopic force sensors that change the tunneling current in response to the forces acting from the surface. An STM equipped with any of these sensors is able to image the short-range Pauli repulsion and thus resolve the inner structure of large organic adsorbate molecules. Differences in the performance of the three studied sensors suggest that the sensor functionality can be tailored by tuning the interaction between the sensor particle and the STM tip.

  19. Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

    PubMed

    Knizia, Gerald

    2013-11-12

    Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

  20. Atomic structure of icosahedral B4C boron carbide from a first principles analysis of NMR spectra.

    PubMed

    Mauri, F; Vast, N; Pickard, C J

    2001-08-20

    Density functional theory is demonstrated to reproduce the 13C and 11B NMR chemical shifts of icosahedral boron carbides with sufficient accuracy to extract previously unresolved structural information from experimental NMR spectra. B4C can be viewed as an arrangement of 3-atom linear chains and 12-atom icosahedra. According to our results, all the chains have a CBC structure. Most of the icosahedra have a B11C structure with the C atom placed in a polar site, and a few percent have a B (12) structure or a B10C2 structure with the two C atoms placed in two antipodal polar sites.

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

    PubMed

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

    2016-04-21

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

  3. Theory of rotational transition in atom-diatom chemical reaction

    NASA Astrophysics Data System (ADS)

    Nakamura, Masato; Nakamura, Hiroki

    1989-05-01

    Rotational transition in atom-diatom chemical reaction is theoretically studied. A new approximate theory (which we call IOS-DW approximation) is proposed on the basis of the physical idea that rotational transition in reaction is induced by the following two different mechanisms: rotationally inelastic half collision in both initial and final arrangement channels, and coordinate transformation in the reaction zone. This theory gives a fairy compact expression for the state-to-state transition probability. Introducing the additional physically reasonable assumption that reaction (particle rearrangement) takes place in a spatially localized region, we have reduced this expression into a simpler analytical form which can explicitly give overall rotational state distribution in reaction. Numerical application was made to the H+H2 reaction and demonstrated its effectiveness for the simplicity. A further simplified most naive approximation, i.e., independent events approximation was also proposed and demonstrated to work well in the test calculation of H+H2. The overall rotational state distribution is expressed simply by a product sum of the transition probabilities for the three consecutive processes in reaction: inelastic transition in the initial half collision, transition due to particle rearrangement, and inelastic transition in the final half collision.

  4. 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.

  5. Nuclear Quadrupole Coupling Constants of Two Chemically Distinct Nitrogen Atoms in 4-Aminobenzonitrile

    PubMed Central

    2014-01-01

    The rotational spectrum of 4-aminobenzonitrile in the gas phase between 2 and 8.5 GHz is reported. Due to the two chemically distinct nitrogen atoms, the observed transitions showed a rich hyperfine structure. From the determination of the nuclear quadrupole coupling constants, information about the electronic environment of these atoms could be inferred. The results are compared to data for related molecules, especially with respect to the absence of dual fluorescence in 4-aminobenzonitrile. In addition, the two-photon ionization spectrum of this molecule was recorded using a time-of-flight mass spectrometer integrated into the setup. This new experimental apparatus is presented here for the first time. PMID:24911139

  6. Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns

    PubMed Central

    Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M.; Mikael, Solomon; Suh, Hyo Seon; Liu, Chi-Chun; Geng, Dalong; Wang, Xudong; Arnold, Michael S.; Ma, Zhenqiang; Nealey, Paul F.

    2016-01-01

    Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyrene-block-poly(methyl methacrylate). Faster assembly kinetics are observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. The rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces. PMID:27528258

  7. Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns.

    PubMed

    Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M; Mikael, Solomon; Suh, Hyo Seon; Liu, Chi-Chun; Geng, Dalong; Wang, Xudong; Arnold, Michael S; Ma, Zhenqiang; Nealey, Paul F

    2016-01-01

    Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyrene-block-poly(methyl methacrylate). Faster assembly kinetics are observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. The rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces.

  8. Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns

    NASA Astrophysics Data System (ADS)

    Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M.; Mikael, Solomon; Suh, Hyo Seon; Liu, Chi-Chun; Geng, Dalong; Wang, Xudong; Arnold, Michael S.; Ma, Zhenqiang; Nealey, Paul F.

    2016-08-01

    Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyrene-block-poly(methyl methacrylate). Faster assembly kinetics are observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. The rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces.

  9. Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns.

    PubMed

    Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M; Mikael, Solomon; Suh, Hyo Seon; Liu, Chi-Chun; Geng, Dalong; Wang, Xudong; Arnold, Michael S; Ma, Zhenqiang; Nealey, Paul F

    2016-01-01

    Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyrene-block-poly(methyl methacrylate). Faster assembly kinetics are observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. The rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces. PMID:27528258

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Ansari, Reza; Ajori, Shahram; Malakpour, Sina

    2016-04-01

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

  12. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

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

    2014-01-01

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

  13. 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

    2014-12-18

    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.

  14. Topological Properties of Atomic Lead Film with Honeycomb Structure.

    PubMed

    Lu, Y H; Zhou, D; Wang, T; Yang, Shengyuan A; Jiang, J Z

    2016-02-25

    Large bandgap is desired for the fundamental research as well as applications of topological insulators. Based on first-principles calculations, here we predict a new family of two-dimensional (2D) topological insulators in functionalized atomic lead films Pb-X (X = H, F, Cl, Br, I and SiH3). All of them have large bandgaps with the largest one above 1 eV, far beyond the recorded gap values and large enough for practical applications even at room temperature. Besides chemical functionalization, external strain can also effectively tune the bandgap while keeping the topological phase. Thus, the topological properties of these materials are quite robust, and as a result there exist 1D topological edge channels against backscattering. We further show that the 2D Pb structure can be encapsulated by SiO2 with very small lattice mismatch and still maintains its topological character. All these features make the 2D atomic Pb films a promising platform for fabricating novel topological electronic devices.

  15. Topological Properties of Atomic Lead Film with Honeycomb Structure

    PubMed Central

    Lu, Y. H.; Zhou, D.; Wang, T.; Yang, Shengyuan A.; Jiang, J. Z.

    2016-01-01

    Large bandgap is desired for the fundamental research as well as applications of topological insulators. Based on first-principles calculations, here we predict a new family of two-dimensional (2D) topological insulators in functionalized atomic lead films Pb-X (X = H, F, Cl, Br, I and SiH3). All of them have large bandgaps with the largest one above 1 eV, far beyond the recorded gap values and large enough for practical applications even at room temperature. Besides chemical functionalization, external strain can also effectively tune the bandgap while keeping the topological phase. Thus, the topological properties of these materials are quite robust, and as a result there exist 1D topological edge channels against backscattering. We further show that the 2D Pb structure can be encapsulated by SiO2 with very small lattice mismatch and still maintains its topological character. All these features make the 2D atomic Pb films a promising platform for fabricating novel topological electronic devices. PMID:26912024

  16. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

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

  17. Theory of quasicrystal surfaces: Probing the chemical reactivity by atomic and molecular adsorption

    NASA Astrophysics Data System (ADS)

    Krajčí, M.; Hafner, J.

    The adsorption of oxygen and carbon atoms and of carbon monoxide molecules on a fivefold surface of icosahedral Al-Pd-Mn quasicrystals has been investigated using ab initio density-functional calculations. The quasicrystalline surface has been modeled by periodically repeated slabs cut from rational approximants to the quasicrystalline structure. Atomic and molecular adsorption have been studied for a large number of possible adsorption sites by performing three-dimensional static relaxations of the adsorbate/substrate complex. Four different scenarios for the dissociative adsorption of the CO molecule have been investigated via nudged-elastic band calculations of the transition states. Al and Mn-metal atoms present at the surface bind C and O atoms rather strongly, while Pd atoms are unstable adsorption sites: during relaxation, the adsorbate drifts to the nearest strong-binding site. The chemical reactivity with respect to a CO molecule varies very strongly across the surface. The adsorption close to Mn sites is promoted by rather strong covalent effects, but CO is only physisorbed at Al sites via weak polarization forces. On the basis of the observed local variations of the adsorption strength, we develop scenarios for dissociation and determine the potential energy barriers for this processes. We find that CO adsorbed close to a transition-metal atom can dissociate via an activated process, but the dissociation rate is expected to be rather low because of a high dissociation barrier and a "late" transition state. CO adsorbed close to Al atoms will desorb before dissociation. Surface vacancies present as a consequence of the irregular coordination of the Mackay cluster in the quasiperiodic structure will act as strongly attractive traps for diffusing molecules. Mn surface atoms are located in the center of truncated Mackay clusters. In scanning tunneling electron microscopy (STM) these truncated clusters are imaged as "white flowers". Surface vacancies are

  18. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    USGS Publications Warehouse

    Dowty, Eric; Clark, J.R.

    1972-01-01

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

  19. Interlayer Potassium And Its Neighboring Atoms in Micas: Crystal-Chemical Modeling And Xanes Spectroscopy

    SciTech Connect

    Brigatti, M.F.; Malferrari, D.; Poppi, M.; Mottana, A.; Cibin, G.; Marcelli, A.; Cinque, G.

    2009-05-12

    A detailed description of the interlayer site in trioctahedral true micas is presented based on a statistical appraisal of crystal-chemical, structural, and spectroscopic data determined on two sets of trioctahedral micas extensively studied by both X-ray diffraction refinement on single crystals (SC-XRD) and X-ray absorption fine spectroscopy (XAFS) at the potassium K-edge. Spectroscopy was carried out on both random powders and oriented cleavage flakes, the latter setting taking advantage of the polarized character of synchrotron radiation. Such an approach (AXANES) is shown to be complementary to crystal-chemical investigation based on SC-XRD refinement. However, the results are not definitive as they focus on few samples having extreme features only (e.g., end-members, unusual compositions, and samples with extreme and well-identified substitution mechanisms). The experimental absorption K-edge (XANES) for potassium was decomposed by calculation and extrapolated into a full in-plane absorption component ({sigma}{parallel}) and a full out-of-plane absorption component ({sigma}{perpendicular}). These two patterns reflect different structural features: {sigma}{parallel}represents the arrangement of the atoms located in the mica interlayer space and facing tetrahedral sheets; {sigma}{perpendicular} is associated with multiple-scattering interactions entering deep into the mica structure, thus also reflecting interactions with the heavy atoms (essentially Fe) located in the octahedral sheet. The out-of-plane patterns also provide insights into the electronic properties of the octahedral cations, such as their oxidation states (e.g., Fe{sup 2+} and Fe{sup 3+}) and their ordering (e.g., trans- vs. cis-setting). It is also possible to distinguish between F- and OH-rich micas due to peculiar absorption features originating from the F vs. OH occupancy of the O4 octahedral site. Thus, combining crystal-chemical, structural, and spectroscopic information is shown to be a

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

    SciTech Connect

    Mantovan, R. Vangelista, S.; Wiemer, C.; Lamperti, A.; Tallarida, G.; Chikoidze, E.; Dumont, Y.; Fanciulli, M.

    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.

  1. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  2. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    PubMed Central

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

    2016-01-01

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

  3. Atomic Structure of Au 329 (SR) 84 Faradaurate Plasmonic Nanomolecules

    SciTech Connect

    Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; Cullen, David A.; Dass, Amala

    2015-05-21

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

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

    DOE PAGES

    Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; Cullen, David; Dass, Amala

    2015-04-03

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

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

    SciTech Connect

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

    2015-04-24

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

  6. Presentation of Atomic Structure in Turkish General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Costu, Bayram

    2009-01-01

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

  7. Mathematical modeling of chemical composition modification and etching of polymers under the atomic oxygen influence

    NASA Astrophysics Data System (ADS)

    Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina

    2016-07-01

    Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.

  8. Extracting chemical information from plane wave calculations by a 3D 'fuzzy atoms' analysis

    NASA Astrophysics Data System (ADS)

    Bakó, I.; Stirling, A.; Seitsonen, A. P.; Mayer, I.

    2013-03-01

    Bond order and valence indices have been calculated by the method of the three-dimensional 'fuzzy atoms' analysis, using the numerical molecular orbitals obtained from plane wave DFT calculations, i.e., without introducing any external atom-centered functions. Weight functions of both Hirshfeld and Becke types have been applied. The results are rather close to the similar 'fuzzy atoms' ones obtained by using atom-centered basis sets and agree well with the chemical expectations, stressing the power of the genuine chemical concepts.

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

    PubMed

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

    2014-05-14

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

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

    SciTech Connect

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

    2014-05-05

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

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

    SciTech Connect

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

    2014-05-05

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

  12. 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…

  13. Atomic structure of highly-charged ions. Final report

    SciTech Connect

    Livingston, A. Eugene

    2002-05-23

    Atomic properties of multiply charged ions have been investigated using excitation of energetic heavy ion beams. Spectroscopy of excited atomic transitions has been applied from the visible to the extreme ultraviolet wavelength regions to provide accurate atomic structure and transition rate data in selected highly ionized atoms. High-resolution position-sensitive photon detection has been introduced for measurements in the ultraviolet region. The detailed structures of Rydberg states in highly charged beryllium-like ions have been measured as a test of long-range electron-ion interactions. The measurements are supported by multiconfiguration Dirac-Fock calculations and by many-body perturbation theory. The high-angular-momentum Rydberg transitions may be used to establish reference wavelengths and improve the accuracy of ionization energies in highly charged systems. Precision wavelength measurements in highly charged few-electron ions have been performed to test the most accurate relativistic atomic structure calculations for prominent low-lying excited states. Lifetime measurements for allowed and forbidden transitions in highly charged few-electron ions have been made to test theoretical transition matrix elements for simple atomic systems. Precision lifetime measurements in laser-excited alkali atoms have been initiated to establish the accuracy of relativistic atomic many-body theory in many-electron systems.

  14. 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)

  15. Atomic-level analysis of membrane-protein structure.

    PubMed

    Hendrickson, Wayne A

    2016-06-01

    Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly underrepresented in structural databases. Recently, focused consortium efforts and advances in methodology for protein production, crystallographic analysis and cryo-EM analysis have accelerated the pace of atomic-level structure determination of membrane proteins.

  16. Chemical assembly of atomically thin transistors and circuits in a large scale

    NASA Astrophysics Data System (ADS)

    Zhao, Mervin; Ye, Yu; Han, Yimo; Xia, Yang; Zhu, Hanyu; Wang, Yuan; Muller, David; Zhang, Xiang

    Next-generation electronics calls for new materials beyond silicon for increased functionality, performance, and scaling in integrated circuits. 2D gapless graphene and semiconducting TMDCs have emerged as promising electronic materials due to their atomic thickness, chemical stability and scalability. However, difficulties in the assembly of 2D electronic structures arise in the precise spatial control over the conducting and semiconducting crystals, typically relying on physically transferring them. Ultimately, this renders them unsuitable for an industrial scale and impedes the maturity of integrating atomic elements in modern electronics. Here, we report the large-scale spatially controlled synthesis of the single-layer MoS2 laterally in electrical contact with graphene using a seeded growth method. TEM studies reveal that the single-layer MoS2 nucleates at the edge of the graphene, creating a lateral van der Waals heterostructure. The graphene allows for electrical injection into MoS2, creating 2D atomic transistors with high transconductance, on-off ratios, and mobility. In addition, we assemble 2D logic circuits, such as a heterostructure NMOS inverter with a high voltage gain, up to 70.

  17. Chemical oscillators in structured media.

    PubMed

    Epstein, Irving R; Vanag, Vladimir K; Balazs, Anna C; Kuksenok, Olga; Dayal, Pratyush; Bhattacharya, Amitabh

    2012-12-18

    Evolution is a characteristic feature of living systems, and many fundamental processes in life, including the cell cycle, take place in a periodic fashion. From a chemistry perspective, these repeating phenomena suggest the question of whether reactions in which concentrations oscillate could provide a basis and/or useful models for the behavior of organisms, and perhaps even their ability to evolve. In this Account, we examine several aspects of the behavior of the prototype oscillating chemical reaction, the Belousov-Zhabotinsky (BZ) system, carried out in microemulsions, arrays of micrometer-sized aqueous droplets suspended in oil, or hydrogels. Each of these environments contains elements of the compartmentalization that likely played a role in the development of the first living cells, and within them we observe behaviors not found in the BZ reaction in simple aqueous solution. Several of these phenomena resemble traits displayed by living organisms. For example, the nanodroplets in a BZ microemulsion "communicate" with each other through a phenomenon analogous to quorum sensing in bacteria to produce a remarkable variety of patterns and waves on length scales 10(5) times the size of a single droplet. A photosensitive version can "remember" an imposed image. Larger, micrometer-sized droplets exhibit similarly rich behavior and allow for the observation and control of individual droplets. These droplets offer promise for building arrays capable of computation by varying the strength and sign of the coupling between drops. Gels that incorporate a BZ catalyst and are immersed in a solution containing the BZ reactants change their shape and volume in oscillations that follow the variation in the redox state of the catalyst. Using this phenomenon, we can construct phototactic gel "worms" or segments of gel that attract one another. Whether such systems will provide more realistic caricatures of life, and whether they can serve as useful materials will largely

  18. Internal and external atomic steps in graphite exhibit dramatically different physical and chemical properties.

    PubMed

    Lee, Hyunsoo; Lee, Han-Bo-Ram; Kwon, Sangku; Salmeron, Miquel; Park, Jeong Young

    2015-04-28

    We report on the physical and chemical properties of atomic steps on the surface of highly oriented pyrolytic graphite (HOPG) investigated using atomic force microscopy. Two types of step edges are identified: internal (formed during crystal growth) and external (formed by mechanical cleavage of bulk HOPG). The external steps exhibit higher friction than the internal steps due to the broken bonds of the exposed edge C atoms, while carbon atoms in the internal steps are not exposed. The reactivity of the atomic steps is manifested in a variety of ways, including the preferential attachment of Pt nanoparticles deposited on HOPG when using atomic layer deposition and KOH clusters formed during drop casting from aqueous solutions. These phenomena imply that only external atomic steps can be used for selective electrodeposition for nanoscale electronic devices.

  19. Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

    PubMed

    Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

    2016-05-01

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

  20. Electronic structure of atomically precise graphene nanoribbons.

    PubMed

    Ruffieux, Pascal; Cai, Jinming; Plumb, Nicholas C; Patthey, Luc; Prezzi, Deborah; Ferretti, Andrea; Molinari, Elisa; Feng, Xinliang; Müllen, Klaus; Pignedoli, Carlo A; Fasel, Roman

    2012-08-28

    Some of the most intriguing properties of graphene are predicted for specifically designed nanostructures such as nanoribbons. Functionalities far beyond those known from extended graphene systems include electronic band gap variations related to quantum confinement and edge effects, as well as localized spin-polarized edge states for specific edge geometries. The inability to produce graphene nanostructures with the needed precision, however, has so far hampered the verification of the predicted electronic properties. Here, we report on the electronic band gap and dispersion of the occupied electronic bands of atomically precise graphene nanoribbons fabricated via on-surface synthesis. Angle-resolved photoelectron spectroscopy and scanning tunneling spectroscopy data from armchair graphene nanoribbons of width N = 7 supported on Au(111) reveal a band gap of 2.3 eV, an effective mass of 0.21 m(0) at the top of the valence band, and an energy-dependent charge carrier velocity reaching 8.2 × 10(5) m/s in the linear part of the valence band. These results are in quantitative agreement with theoretical predictions that include image charge corrections accounting for screening by the metal substrate and confirm the importance of electron-electron interactions in graphene nanoribbons.

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

    ERIC Educational Resources Information Center

    Rittenhouse, Robert C.

    2015-01-01

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

  2. Chemical structure and dynamics. Annual report 1995

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a 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; (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; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  3. Chemical structure and dynamics: Annual report 1996

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a 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; (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; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  4. 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.

  5. Physical Construction of the Chemical Atom: Is It Convenient to Go All the Way Back?

    ERIC Educational Resources Information Center

    Izquierdo-Aymerich, Merce; Aduriz-Bravo, Agustin

    2009-01-01

    In this paper we present an analysis of chemistry texts (mainly textbooks) published during the first half of the 20th century. We show the evolution of the explanations therein in terms of atoms and of atomic structure, when scientists were interpreting phenomena as evidence of the discontinuous, corpuscular structure of matter. In this process…

  6. 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.

  7. 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

  8. Structure and stability of a silicon cluster on sequential doping with carbon atoms

    NASA Astrophysics Data System (ADS)

    AzeezullaNazrulla, Mohammed; Joshi, Krati; Israel, S.; Krishnamurty, Sailaja

    2016-02-01

    SiC is a highly stable material in bulk. On the other hand, alloys of silicon and carbon at nanoscale length are interesting from both technological as well fundamental view point and are being currently synthesized by various experimental groups (Truong et. al., 2015 [26]). In the present work, we identify a well-known silicon cluster viz., Si10 and dope it sequentially with carbon atoms. The evolution of electronic structure (spin state and the structural properties) on doping, the charge redistribution and structural properties are analyzed. It is interesting to note that the ground state SiC clusters prefer to be in the lowest spin state. Further, it is seen that carbon atoms are the electron rich centres while silicon atoms are electron deficient in every SiC alloy cluster. The carbon-carbon bond lengths in alloy clusters are equivalent to those seen in fullerene molecules. Interestingly, the carbon atoms tend to aggregate together with silicon atoms surrounding them by donating the charge. As a consequence, very few Si-Si bonds are noted with increasing concentrations of C atoms in a SiC alloy. Physical and chemical stability of doped clusters is studied by carrying out finite temperature behaviour and adsorbing O2 molecule on Si9C and Si8C2 clusters, respectively.

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

    SciTech Connect

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

    2015-10-10

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

  10. Atomic structure and phason modes of the Sc-Zn icosahedral quasicrystal.

    PubMed

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-07-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = -0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye-Waller factor, which explains the vanishing of 'high-Q perp' reflections. PMID:27437112

  11. Atomic structure and phason modes of the Sc-Zn icosahedral quasicrystal.

    PubMed

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-07-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = -0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye-Waller factor, which explains the vanishing of 'high-Q perp' reflections.

  12. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    PubMed Central

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-01-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112

  13. The PubChem chemical structure sketcher.

    PubMed

    Ihlenfeldt, Wolf D; Bolton, Evan E; Bryant, Stephen H

    2009-12-17

    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.

  14. On a new method for chemical production of iodine atoms in a chemical oxygen-iodine laser

    SciTech Connect

    Andreeva, Tamara L; Kuznetsova, S V; Maslov, A I; Sorokin, Vadim N

    2004-11-30

    A new method is proposed for generating iodine atoms in a chemical oxygen-iodine laser. The method is based on a branched chain reaction of dissociation of the alkyl iodide CH{sub 3}I in a medium of singlet oxygen and chlorine. (active media)

  15. 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.

  16. 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.

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

    SciTech Connect

    Osmera, Pavel

    2010-06-17

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

  18. 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

  19. 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.

  20. Atomic-Scale Observations of Catalyst Structures under Reaction Conditions and during Catalysis.

    PubMed

    Tao, Franklin Feng; Crozier, Peter A

    2016-03-23

    Heterogeneous catalysis is a chemical process performed at a solid-gas or solid-liquid interface. Direct participation of catalyst atoms in this chemical process determines the significance of the surface structure of a catalyst in a fundamental understanding of such a chemical process at a molecular level. High-pressure scanning tunneling microscopy (HP-STM) and environmental transmission electron microscopy (ETEM) have been used to observe catalyst structure in the last few decades. In this review, instrumentation for the two in situ/operando techniques and scientific findings on catalyst structures under reaction conditions and during catalysis are discussed with the following objectives: (1) to present the fundamental aspects of in situ/operando studies of catalysts; (2) to interpret the observed restructurings of catalyst and evolution of catalyst structures; (3) to explore how HP-STM and ETEM can be synergistically used to reveal structural details under reaction conditions and during catalysis; and (4) to discuss the future challenges and prospects of atomic-scale observation of catalysts in understanding of heterogeneous catalysis. This Review focuses on the development of HP-STM and ETEM, the in situ/operando characterizations of catalyst structures with them, and the integration of the two structural analytical techniques for fundamentally understanding catalysis.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

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

    DOE PAGES

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

    2014-12-02

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » 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.« less

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

    SciTech Connect

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

    2014-12-01

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 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 FeTe{sub 1−x}Se{sub x} 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.

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

    SciTech Connect

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

    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.

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

    PubMed

    Chen, Lei; Yang, Jing; 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

  8. Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties.

    PubMed

    Lazar, Petr; Zbořil, Radek; Pumera, Martin; Otyepka, Michal

    2014-07-21

    Boron and nitrogen doped graphenes are highly promising materials for electrochemical applications, such as energy storage, generation and sensing. The doped graphenes can be prepared by a broad variety of chemical approaches. The substitution of a carbon atom should induce n-type behavior in the case of nitrogen and p-type behavior in the case of boron-doped graphene; however, the real situation is more complex. The electrochemical experiments show that boron-doped graphene prepared by hydroboration reaction exhibits similar properties as the nitrogen doped graphene; according to theory, the electrochemical behavior of B and N doped graphenes should be opposite. Here we analyze the electronic structure of N/B-doped graphene (at ∼5% coverage) by theoretical calculations. We consider graphene doped by both substitution and addition reactions. The density of states (DOS) plots show that graphene doped by substitution of the carbon atom by N/B behaves as expected, i.e., as an n/p-doped material. N-doped graphene also has a lower value of the workfunction (3.10 eV) with respect to that of the pristine graphene (4.31 eV), whereas the workfunction of B-doped graphene is increased to the value of 5.57 eV. On the other hand, the workfunctions of graphene doped by addition of -NH2 (4.77 eV) and -BH2 (4.54 eV) groups are both slightly increased and therefore the chemical nature of the dopant is less distinguishable. This shows that mode of doping depends significantly on the synthesis method used, as it leads to different types of behaviour, and, in turn, different electronic and electrochemical properties of doped graphene, as observed in electrocatalytic experiments. This study has a tremendous impact on the design of doped graphene systems from the point of view of synthetic chemistry.

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

    SciTech Connect

    1981-03-01

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

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

    PubMed

    Sobel, Nicolas; Hess, Christian

    2015-12-01

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

  11. Formation and atomic structure of ordered Sr-induced nanostrips on Ge(100)

    NASA Astrophysics Data System (ADS)

    Lukanov, Boris R.; Garrity, Kevin F.; Ismail-Beigi, Sohrab; Altman, Eric I.

    2014-04-01

    The deposition of alkaline earths onto Ge(100) surfaces leads to well-ordered arrays of narrow trenches and elongated plateaus that extend for thousands of angstroms. Using scanning tunneling microscopy (STM) in conjunction with density functional theory (DFT), the atomic scale details of these nanostructures are revealed and the driving force responsible for their formation is evaluated. The STM data reveal a dramatic contrast reversal when the polarity of the imaging bias is switched. An energetically favorable structure for the plateaus was found using DFT that can reproduce all of the observed features. This structure is based upon a double dimer vacancy model in which Sr atoms displace two Ge dimers from the surface. Interestingly, the ordered plateau-trench structure is unique to Ge(100) despite the structural and chemical similarities to the Si(100) surface.

  12. Chemical Structure and Dynamics annual report 1997

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a 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; (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; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

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

    NASA Astrophysics Data System (ADS)

    Alloyeau, D.; Oikawa, T.; Nelayah, J.; Wang, G.; Ricolleau, C.

    2012-09-01

    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. Atomic and electronic structure of gold clusters: understanding flakes, cages and superatoms from simple concepts.

    PubMed

    Häkkinen, Hannu

    2008-09-01

    Atomic structure and electronic structure are intimately interrelated properties of nanoclusters and nanoparticles, defining their stability, electronic, optical and chemical properties, in other words, their usability as potential components for nanoscale devices. This tutorial review attempts to describe the development in understanding the structures of bare and ligand-protected gold clusters over the past decade, based on selected density-functional-theory calculations. This review should be of interest both to newcomers in the field and to an interdisciplinary community of researchers working in synthesis, characterization and utilization of ligand-protected gold clusters.

  15. The shells of atomic structure in metallic glasses

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  16. Likelihood of atom–atom contacts in crystal structures of halogenated organic compounds

    PubMed Central

    Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

    2015-01-01

    The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C—H⋯Cl and O—H⋯O are the preferred interactions in compounds containing both O and Cl. PMID:25995842

  17. Atomic structure of [110] tilt grain boundaries in FCC materials

    SciTech Connect

    Merkle, K.L.; Thompson, L.J.

    1997-04-01

    High-resolution electron microscopy (HREM) has been used to study the atomic-scale structure and localized relaxations at grain boundaries (GBs) in Au, Al, and MgO. The [110] tilt GBs play an important role in polycrystalline fcc metals since among all of the possible GB geometries this series of misorientations as a whole contains the lowest energies, including among others the two lowest energy GBs, the (111) and (113) twins. Therefore, studies of the atomic-scale structure of [110] tilt GBs in fcc metals and systematic investigations of their dependence on misorientation and GB plane is of considerable importance to materials science. [110] tilt GBs in ceramic oxides of the fcc structure are also of considerable interest, since in this misorientation range polar GBs exist, i.e. GBs in which crystallographic planes that are made up of complete layers of cations or anions can join to form a GB.

  18. Volcano structure in atomic resolution core-loss images.

    PubMed

    D'Alfonso, A J; Findlay, S D; Oxley, M P; Allen, L J

    2008-06-01

    A feature commonly present in simulations of atomic resolution electron energy loss spectroscopy images in the scanning transmission electron microscope is the volcano or donut structure. In the past this has been understood in terms of a geometrical perspective using a dipole approximation. It is shown that the dipole approximation for core-loss spectroscopy begins to break down as the probe forming aperture semi-angle increases, necessitating the inclusion of higher order terms for a quantitative understanding of volcano formation. Using such simulations we further investigate the mechanisms behind the formation of such structures in the single atom case and extend this to the case of crystals. The cubic SrTiO3 crystal is used as a test case to show the effects of nonlocality, probe channelling and absorption in producing the volcano structure in crystal images.

  19. Atomic Structure of an Amorphous/Crystal Interface

    SciTech Connect

    Shibata, Naoya; Painter, Gayle S; Becher, Paul F; Pennycook, Stephen J

    2006-01-01

    In this study, the authors report atomic-resolution images that illustrate the transition from a crystalline Si{sub 3}N{sub 4} grain across the interface into an amorphous Lu-Si-Mg-N-O glassy phase. The interface is not atomically abrupt, but is comprised of sub-nanometer-scale ordered regions that resemble a LuN-like structure. These ordered clusters bind to the prismatic surface of the Si{sub 3}N{sub 4} grains at specific low energy positions for Lu adsorption as predicted by first-principles calculations. The ordered regions are filamentary in nature, extending for at least two atomic layers into the amorphous pockets at multigrain junctions before disappearing.

  20. Structural properties of lithium atom under weakly coupled plasma environment

    NASA Astrophysics Data System (ADS)

    Dutta, S.; Saha, J. K.; Chandra, R.; Mukherjee, T. K.

    2016-04-01

    The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. The excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.

  1. 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.

  2. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a 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; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  3. Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

    PubMed Central

    van den Bedem, Henry; Fraser, James S.

    2015-01-01

    Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

  4. Stable atomic structure of NiTi austenite

    SciTech Connect

    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.

  5. Atomic Structure of Twin Boundaries in CdTe

    SciTech Connect

    Yan, Y.; Jones, K. M.; Al-Jassim, M. M.

    2003-05-01

    Using the combination of high-resolution transmission electron microscopy, first-principles density-functional total energy calculations, and image simulations, we determined the atomic structure of lamellar twin and double-positioning twin boundaries in CdTe. We find that the structure of lamellar twin boundaries has no dangling bonds or wrong bonds; thus, it results in negligible effects on the electronic properties. The structure of double-positioning twin boundaries, however, contain both Cd and Te dangling bonds, and therefore produce energy states in the bandgap that are detrimental to the electronic properties of CdTe.

  6. Method for quantitative determination and separation of trace amounts of chemical elements in the presence of large quantities of other elements having the same atomic mass

    DOEpatents

    Miller, C.M.; Nogar, N.S.

    1982-09-02

    Photoionization via autoionizing atomic levels combined with conventional mass spectroscopy provides a technique for quantitative analysis of trace quantities of chemical elements in the presence of much larger amounts of other elements with substantially the same atomic mass. Ytterbium samples smaller than 10 ng have been detected using an ArF* excimer laser which provides the atomic ions for a time-of-flight mass spectrometer. Elemental selectivity of greater than 5:1 with respect to lutetium impurity has been obtained. Autoionization via a single photon process permits greater photon utilization efficiency because of its greater absorption cross section than bound-free transitions, while maintaining sufficient spectroscopic structure to allow significant photoionization selectivity between different atomic species. Separation of atomic species from others of substantially the same atomic mass is also described.

  7. Atom-scale depth localization of biologically important chemical elements in molecular layers.

    PubMed

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-08-23

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

  8. Atom-scale depth localization of biologically important chemical elements in molecular layers

    PubMed Central

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-01-01

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers’ global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

  9. Atom-scale depth localization of biologically important chemical elements in molecular layers.

    PubMed

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-08-23

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces.

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

    PubMed

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

    2016-02-18

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

  11. Interfacial Atomic Structure of Twisted Few-Layer Graphene

    PubMed Central

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

    2016-01-01

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene. PMID:26888259

  12. Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures.

    PubMed

    Bar Sadan, Maya; Houben, Lothar; Enyashin, Andrey N; Seifert, Gotthard; Tenne, Reshef

    2008-10-14

    The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS(2) nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS(2) nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism.

  13. Zero-Temperature Structures of Atomic Metallic Hydrogen

    NASA Astrophysics Data System (ADS)

    McMahon, Jeffrey; Ceperley, David

    2011-03-01

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

  14. Metal oxide nanoparticle growth on graphene via chemical activation with atomic oxygen.

    PubMed

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

    2013-12-01

    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 that 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.

  15. Revealing the angular symmetry of chemical bonds by atomic force microscopy.

    PubMed

    Welker, Joachim; Giessibl, Franz J

    2012-04-27

    We have measured the angular dependence of chemical bonding forces between a carbon monoxide molecule that is adsorbed to a copper surface and the terminal atom of the metallic tip of a combined scanning tunneling microscope and atomic force microscope. We provide tomographic maps of force and current as a function of distance that revealed the emergence of strongly directional chemical bonds as tip and sample approach. The force maps show pronounced single, dual, or triple minima depending on the orientation of the tip atom, whereas tunneling current maps showed a single minimum for all three tip conditions. We introduce an angular dependent model for the bonding energy that maps the observed experimental data for all observed orientations and distances.

  16. Atomic force microscopy of DNA on mica and chemically modified mica.

    PubMed

    Thundat, T; Allison, D P; Warmack, R J; Brown, G M; Jacobson, K B; Schrick, J J; Ferrell, T L

    1992-12-01

    Atomic force microscopy (AFM) was used to image circular DNA adsorbed on freshly cleaved mica and mica chemically modified with Mg(II), Co(II), La(III), and Zr(IV). Images obtained on unmodified mica show coiling of DNA due to forces involved during the drying process. The coiling or super twisting appeared to be right handed and the extent of super twisting could be controlled by the drying conditions. Images of DNA observed on chemically modified surfaces show isolated open circular DNA that is free from super twisting, presumably due to strong binding of DNA on chemically modified surfaces.

  17. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

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

    2015-11-15

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

  18. 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.

  19. Structure and electronic behavior of 26-atom Cu-Ag and Cu-Au nanoalloys

    NASA Astrophysics Data System (ADS)

    Guzmán-Ramírez, Gregorio; Robles, Juvencio; Aguilera-Granja, Faustino

    2016-09-01

    We hereby present a density functional theory (DFT) study of the structural, energetic, and electronic properties of the binary clusters Cu n X26- n (with X = Ag and Au). Our electronic calculations were performed with the DFT package GAUSSIAN 09, and we chose the BPW91 exchange correlation functional in combination with an effective core potential LANL2DZ basis set as our level of theory. We find that in the case of these clusters and in a completely different way - as compared to the bulk chemical order observed in both alloys CuAg (segregation) and CuAu (ordering) -, for small n both Ag and Au clusters exhibit a similar chemical order, finding the Cu atoms in the center of the cluster with the tendency to form core shell structures. On the other hand, for large n values the Ag and Au atoms tend to occupy surface positions forming separated surface islands that keep the two metal atoms separated as long as the concentration allows it. Concerning the structural properties, a clear increase in the interatomic distance of the Ag-Ag and Au-Au surface pairs is observed, particularly in the equiatomic region. In conclusion, both nanoalloys CuAg and CuAu behave quite similarly in contrast to their respective bulk cases.

  20. Evolution of crystal structure during the initial stages of ZnO atomic layer deposition

    DOE PAGES

    Boichot, R.; Tian, L.; Richard, M. -I.; Crisci, A.; Chaker, A.; Cantelli, V.; Coindeau, S.; Lay, S.; Ouled, T.; Guichet, C.; et al

    2016-01-05

    In this study, a complementary suite of in situ synchrotron X-ray techniques is used to investigate both structural and chemical evolution during ZnO growth by atomic layer deposition. Focusing on the first 10 cycles of growth, we observe that the structure formed during the coalescence stage largely determines the overall microstructure of the film. Furthermore, by comparing ZnO growth on silicon with a native oxide with that on Al2O3(001), we find that even with lattice-mismatched substrates and low deposition temperatures, the crystalline texture of the films depend strongly on the nature of the interfacial bonds.

  1. The crystal structure of samarosporin I at atomic resolution.

    PubMed

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  2. Structural defects and chemical interaction of implanted ions with substrate structure in amorphous SiO2

    NASA Astrophysics Data System (ADS)

    Hosono, Hideo; Matsunami, Noriaki

    1993-11-01

    Structural defects in SiO2 glasses implanted with Li+, N+, O+, F+, Si+, and P+ ions were examined by vacuum-ultraviolet-absorption and electron-paramagnetic-resonance spectroscopies as well as thermal-gas-release analysis. The chemical interaction of implanted ions with substrate structure was considered on the basis of the obtained results. It is found that the type of predominant defects is controlled by the electronegative nature of implants. Silicon-silicon homobonds, which are oxygen-vacancy-type defects, are produced by electropositive implants (i.e., Li, P, and Si) at concentrations comparable to those of the implants. On the other hand, in the case of electronegative implants (F and O) O2 molecules and peroxy radicals (POR), both of which may be regarded as oxygen-interstitial-type defects, are the major defects and the total concentrations of these two defects are comparable to implant concentrations. These results indicate that chemical interaction of implanted ions with SiO2 is primarily controlled by the electronegative nature of implants. Electropositive implants (M) react chemically with oxygen atoms in the substrate structure to form M-O bonds, leaving Si-Si bonds. Electronegative implants (A) react chemically with silicon atoms to form Si-A bonds and oxygen atoms recoiled with implants combine with each other to form O2 molecules or react with the silica-network structure to form POR's. Concentrations of these predominant defects relative to implants can be used quantitatively to describe the strength of chemical interactions. When the chemical interaction is strong, both concentrations are comparable. On the other hand, when the chemical interaction is weak, concentrations of these defects are much smaller than those of implants because the major fraction of implants occur in a neutral state without forming chemical bonds with constituents of the substrate. Nitrogen is an example of this category and the major fraction of implanted nitrogen atoms

  3. Direct structure determination by atomic-resolution incoherent STEM imaging

    SciTech Connect

    Nellist, P.D.; Xin, Y.; Pennycook, S.J.

    1997-11-01

    Use of a large, annular dark-field (ADF) detector in a scanning transmission electron microscope is shown to give images that can allow direct structure determination, being a convolution between the illuminating probe intensity and an object function localized at the atomic column positions. The ADF image is also shown to resolve crystal spacings more than twice smaller than the phase contrast point resolution limit of the microscope used, with sub-angstrom structural information being retrieved. ADF image of several semiconductor materials are studied.

  4. Chemical quantification of atomic-scale EDS maps under thin specimen conditions.

    PubMed

    Lu, Ping; Romero, Eric; Lee, Shinbuhm; MacManus-Driscoll, Judith L; Jia, Quanxi

    2014-12-01

    We report our effort to quantify atomic-scale chemical maps obtained by collecting energy-dispersive X-ray spectra (EDS) using scanning transmission electron microscopy (STEM) (STEM-EDS). With thin specimen conditions and localized EDS scattering potential, the X-ray counts from atomic columns can be properly counted by fitting Gaussian peaks at the atomic columns, and can then be used for site-by-site chemical quantification. The effects of specimen thickness and X-ray energy on the Gaussian peak width are investigated using SrTiO3 (STO) as a model specimen. The relationship between the peak width and spatial resolution of an EDS map is also studied. Furthermore, the method developed by this work is applied to study cation occupancy in a Sm-doped STO thin film and antiphase boundaries (APBs) present within the STO film. We find that Sm atoms occupy both Sr and Ti sites but preferably the Sr sites, and Sm atoms are relatively depleted at the APBs likely owing to the effect of strain.

  5. Chemical Quantification of Atomic-Scale EDS Maps under Thin Specimen Conditions

    DOE PAGES

    Lu, Ping; Romero, Eric; Lee, Shinbuhm; MacManus-Driscoll, Judith L.; Jia, Quanxi

    2014-10-13

    We report our effort to quantify atomic-scale chemical maps obtained by collecting energy-dispersive X-ray spectra (EDS) using scanning transmission electron microscopy (STEM) (STEM-EDS). Under a thin specimen condition and when the EDS scattering potential is localized, the X-ray counts from atomic columns can be properly counted by fitting Gaussian peaks at the atomic columns, and can then be used for site-by-site chemical quantification. The effects of specimen thickness and X-ray energy on the Gaussian peak-width are investigated by using SrTiO3 (STO) as a model specimen. The relationship between the peak-width and spatial-resolution of an EDS map is also studied. Furthermore,more » the method developed by this work is applied to study a Sm-doped STO thin film and antiphase boundaries present within the STO film. We find that Sm atoms occupy both Sr and Ti sites but preferably the Sr sites, and Sm atoms are relatively depleted at the antiphase boundaries likely due to the effect of strain.« less

  6. Chemical Quantification of Atomic-Scale EDS Maps under Thin Specimen Conditions

    SciTech Connect

    Lu, Ping; Romero, Eric; Lee, Shinbuhm; MacManus-Driscoll, Judith L.; Jia, Quanxi

    2014-10-13

    We report our effort to quantify atomic-scale chemical maps obtained by collecting energy-dispersive X-ray spectra (EDS) using scanning transmission electron microscopy (STEM) (STEM-EDS). Under a thin specimen condition and when the EDS scattering potential is localized, the X-ray counts from atomic columns can be properly counted by fitting Gaussian peaks at the atomic columns, and can then be used for site-by-site chemical quantification. The effects of specimen thickness and X-ray energy on the Gaussian peak-width are investigated by using SrTiO3 (STO) as a model specimen. The relationship between the peak-width and spatial-resolution of an EDS map is also studied. Furthermore, the method developed by this work is applied to study a Sm-doped STO thin film and antiphase boundaries present within the STO film. We find that Sm atoms occupy both Sr and Ti sites but preferably the Sr sites, and Sm atoms are relatively depleted at the antiphase boundaries likely due to the effect of strain.

  7. 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 .

  8. Chemical mapping and quantification at the atomic scale by scanning transmission electron microscopy.

    PubMed

    Chu, Ming-Wen; Chen, Cheng Hsuan

    2013-06-25

    With innovative modern material-growth methods, a broad spectrum of fascinating materials with reduced dimensions-ranging from single-atom catalysts, nanoplasmonic and nanophotonic materials to two-dimensional heterostructural interfaces-is continually emerging and extending the new frontiers of materials research. A persistent central challenge in this grand scientific context has been the detailed characterization of the individual objects in these materials with the highest spatial resolution, a problem prompting the need for experimental techniques that integrate both microscopic and spectroscopic capabilities. To date, several representative microscopy-spectroscopy combinations have become available, such as scanning tunneling microscopy, tip-enhanced scanning optical microscopy, atom probe tomography, scanning transmission X-ray microscopy, and scanning transmission electron microscopy (STEM). Among these tools, STEM boasts unique chemical and electronic sensitivity at unparalleled resolution. In this Perspective, we elucidate the advances in STEM and chemical mapping applications at the atomic scale by energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy with a focus on the ultimate challenge of chemical quantification with atomic accuracy.

  9. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies

    NASA Astrophysics Data System (ADS)

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-01

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE

  10. Annual Report 2002. Chemical Structure & Dynamics

    SciTech Connect

    Colson, Steven D.; Gephart, Roy E.

    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 CS&D program supports the Department of Energy?s mission of fostering fundamental research in the natural sciences to provide a basis for new and improved energy technologies and for understanding and mitigating the environmental impacts of energy use and contaminant releases.

  11. 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

  12. Nanoscale fabrication and characterization of chemically modified silicon surfaces using conductive atomic force microscopy in liquids

    NASA Astrophysics Data System (ADS)

    Kinser, Christopher Reagan

    This dissertation examines the modification and characterization of hydrogen-terminated silicon surfaces in organic liquids. Conductive atomic force microscope (cAFM) lithography is used to fabricate structures with sub-100 nm line width on H:Si(111) in n-alkanes, 1-alkenes, and 1-alkanes. Nanopatterning is accomplished by applying a positive (n-alkanes and 1-alkenes) or a negative (1-alkanes) voltage pulse to the silicon substrate with the cAFM tip connected to ground. The chemical and kinetic behavior of the patterned features is characterized using AFM, lateral force microscopy, time-of-flight secondary ion mass spectroscopy (TOF SIMS), and chemical etching. Features patterned in hexadecane, 1-octadecene, and undecylenic acid methyl ester exhibited chemical and kinetic behavior consistent with AFM field induced oxidation. The oxide features are formed due to capillary condensation of a water meniscus at the AFM tip-sample junction. A space-charge limited growth model is proposed to explain the observed growth kinetics. Surface modifications produced in the presence of neat 1-dodecyne and 1-octadecyne exhibited a reduced lateral force compared to the background H:Si(111) substrate and were resistant to a hydrofluoric acid etch, characteristics which indicate that the patterned features are not due to field induced oxidation and which are consistent with the presence of the methyl-terminated 1-alkyne bound directly to the silicon surface through silicon-carbon bonds. In addition to the cAFM patterned surfaces, full monolayers of undecylenic acid methyl ester (SAM-1) and undec-10-enoic acid 2-bromoethyl ester (SAM-2) were grown on H:Si(111) substrates using ultraviolet light. The structure and chemistry of the monolayers were characterized using AFM, TOF SIMS, X-ray photoelectron spectroscopy (XPS), X-ray reflectivity (XRR), X-ray standing waves (XSW), and X-ray fluorescence (XRF). These combined analyses provide evidence that SAM-1 and SAM-2 form dense monolayers

  13. Structure of a Quantized Vortex in Fermi Atom Gas

    SciTech Connect

    Machida, Masahiko; Koyama, Tomio

    2006-09-07

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

  14. Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

    DOEpatents

    Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

    2015-01-13

    Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

  15. Radical and Atom Transfer Halogenation (RATH): A Facile Route for Chemical and Polymer Functionalization.

    PubMed

    Han, Yi-Jen; Lin, Chia-Yu; Liang, Mong; Liu, Ying-Ling

    2016-05-01

    This work demonstrates a new halogenation reaction through sequential radical and halogen transfer reactions, named as "radical and atom transfer halogenation" (RATH). Both benzoxazine compounds and poly(2,6-dimethyl-1,4-phenylene oxide) have been demonstrated as active species for RATH. Consequently, the halogenated compound becomes an active initiator of atom transfer radical polymerization. Combination of RATH and sequential ATRP provides an convenient and effective approach to prepare reactive and crosslinkable polymers. The RATH reaction opens a new window both to chemical synthesis and molecular design and preparation of polymeric materials.

  16. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    SciTech Connect

    Thurmer, Konrad; Feibelman, Peter J.

    2014-09-01

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

  17. 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.

  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. Atom type preferences, structural diversity, and property profiles of known drugs, leads, and nondrugs: a comparative assessment.

    PubMed

    Viswanadhan, Vellarkad N; Rajesh, Hariharan; Balaji, Vitukudi N

    2011-05-01

    A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose−Viswanadhan−Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads.

  20. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms.

    PubMed

    Lee, Louis P; Limas, Nidia Gabaldon; Cole, Daniel J; Payne, Mike C; Skylaris, Chris-Kriton; Manz, Thomas A

    2014-12-01

    The density derived electrostatic and chemical (DDEC/c3) method is implemented into the onetep program to compute net atomic charges (NACs), as well as higher-order atomic multipole moments, of molecules, dense solids, nanoclusters, liquids, and biomolecules using linear-scaling density functional theory (DFT) in a distributed memory parallel computing environment. For a >1000 atom model of the oxygenated myoglobin protein, the DDEC/c3 net charge of the adsorbed oxygen molecule is approximately -1e (in agreement with the Weiss model) using a dynamical mean field theory treatment of the iron atom, but much smaller in magnitude when using the generalized gradient approximation. For GaAs semiconducting nanorods, the system dipole moment using the DDEC/c3 NACs is about 5% higher in magnitude than the dipole computed directly from the quantum mechanical electron density distribution, and the DDEC/c3 NACs reproduce the electrostatic potential to within approximately 0.1 V on the nanorod's solvent-accessible surface. As examples of conducting materials, we study (i) a 55-atom Pt cluster with an adsorbed CO molecule and (ii) the dense solids Mo2C and Pd3V. Our results for solid Mo2C and Pd3V confirm the necessity of a constraint enforcing exponentially decaying electron density in the tails of buried atoms. PMID:26583221

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

    PubMed

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

    2015-05-28

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

  2. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

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

    2015-01-01

    Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA 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. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  3. Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography

    SciTech Connect

    Pentelute, Brad L.; Mandal, Kalyaneswar; Gates, Zachary P.; Sawaya, Michael R.; Yeates, Todd O.; Kent, Stephen B.H.

    2010-11-05

    Here we report the total synthesis of kaliotoxin by 'one pot' native chemical ligation of three synthetic peptides. A racemic mixture of D- and L-kaliotoxin synthetic protein molecules gave crystals in the centrosymmetric space groupP that diffracted to atomic-resolution (0.95 {angstrom}), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

  4. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

    PubMed

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-19

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum. PMID:27160891

  5. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

    PubMed

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-19

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.

  6. 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

  7. 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

  8. Mesoscale effects in electrochemical conversion: coupling of chemistry to atomic- and nanoscale structure in iron-based electrodes.

    PubMed

    Wiaderek, Kamila M; Borkiewicz, Olaf J; Pereira, Nathalie; Ilavsky, Jan; Amatucci, Glenn G; Chupas, Peter J; Chapman, Karena W

    2014-04-30

    The complex coupling of atomic, chemical, and electronic transformations across multiple length scales underlies the performance of electrochemical energy storage devices. Here, the coupling of chemistry with atomic- and nanoscale structure in iron conversion electrodes is resolved by combining pair distribution function (PDF) and small-angle X-ray scattering (SAXS) analysis for a series of Fe fluorides, oxyfluorides, and oxides. The data show that the anion chemistry of the initial electrode influences the abundance of atomic defects in the Fe atomic lattice. This, in turn, is linked to different atom mobilities and propensity for particle growth. Competitive nanoparticle growth in mixed anion systems contributes to a distinct nanostructure, without the interconnected metallic nanoparticles formed for single anion systems.

  9. 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

  10. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

    Emberson, R.; Hovius, N.; Hsieh, M.; Galy, A.

    2013-12-01

    Material eroded from active mountain belts can spend extended periods in depositional structures within the mountain catchments before reaching its final destination. This can be in the form of colluvial fills, debris fans, or alluvial valley fills and terraces. The existence of these landforms is testament to the catastrophic nature of the events that lead to their formation. Sourced by landslides or debris flows, the material that forms them is in many cases either unweathered or incompletely weathered (e.g. Hsieh and Chyi 2010). Due to their porosity and permeability, these deposits likely serve as locations for extensive chemical weathering within bedrock landscapes. Recent studies considering the weathering flux from active mountain belts (e.g. Calmels et al. 2011) have distinguished between shallow and deep groundwater in terms of the contribution to the solute budget from a catchment; in this study we have attempted to more tightly constrain the sources of these groundwater components in the context of the previously mentioned depositional structures. We have collected water samples from a large number of sites within the Chen-you-lan catchment (370 km2) in central west Taiwan to elucidate the location of chemical weathering as well as how the sourcing of weathering products varies depending on the meteorological conditions. Central Taiwan has good attributes for this work considering both the extremely active tectonics and tropical climate, (including extensive cyclonic activity) which stimulate both extensive physical erosion (Dadson et al. 2003) and chemical weathering (Calmels et al. 2011). The Chen-you-lan catchment in particular contains some of the largest alluvial deposits inside the Taiwan mountain belt (Hsieh and Chyi 2010). Our preliminary results suggest that weathering within intramontane deposits may be a significant source of solutes, with the hyporheic systems within mountain rivers of particular import. This input of solutes occurs over

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

    PubMed

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

    2013-01-01

    : We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics. PMID:23718316

  12. AMO Database in KAERI and Atomic Structure Studies

    NASA Astrophysics Data System (ADS)

    Rhee, Yongjoo; Park, H. M.; Kwon, D. H.

    2005-05-01

    Atomic spectroscopy studies carried out at the Laboratory for Quantum Optics in Korea Atomic Energy Research Institute are introduced together with the AMO (Atomic, Molecular, and Optical) database established based upon those studies.

  13. Atomic structure calculations on the CRAY X-MP

    SciTech Connect

    Fischer, C.F.

    1988-01-01

    Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. Some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and CRAY 2. These show that the workload can easily be distributed evenly among available processors with dynamic scheduling. 18 refs., 1 fig., 3 tabs.

  14. Quasicrystal surfaces: structure and growth of atomic overlayers

    NASA Astrophysics Data System (ADS)

    Sharma, H. R.; Shimoda, M.; Tsai, A. P.

    2007-05-01

    We review recent developments in surface studies of single-grain quasicrystals under ultra high-vacuum conditions, focusing on two different topics: surface structure and growth of atomic overlayers on surfaces. Quasicrystalline phases are currently used for investigation of the first topic are icosahedral (i) Al-Pd-Mn, i-Al-Cu-Fe, i-Al-Cu-Ru, i-Ag-In-Yb and decagonal (d) Al-Ni-Co, and d-Al-Cu-Co. We report the progress made with all of these phases. The second topic covers the study of single-element overlayer growth by vapor deposition.

  15. A collaboration of labs: The Institute for Atom-Efficient Chemical Transformations (IACT)

    ScienceCinema

    Lobo, Rodrigo; Marshall, Chris; Cheng, Lei; Stair, Peter; Wu, Tianpan; Ray, Natalie; O'Neil, Brandon; Dietrich, Paul

    2016-07-12

    The Institute for Atom-Efficient Chemical Transformations (IACT) is an Energy Frontier Research Center funded by the U.S. Department of Energy. IACT focuses on advancing the science of catalysis to improve the efficiency of producing fuels from biomass and coal. IACT is a collaborative effort that brings together a diverse team of scientists from Argonne National Laboratory, Brookhaven National Laboratory, Northwestern University, Purdue University and the University of Wisconsin. For more information, visit www.iact.anl.gov

  16. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale

    NASA Astrophysics Data System (ADS)

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-11-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo phase

  17. Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

    PubMed

    Yong, Chin W

    2016-08-22

    DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense. PMID:27455451

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

    PubMed

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

    2014-02-12

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

  19. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    PubMed

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

    2016-08-01

    Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation. PMID:27355699

  20. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    PubMed

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

    2016-08-01

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

  1. Functional cavitands: Chemical reactivity in structured environments

    PubMed Central

    Purse, Byron W.; Rebek, Julius

    2005-01-01

    Container-shaped molecules provide structured environments that impart geometric bounds on the motions and conformations of smaller molecular occupants. Moreover, they provide “solvation” that is constrained in time and space. When inwardly directed functional groups are present, they can interact chemically with the occupants. Additionally, the potential for reactivity and catalysis is greatly enhanced. Deep cavitands, derived from resorcinarenes, nearly surround smaller molecules and have been one of the most successful platforms for elaboration with functional groups. Derivatives bearing organic and metal-binding functional groups have been shown to affect recognition properties and selectively accelerate diverse reactions. In this review, we examine recent examples of these systems with an emphasis on how and why ordered nanoenvironments impart changes in the properties and reactivity of their occupants. PMID:16043720

  2. Use of radiation effects for a controlled change in the chemical composition and properties of materials by intentional addition or substitution of atoms of a certain kind

    SciTech Connect

    Gurovich, B. A.; Prikhod'ko, K. E. Kuleshova, E. A.; Maslakov, K. I.; Komarov, D. A.

    2013-06-15

    This study is a continuation of works [1-12] dealing with the field developed by the authors, namely, to widen the possibilities of radiation methods for a controlled change in the atomic composition and properties of thin-film materials. The effects under study serve as the basis for the following two methods: selective atom binding and selective atom substitution. Such changes in the atomic composition are induced by irradiation by mixed beams consisting of protons and other ions, the energy of which is sufficient for target atom displacements. The obtained experimental data demonstrate that the changes in the chemical composition of thin-film materials during irradiation by an ion beam of a complex composition take place according to mechanisms that differ radically from the well-known mechanisms controlling the corresponding chemical reactions in these materials. These radical changes are shown to be mainly caused by the accelerated ioninduced atomic displacements in an irradiated material during irradiation; that is, they have a purely radiation nature. The possibilities of the new methods for creating composite structures consisting of regions with a locally changed chemical composition and properties are demonstrated for a wide class of materials.

  3. Characterization of atomic-layer MoS2 synthesized using a hot filament chemical vapor deposition method

    NASA Astrophysics Data System (ADS)

    Ying-Zi, Peng; Yang, Song; Xiao-Qiang, Xie; Yuan, Li; Zheng-Hong, Qian; Ru, Bai

    2016-05-01

    Atomic-layer MoS2 ultrathin films are synthesized using a hot filament chemical vapor deposition method. A combination of atomic force microscopy (AFM), x-ray diffraction (XRD), high-resolution transition electron microscopy (HRTEM), photoluminescence (PL), and x-ray photoelectron spectroscopy (XPS) characterization methods is applied to investigate the crystal structures, valence states, and compositions of the ultrathin film areas. The nucleation particles show irregular morphology, while for a larger size somewhere, the films are granular and the grains have a triangle shape. The films grow in a preferred orientation (002). The HRTEM images present the graphene-like structure of stacked layers with low density of stacking fault, and the interlayer distance of plane is measured to be about 0.63 nm. It shows a clear quasi-honeycomb-like structure and 6-fold coordination symmetry. Room-temperature PL spectra for the atomic layer MoS2 under the condition of right and left circular light show that for both cases, the A1 and B1 direct excitonic transitions can be observed. In the meantime, valley polarization resolved PL spectra are obtained. XPS measurements provide high-purity samples aside from some contaminations from the air, and confirm the presence of pure MoS2. The stoichiometric mole ratio of S/Mo is about 2.0–2.1, suggesting that sulfur is abundant rather than deficient in the atomic layer MoS2 under our experimental conditions. Project supported by the Natural Science Foundation of Zhejiang Province, China (Grant Nos. LY16F040003 and LY16A040007) and the National Natural Science Foundation of China (Grant Nos. 51401069 and 11574067).

  4. Trends in information theory-based chemical structure codification.

    PubMed

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  5. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

    PubMed

    Gumbart, James C; Beeby, Morgan; Jensen, Grant J; Roux, Benoît

    2014-02-01

    Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.

  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.

  7. Atomic structure of amorphous shear bands in boron carbide.

    PubMed

    Reddy, K Madhav; Liu, P; Hirata, A; Fujita, T; Chen, M W

    2013-01-01

    Amorphous shear bands are the main deformation and failure mode of super-hard boron carbide subjected to shock loading and high pressures at room temperature. Nevertheless, the formation mechanisms of the amorphous shear bands remain a long-standing scientific curiosity mainly because of the lack of experimental structure information of the disordered shear bands, comprising light elements of carbon and boron only. Here we report the atomic structure of the amorphous shear bands in boron carbide characterized by state-of-the-art aberration-corrected transmission electron microscopy. Distorted icosahedra, displaced from the crystalline matrix, were observed in nano-sized amorphous bands that produce dislocation-like local shear strains. These experimental results provide direct experimental evidence that the formation of amorphous shear bands in boron carbide results from the disassembly of the icosahedra, driven by shear stresses.

  8. Structure of human chromosomes studied by atomic force microscopy.

    PubMed

    Tamayo, Javier

    2003-03-01

    In this work human chromosomes have been treated with RNase and pepsin to remove the layer of cellular material that covers the standard preparations on glass slides. This allows characterization of the topography of chromosomes at nanometer scale in air and in physiological solution by atomic force microscopy. Imaging of the dehydrated structure in air indicates radial arrangement of chromatin loops as the last level of DNA packing. However, imaging in liquid reveals a last level of organization consisting of a hierarchy of bands and coils. Additionally force curves between the tip and the chromosome in liquid are consistent with radial chromatin loops. These results and previous electron microscopy studies are analyzed, and a model is proposed for the chromosome structure in which radial loops and helical coils coexist.

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

    PubMed Central

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

    2015-01-01

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

  10. Unambiguous identification of the role of a single Cu atom in the ZnO structured green band.

    PubMed

    Byrne, D; Herklotz, F; Henry, M O; McGlynn, E

    2012-05-30

    High quality and purity single crystal ZnO samples doped with single isotopes of (63)Cu and (65)Cu, with equal concentrations of both these isotopes, and with natural Cu using a wet chemical atomic substitution reaction and anneal were studied using low temperature optical spectroscopy. Our data on the zero phonon line of the structured green band in ZnO confirm unambiguously the involvement of a single Cu atom in this defect emission. These data allow us to confirm the main features of the assignment proposed by Dingle in 1969 and to comment further on the defect structure.

  11. Images of Atoms.

    ERIC Educational Resources Information Center

    Wright, Tony

    2003-01-01

    Recommends using a simple image, such as the fuzzy atom ball to help students develop a useful understanding of the molecular world. Explains that the image helps students easily grasp ideas about atoms and molecules and leads naturally to more advanced ideas of atomic structure, chemical bonding, and quantum physics. (Author/NB)

  12. Effects of xenon insertion into hydrogen bromide. Comparison of the electronic structure of the HBr···CO2 and HXeBr···CO2 complexes using quantum chemical topology methods: electron localization function, atoms in molecules and symmetry adapted perturbation theory.

    PubMed

    Makarewicz, Emilia; Gordon, Agnieszka J; Mierzwicki, Krzysztof; Latajka, Zdzislaw; Berski, Slawomir

    2014-06-01

    Quantum chemistry methods have been applied to study the influence of the Xe atom inserted into the hydrogen-bromine bond (HBr → HXeBr), particularly on the nature of atomic interactions in the HBr···CO2 and HXeBr···CO2 complexes. Detailed analysis of the nature of chemical bonds has been carried out using topological analysis of the electron localization function, while topological analysis of electron density was used to gain insight into the nature of weak nonbonding interactions. Symmetry-adapted perturbation theory within the orbital approach was applied for greater understanding of the physical contributions to the total interaction energy.

  13. To What Extent are "Atoms in Molecules" Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

    PubMed

    Keyvani, Zahra Alimohammadi; Shahbazian, Shant; Zahedi, Mansour

    2016-03-24

    The "atoms in molecules" structures of 225 unsubstituted hydrocarbons are derived from both the optimized and the promolecule electron densities. A comparative analysis demonstrates that the molecular graphs derived from these two types of electron densities at the same geometry are equivalent for almost 90 % of the hydrocarbons containing the same number and types of critical points. For the remaining 10 % of molecules, it is demonstrated that by inducing small perturbations, through the variation of the used basis set or slight changes in the used geometry, the emerging molecular graphs from both densities are also equivalent. Interestingly, the (3, -1) critical point between two "non-bonded" hydrogen atoms, which triggered "H-H bonding" controversy is also observed in the promolecule densities of certain hydrocarbons. Evidently, the topology of the electron density is not dictated by chemical bonds or strong interactions and deformations induced by the interactions of atoms in molecules have a quite marginal role, virtually null, in shaping the general traits of the topology of molecular electron densities of the studied hydrocarbons, whereas the key factor is the underlying atomic densities.

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    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.

  15. Chemical vapor deposition of atomically thin materials for membrane dialysis applications

    NASA Astrophysics Data System (ADS)

    Kidambi, Piran; Mok, Alexander; Jang, Doojoon; Boutilier, Michael; Wang, Luda; Karnik, Rohit; Microfluidics; Nanofluidics Research Lab Team

    2015-11-01

    Atomically thin 2D materials like graphene and h-BN represent a new class of membranes materials. They offer the possibility of minimum theoretical membrane transport resistance along with the opportunity to tune pore sizes at the nanometer scale. Chemical vapor deposition has emerged as the preferable route towards scalable, cost effective synthesis of 2D materials. Here we show selective molecular transport through sub-nanometer diameter pores in graphene grown via chemical vapor deposition processes. A combination of pressure driven and diffusive transport measurements shows evidence for size selective transport behavior which can be used for separation by dialysis for applications such as desalting of biomolecular or chemical solutions. Principal Investigator

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

    SciTech Connect

    An, Nguyen Ba; Kim, Jaewan; Kim, Kisik

    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.

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

    SciTech Connect

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

    2015-06-24

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

  18. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance. PMID:23701000

  19. Magnetic and atomic structure parameters of Sc-doped barium hexagonal ferrites

    NASA Astrophysics Data System (ADS)

    Yang, Aria; Chen, Yajie; Chen, Zhaohui; Vittoria, Carmine; Harris, V. G.

    2008-04-01

    Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12-xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x =0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

  20. Quantum chemical simulations of atomic layer deposition of metal oxides and metal nitrides

    NASA Astrophysics Data System (ADS)

    Xu, Ye

    Scaling of SiO2 gate dielectrics to extend the miniaturization of complementary metal oxide semiconductor (CMOS) devices in accordance with Moore's Law has resulted in unacceptable tunneling current leakage levels. The projection that this challenge could significantly limit CMOS performance has prompted the intense search for alternative gate dielectric materials that can achieve high capacitances with physically thicker films which minimize tunneling leakage current. Atomic layer deposition is an ideal deposition method for high-k films because it controls the film thickness with atomic layer precision and can achieve high film conformality and uniformity. We use density functional theory (DFT) to explore chemical reactions involved in ALD processes at the atomic level. We have investigated different metal precursors for ALD process. Compared to halides, metal alkylamides are more favorable on nitrided silicon surfaces and subsequent film growth. Likewise, hafnium alkylamide is more favorable than water to initiate the nucleation on hydrogen terminated silicon surfaces. For deposition on organic self-assembled monolayers, different end groups significantly affect the selectivity towards ALD reactions. The chemical mechanisms involved in ALD of hafnium nitride, aluminum nitride are developed which provide an understanding to the difficulty in producing oxygen free metal nitrides by ALD. By combining ALD of metal oxide and metal nitride, a new method for incorporating nitrogen into oxide films is proposed. In TMA and ozone reaction, it's found that by-product water can be a catalyzer for this reaction.

  1. Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

    PubMed

    Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, Lucie; Pichová, Iva; Řezáčová, Pavlina; Lepšík, Martin; Brynda, Jiří

    2015-12-01

    The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

  2. Electronic Structure of Helium Atom in a Quantum Dot

    NASA Astrophysics Data System (ADS)

    Saha, Jayanta K.; Bhattacharyya, S.; Mukherjee, T. K.

    2016-03-01

    Bound and resonance states of helium atom have been investigated inside a quantum dot by using explicitly correlated Hylleraas type basis set within the framework of stabilization method. To be specific, precise energy eigenvalues of bound 1sns (1Se) (n = 1-6) states and the resonance parameters i.e. positions and widths of 1Se states due to 2sns (n = 2-5) and 2pnp (n = 2-5) configurations of confined helium below N = 2 ionization threshold of He+ have been estimated. The two-parameter (Depth and Width) finite oscillator potential is used to represent the confining potential due to the quantum dot. It has been explicitly demonstrated that the electronic structural properties become sensitive functions of the dot size. It is observed from the calculations of ionization potential that the stability of an impurity ion within a quantum dot may be manipulated by varying the confinement parameters. A possibility of controlling the autoionization lifetime of doubly excited states of two-electron ions by tuning the width of the quantum cavity is also discussed here. TKM Gratefully Acknowledges Financial Support under Grant No. 37(3)/14/27/2014-BRNS from the Department of Atomic Energy, BRNS, Government of India. SB Acknowledges Financial Support under Grant No. PSW-160/14-15(ERO) from University Grants Commission, Government of India

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2016-08-01

    Electrochemical interfaces between immiscible liquids have lately received renewed interest, both for gaining fundamental insight as well as for applications in nanomaterial synthesis. In this feature article we demonstrate that the atomic scale structure of these previously inaccessible interfaces nowadays can be explored by in situ synchrotron based X-ray scattering techniques. Exemplary studies of a prototypical electrochemical system - a liquid mercury electrode in pure NaCl solution - reveal that the liquid metal is terminated by a well-defined atomic layer. This layering decays on length scales of 0.5 nm into the Hg bulk and displays a potential and temperature dependent behaviour that can be explained by electrocapillary effects and contributions of the electronic charge distribution on the electrode. In similar studies of nanomaterial growth, performed for the electrochemical deposition of PbFBr, a complex nucleation and growth behaviour is found, involving a crystalline precursor layer prior to the 3D crystal growth. Operando X-ray scattering measurements provide detailed data on the processes of nanoscale film formation. PMID:27301317

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

    PubMed

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

    2016-08-01

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

  6. Defects in p-GaN and their atomic structure

    SciTech Connect

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

    2004-10-08

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

  7. Interfacial atomic structure analysis at sub-angstrom resolution using aberration-corrected STEM

    NASA Astrophysics Data System (ADS)

    Hsiao, Chien-Nan; Kuo, Shou-Yi; Lai, Fang-I.; Chen, Wei-Chun

    2014-10-01

    The atomic structure of a SiGe/Si epitaxial interface grown via molecular beam epitaxy on a single crystal silicon substrate was investigated using an aberration-corrected scanning transmittance electron microscope equipped with a high-angle annular dark-field detector and an energy-dispersive spectrometer. The accuracy required for compensation of the various residual aberration coefficients to achieve sub-angstrom resolution with the electron optics system was also evaluated. It was found that the interfacial layer was composed of a silicon single crystal, connected coherently to epitaxial SiGe nanolaminates. In addition, the distance between the dumbbell structures of the Si and Ge atoms was approximately 0.136 nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78 Å. Furthermore, the relative positions of the atoms in the chemical composition line scan signals could be directly interpreted from the corresponding incoherent high-angle annular dark-field image.

  8. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance.

    PubMed

    Bender, Andreas; Mussa, Hamse Y; Glen, Robert C; Reiling, Stephan

    2004-01-01

    A molecular similarity searching technique based on atom environments, information-gain-based feature selection, and the naive Bayesian classifier has been applied to a series of diverse datasets and its performance compared to those of alternative searching methods. Atom environments are count vectors of heavy atoms present at a topological distance from each heavy atom of a molecular structure. In this application, using a recently published dataset of more than 100000 molecules from the MDL Drug Data Report database, the atom environment approach appears to outperform fusion of ranking scores as well as binary kernel discrimination, which are both used in combination with Unity fingerprints. Overall retrieval rates among the top 5% of the sorted library are nearly 10% better (more than 14% better in relative numbers) than those of the second best method, Unity fingerprints and binary kernel discrimination. In 10 out of 11 sets of active compounds the combination of atom environments and the naive Bayesian classifier appears to be the superior method, while in the remaining dataset, data fusion and binary kernel discrimination in combination with Unity fingerprints is the method of choice. Binary kernel discrimination in combination with Unity fingerprints generally comes second in performance overall. The difference in performance can largely be attributed to the different molecular descriptors used. Atom environments outperform Unity fingerprints by a large margin if the combination of these descriptors with the Tanimoto coefficient is compared. The naive Bayesian classifier in combination with information-gain-based feature selection and selection of a sensible number of features performs about as well as binary kernel discrimination in experiments where these classification methods are compared. When used on a monoaminooxidase dataset, atom environments and the naive Bayesian classifier perform as well as binary kernel discrimination in the case of a 50

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

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

    2015-10-15

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

  12. On the atomic structure of cocaine in solution.

    PubMed

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

    2016-01-14

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

  13. An atomic structure of the human 26S proteasome.

    PubMed

    Huang, Xiuliang; Luan, Bai; Wu, Jianping; Shi, Yigong

    2016-09-01

    We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.

  14. First Optical Hyperfine Structure Measurement in an Atomic Anion

    SciTech Connect

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

    2010-02-19

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

  15. 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.

  16. Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation.

    PubMed

    Orfield, Noah J; McBride, James R; Wang, Feng; Buck, Matthew R; Keene, Joseph D; Reid, Kemar R; Htoon, Han; Hollingsworth, Jennifer A; Rosenthal, Sandra J

    2016-02-23

    Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. Herein, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking "giant" CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging, rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive "dark" fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be "dark". Therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.

  17. Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

    SciTech Connect

    Bai, Yanwen; Bian, Xiufang Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng; Zhang, Shuo; Huang, Yuying

    2014-01-28

    Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Ag and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.

  18. 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

  19. Structure and local chemical properties of boron-terminated tetravacancies in hexagonal boron nitride.

    PubMed

    Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H G; Liu, Zheng; Suenaga, Kazutomo

    2015-02-20

    Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride. We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sample regions. We correlate our experimental data with calculations which help explain our observations. PMID:25763963

  20. 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

  1. Atomic structures and compositions of internal interfaces. Progress report, September 1, 1991--August 31, 1992

    SciTech Connect

    Seidman, D.N.; Merkle, K.L.

    1992-03-01

    This research program addresses fundamental questions concerning the relationships between atomic structures and chemical compositions of metal/ceramic heterophase interfaces. The chemical composition profile across a Cu/MgO {l_brace}111{r_brace}-type heterophase interface, produced by the internal oxidation of a Cu(Mg) single phase alloy, is measured via atom-probe field-ion microscopy with a spatial resolution of 0.121 nm; this resolution is equal to the interplanar space of the {l_brace}222{r_brace} MgO planes. In particular, we demonstrate for the first time that the bonding across a Cu/MgO {l_brace}111{r_brace}-type heterophase interface, along a <111> direction common to both the Cu matrix and an MgO precipitate, has the sequence Cu{vert_bar}O{vert_bar}Mg{hor_ellipsis} and not Cu{vert_bar}Mg{vert_bar}O{hor_ellipsis}; this result is achieved without any deconvolution of the experimental data. Before determining this chemical sequence it was established, via high resolution electron microscopy, that the morphology of an MgO precipitate in a Cu matrix is an octahedron faceted on {l_brace}111{r_brace} planes with a cube-on-cube relationship between a precipitate and the matrix. First results are also presented for the Ni/Cr{sub 2}O{sub 4} interface; for this system selected area atom probe microscopy was used to analyze this interface; Cr{sub 2}O{sub 4} precipitates are located in a field-ion microscope tip and a precipitate is brought into the tip region via a highly controlled electropolishing technique.

  2. Trapping and manipulation of isolated atoms using nanoscale plasmonic structures.

    PubMed

    Chang, D E; Thompson, J D; Park, H; Vuletić, V; Zibrov, A S; Zoller, P; Lukin, M D

    2009-09-18

    We propose and analyze a scheme to interface individual neutral atoms with nanoscale solid-state systems. The interface is enabled by optically trapping the atom via the strong near-field generated by a sharp metallic nanotip. We show that under realistic conditions, a neutral atom can be trapped with position uncertainties of just a few nanometers, and within tens of nanometers of other surfaces. Simultaneously, the guided surface plasmon modes of the nanotip allow the atom to be optically manipulated, or for fluorescence photons to be collected, with very high efficiency. Finally, we analyze the surface forces, heating and decoherence rates acting on the trapped atom.

  3. 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.; Kotochigova, Svetlana; Petrov, Alexander

    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.

  4. Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  5. Tooth structure studied using the atomic force microscope

    NASA Astrophysics Data System (ADS)

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

    1993-06-01

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

  6. An atomic structure of human γ-secretase.

    PubMed

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

    2015-09-10

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

  7. A near atomic structure of the active human apoptosome

    PubMed Central

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

    2016-01-01

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

  8. An atomic structure of human γ-secretase

    PubMed Central

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

    2015-01-01

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

  9. An atomic structure of human γ-secretase

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  10. Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the STEM

    SciTech Connect

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

    1993-12-01

    The macroscopic properties of many materials are controlled by the structure and chemistry at the grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. The high-resolution Z-contrast imaging technique in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition can be interpreted intuitively. This direct image allows the electron probe to be positioned over individual atomic columns for parallel detection electron energy loss spectroscopy (PEELS) at a spatial resolution approaching 0.22nm. The bonding information which can be obtained from the fine structure within the PEELS edges can then be used in conjunction with the Z-contrast images to determine the structure at the grain boundary. In this paper we present 3 examples of correlations between the structural, chemical and electronic properties at materials interfaces in metal-semiconductor systems, superconducting and ferroelectric materials.

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

    ERIC Educational Resources Information Center

    Inner London Education Authority (England).

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

  12. Investigating the Internal Structure of Individual Aerosol Particles Using Atomic Force and Raman Microscopies

    NASA Astrophysics Data System (ADS)

    Freedman, M. A.; Baustian, K. J.; Wise, M. E.; Tolbert, M. A.

    2009-12-01

    We have used Atomic Force Microscopy (AFM) and Raman Microscopy to probe aerosol internal structures in order to understand the optical properties of aerosols composed of mixtures of organic and inorganic components. While AFM gives only topographical information about the particles, indirect chemical information can be obtained by using substrates with different surface properties. With Raman microscopy, chemical signatures of the components of the aerosol are obtained, but we have limited spatial resolution. We have explored the use of these two techniques to look at aerosol internal structure using a range of different model aerosols composed of mixtures of ammonium sulfate with organic compounds of various solubilities such as sucrose, succinic acid, and palmitic acid. At the extremes of solubility, AFM provides suitable information for interpreting aerosol microstructure. For example, AFM clearly shows the presence of core-shell structures for aerosol particles composed of palmitic acid and ammonium sulfate, while the results for aerosol particles composed of succinic acid and ammonium sulfate are more difficult to interpret. Information about size and shape can be obtained when hydrophilic particles are impacted on hydrophobic substrates and vise versa. With Raman microscopy, core-shell structures were readily identified for ammonium sulfate with palmitic acid or succinic acid coatings. For the case of succinic acid and ammonium sulfate mixtures, we are using microscopy results to aid in interpreting the refractive indices we retrieved from cavity ring-down studies.

  13. 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 MΩ 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.

  14. Atomic layer chemical vapor deposition of ZrO2-based dielectric films: Nanostructure and nanochemistry

    NASA Astrophysics Data System (ADS)

    Dey, S. K.; Wang, C.-G.; Tang, D.; Kim, M. J.; Carpenter, R. W.; Werkhoven, C.; Shero, E.

    2003-04-01

    A 4 nm layer of ZrOx (targeted x˜2) was deposited on an interfacial layer (IL) of native oxide (SiO, t˜1.2 nm) surface on 200 mm Si wafers by a manufacturable atomic layer chemical vapor deposition technique at 300 °C. Some as-deposited layers were subjected to a postdeposition, rapid thermal annealing at 700 °C for 5 min in flowing oxygen at atmospheric pressure. The experimental x-ray diffraction, x-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, and high-resolution parallel electron energy loss spectroscopy results showed that a multiphase and heterogeneous structure evolved, which we call the Zr-O/IL/Si stack. The as-deposited Zr-O layer was amorphous ZrO2-rich Zr silicate containing about 15% by volume of embedded ZrO2 nanocrystals, which transformed to a glass nanoceramic (with over 90% by volume of predominantly tetragonal-ZrO2 (t-ZrO2) and monoclinic-ZrO2 (m-ZrO2) nanocrystals) upon annealing. The formation of disordered amorphous regions within some of the nanocrystals, as well as crystalline regions with defects, probably gave rise to lattice strains and deformations. The interfacial layer (IL) was partitioned into an upper SiO2-rich Zr silicate and the lower SiOx. The latter was substoichiometric and the average oxidation state increased from Si0.86+ in SiO0.43 (as-deposited) to Si1.32+ in SiO0.66 (annealed). This high oxygen deficiency in SiOx was indicative of the low mobility of oxidizing specie in the Zr-O layer. The stacks were characterized for their dielectric properties in the Pt/{Zr-O/IL}/Si metal oxide-semiconductor capacitor (MOSCAP) configuration. The measured equivalent oxide thickness (EOT) was not consistent with the calculated EOT using a bilayer model of ZrO2 and SiO2, and the capacitance in accumulation (and therefore, EOT and kZr-O) was frequency dispersive, trends well documented in literature. This behavior is qualitatively explained in terms of the multilayer nanostructure and nanochemistry that

  15. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  16. Electronic and atomic structure of the AlnHn+2 clusters

    NASA Astrophysics Data System (ADS)

    Martínez, J. I.; Alonso, J. A.

    2008-08-01

    The electronic and atomic structure of the family of hydrogenated Al clusters AlnHn+2 with n=4-11 has been studied using the density functional theory with the generalized gradient approximation (GGA) for exchange and correlation. All these clusters have substantial gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) and, consequently, they are chemically very stable. The largest gap of 2.81 eV occurs for Al6H8. Five clusters of the family, Al4H6, Al5H7, Al6H8, Al7H9, and Al10H12, fulfill the Wade-Mingos rule. That is, in AlnHn+2, the Al matrix forms a polyhedron of n vertices and n H atoms form strong H-Al terminal bonds; one pair of electrons is involved in each of those bonds. The remaining n+1 electron pairs form a delocalized cloud over the surface of the Al cage. The clusters fulfilling the Wade-Mingos rule have wider HOMO-LUMO gaps and are chemically more stable. The trends in the gap have some reflections in the form of the photoabsorption spectra, calculated in the framework of time-dependent density functional theory using the GGA single-particle energies and orbitals and a local density approximation exchange-correlation kernel.

  17. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    SciTech Connect

    Sakai, Osamu Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-15

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH{sub 3} in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

  18. Growth mechanisms for Si epitaxy on O atomic layers: Impact of O-content and surface structure

    NASA Astrophysics Data System (ADS)

    Jayachandran, Suseendran; Billen, Arne; Douhard, Bastien; Conard, Thierry; Meersschaut, Johan; Moussa, Alain; Caymax, Matty; Bender, Hugo; Vandervorst, Wilfried; Heyns, Marc; Delabie, Annelies

    2016-10-01

    The epitaxial growth of Si layers on Si substrates in the presence of O atoms is generally considered a challenge, as O atoms degrade the epitaxial quality by generating defects. Here, we investigate the growth mechanisms for Si epitaxy on O atomic layers (ALs) with different O-contents and structures. O ALs are deposited by ozone (O3) or oxygen (O2) exposure on H-terminated Si at 50 °C and 300 °C respectively. Epitaxial Si is deposited by chemical vapor deposition using silane (SiH4) at 500 °C. After O3 exposure, the O atoms are uniformly distributed in Si-Si dimer/back bonds. This O layer still allows epitaxial seeding of Si. The epitaxial quality is enhanced by lowering the surface distortions due to O atoms and by decreasing the arrival rate of SiH4 reactants, allowing more time for surface diffusion. After O2 exposure, the O atoms are present in the form of SiOx clusters. Regions of hydrogen-terminated Si remain present between the SiOx clusters. The epitaxial seeding of Si in these structures is realized on H-Si regions, and an epitaxial layer grows by a lateral overgrowth mechanism. A breakdown in the epitaxial ordering occurs at a critical Si thickness, presumably by accumulation of surface roughness.

  19. Enhanced Sensitivity of Micro Mechanical Chemical Sensors Through Structural Variation

    SciTech Connect

    Harris, J.C.

    2001-04-16

    Chemical detection devices are very effective; however, their bulkiness makes them undesirable for portable applications. The next generation of chemical detectors is microscopic mechanical devices capable of measuring trace amounts of chemical vapor within the environment. The chemicals do not react directly with the detector, instead intermolecular forces cause chemicals to adhere to the surface. This surface adhesion of the chemical creates surface stress on the detectors leading to measurable movement. Modifications to the structural design of these microstructures have resulted in signal enhancement to over seven hundred percent.

  20. Three-dimensionality of space in the structure of the periodic table of chemical elements

    SciTech Connect

    Veremeichik, T. F.

    2006-07-15

    The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed.

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

    SciTech Connect

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-17

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

  2. Voronoi analysis of the short-range atomic structure in iron and iron-carbon melts

    NASA Astrophysics Data System (ADS)

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-01

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

  3. Materials by Design—A Perspective From Atoms to Structures

    PubMed Central

    Buehler, Markus J.

    2013-01-01

    Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499

  4. Materials by Design-A Perspective From Atoms to Structures.

    PubMed

    Buehler, Markus J

    2013-02-01

    Biological materials are effectively synthesized, controlled, and used for a variety of purposes-in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499

  5. Materials by Design-A Perspective From Atoms to Structures.

    PubMed

    Buehler, Markus J

    2013-02-01

    Biological materials are effectively synthesized, controlled, and used for a variety of purposes-in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science.

  6. 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 μA 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

  7. 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; Drndić, 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 μA 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.

  8. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  9. Atomic structure of intracellular amorphous calcium phosphate deposits.

    PubMed

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

    1975-06-01

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

  10. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  11. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale.

    PubMed

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-12-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo

  12. 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

    2014-12-22

    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.

  13. Role of hydrogen in the chemical vapor deposition growth of MoS2 atomic layers

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Li, Xinming; Zang, Xiaobei; Zhu, Miao; He, Yijia; Wang, Kunlin; Xie, Dan; Zhu, Hongwei

    2015-04-01

    Hydrogen plays a crucial role in the chemical vapor deposition (CVD) growth of graphene. Here, we have revealed the roles of hydrogen in the two-step CVD growth of MoS2. Our study demonstrates that hydrogen acts as the following: (i) an inhibitor of the thermal-induced etching effect in the continuous film growth process; and (ii) a promoter of the desulfurization reaction by decreasing the S/Mo atomic ratio and the oxidation reaction of the obtained MoSx (0 < x < 2) films. A high hydrogen content of more than 100% in argon forms nano-sized circle-like defects and damages the continuity and uniformity of the film. Continuous MoS2 films with a high crystallinity and a nearly perfect S/Mo atomic ratio were finally obtained after sulfurization annealing with a hydrogen content in the range of 20%-80%. This insightful understanding reveals the crucial roles of hydrogen in the CVD growth of MoS2 and paves the way for the controllable synthesis of two-dimensional materials.Hydrogen plays a crucial role in the chemical vapor deposition (CVD) growth of graphene. Here, we have revealed the roles of hydrogen in the two-step CVD growth of MoS2. Our study demonstrates that hydrogen acts as the following: (i) an inhibitor of the thermal-induced etching effect in the continuous film growth process; and (ii) a promoter of the desulfurization reaction by decreasing the S/Mo atomic ratio and the oxidation reaction of the obtained MoSx (0 < x < 2) films. A high hydrogen content of more than 100% in argon forms nano-sized circle-like defects and damages the continuity and uniformity of the film. Continuous MoS2 films with a high crystallinity and a nearly perfect S/Mo atomic ratio were finally obtained after sulfurization annealing with a hydrogen content in the range of 20%-80%. This insightful understanding reveals the crucial roles of hydrogen in the CVD growth of MoS2 and paves the way for the controllable synthesis of two-dimensional materials. Electronic supplementary

  14. Structure of ultrathin oxide layers on metal surfaces from grazing scattering of fast atoms

    NASA Astrophysics Data System (ADS)

    Winter, H.; Seifert, J.; Blauth, D.; Busch, M.; Schüller, A.; Wethekam, S.

    2009-10-01

    The structure of ultrathin oxide layers grown on metal substrates is investigated by grazing scattering of fast atoms from the film surface. We present three recent experimental techniques which allow us to study the structure of ordered oxide films on metal substrates in detail. (1) A new variant of a triangulation method with fast atoms based on the detection of emitted electrons, (2) rainbow scattering under axial surface channeling conditions, and (3) fast atom diffraction (FAD) for studies on the structure of oxide films. Our examples demonstrate the attractive features of grazing fast atom scattering as a powerful analytical tool in surface physics.

  15. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

    ) fabricate graphene/metal interfaces and metal/graphene/metal sandwich structures evidencing classical anisotropic umpolung chemistry from carbon pz-orbrital charge pinning, and (Chapter 5) engineer graphene/dielectric interfaces showing electron depletion from carbon atoms at the HfO2/graphene interface. The fabrication of graphene interfaces remains a critical gap for successful commercialization of graphene-based devices, yet we demonstrate that interfacial hybridization, anisotropic charge redistribution, local chemical bonding, and discrete electronic hybridization regimes play a critical role in the electronic structure at graphene interfaces.

  16. 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.

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

    DOE PAGES

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

    2015-01-01

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

  18. Gyration-radius dynamics in structural transitions of atomic clusters.

    PubMed

    Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

    2007-03-28

    This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present

  19. 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.

  20. Structures and chemical properties of silicene: unlike graphene.

    PubMed

    Jose, Deepthi; Datta, Ayan

    2014-02-18

    The discovery of graphene and its remarkable and exotic properties have aroused interest in other elements and molecules that form 2D atomic layers, such as metal chalcogenides, transition metal oxides, boron nitride, silicon, and germanium. Silicene and germanene, the Si and Ge counterparts of graphene, have interesting fundamental physical properties with potential applications in technology. For example, researchers expect that silicene will be relatively easy to incorporate within existing silicon-based electronics. In this Account, we summarize the challenges and progress in the field of silicene research. Theoretical calculations have predicted that silicene possesses graphene-like properties such as massless Dirac fermions that carry charge and the quantum spin Hall effect. Researchers are actively exploring the physical and chemical properties of silicene and tailoring it for wide variety of applications. The symmetric buckling in each of the six-membered rings of silicene differentiates it from graphene and imparts a variety of interesting properties with potential technological applications. The pseudo-Jahn-Teller (PJT) distortion breaks the symmetry and leads to the buckling in silicenes. In graphene, the two sublattice structures are equivalent, which does not allow for the opening of the band gap by an external electric field. However, in silicene where the neighboring Si atoms are displaced alternatively perpendicular to the plane, the intrinsic buckling permits a band gap opening in silicene in the presence of external electric field. Silicene's stronger spin orbit coupling than graphene has far reaching applications in spintronic devices. Because silicon prefers sp(3) hybridization over sp(2), hydrogenation is much easier in silicene. The hydrogenation of silicene to form silicane opens the band gap and increases the puckering angle. Lithiation can suppress the pseudo-Jahn-Teller distortion in silicene and hence can flatten silicene's structure

  1. Software for relativistic atomic structure theory: The grasp project at oxford

    SciTech Connect

    Parpia, F.A.; Grant, I.P. )

    1991-08-05

    GRASP is an acronym for General-purpose Relativistic Atomic Structure Program. The objective of the GRASP project at Oxford is to produce user-friendly state-of-the-art multiconfiguration Dirac-Fock (MCDF) software packages for rleativistic atomic structure theory.

  2. Survey of reproductive hazards among oil, chemical, and atomic workers exposed to halogenated hydrocarbons

    SciTech Connect

    Savitz, D.A.; Harley, B.; Krekel, S.; Marshall, J.; Bondy, J.; Orleans, M.

    1984-01-01

    Several halogenated hydrocarbons are suspected of causing adverse reproductive effects. Because of such concerns, the Oil, Chemical, and Atomic Workers International Union surveyed the reproductive histories of two groups of workers. One group worked at plants engaged in the production or use of halogenated hydrocarbons (exposed) whereas the others had no such opportunity for exposure (nonexposed). Although a low response rate precludes firm conclusions, the 1,280 completed questionnaires provide useful data for generating hypotheses in this developing field of interest. A history of diagnosed cancer was reported more frequently among exposed workers. The infant mortality rate was also significantly elevated among the offspring of exposed workers. No risk gradient was observed for episodes of infertility, fetal loss, congenital defects, or low-birthweight offspring. Concerns with nonresponse, exposure characterization, possible confounding factors, and limited statistical power are addressed. The results provide further suggestions which help to direct studies of occupational reproductive risks.

  3. 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.

  4. 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

  5. Multi-element analysis of manganese nodules by atomic absorption spectrometry without chemical separation

    USGS Publications Warehouse

    Kane, J.S.; Harnly, J.M.

    1982-01-01

    Five manganese nodules, including the USGS reference nodules A-1 and P-1, were analyzed for Co, Cu, Fe, K, Mg, Mn, Na, Ni and Zn without prior chemical separation by using a simultaneous multi-element atomic absorption spectrometer with an air-cetylene flame. The nodules were prepared in three digestion matrices. One of these solutions was measured using sixteen different combinations of burner height and air/acetylene ratios. Results for A-1 and P-1 are compared to recommended values and results for all nodules are compared to those obtained with an inductively coupled plasma. The elements Co, Cu, Fe, K, Mg, Mn, Na, Ni, and Zn are simultaneously determined with a composite recovery for all elements of 100 ?? 7%, independent of the digestion matrices, heights in the flame, or flame stoichiometries examined. Individual recoveries for Co, K, and Ni are considerably poorer in two digests than this composite figure, however. The optimum individual recoveries of 100 ?? 5% and imprecisions of 1-4%, except for zinc, are obtained when Co, K, Mn, Na and Ni are determined simultaneously in a concentrated digest, and in another analytical sequence, when Cu, Fe, Mg, Mn and Zn are measured simultaneously after dilution. Determination of manganese is equally accurate in the two sequences; its measurement in both assures internal consistency between the two measurement sequences. This approach improves analytical efficiency over that for conventional atomic absorption methods, while minimizing loss of accuracy or precision for individual elements. ?? 1982.

  6. Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

    SciTech Connect

    Asta, M.; Morgan, D.; Hoyt, J.J.; Sadigh, B.; Althoff, J.D.; de Fontaine, D.; Foiles, S.M.

    1999-06-01

    Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. {bold 2}, 5 (1987)], Voter and Chen (VC) [in {ital Characterization of Defects in Materials}, edited by R. W. Siegel {ital et al.} MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. {bold 3}, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni{sub 20}Al{sub 80} alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic {percent}, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for Ni{sub x}Al{sub 1{minus}x} liquid alloys with x{ge}0.75, and point to the limitations of EAM potentials for alloys richer in Al. {copyright} {ital 1999} {ital The American Physical Society}

  7. Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

    NASA Astrophysics Data System (ADS)

    Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

    1999-06-01

    Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

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

    SciTech Connect

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

    2014-04-28

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

  9. Atom-specific look at the surface chemical bond using x-ray emission spectroscopy

    SciTech Connect

    Nilsson, A.; Wassdahl, N.; Weinelt, M.

    1997-04-01

    CO and N{sub 2} adsorbed on the late transition metals have become prototype systems regarding the general understanding of molecular adsorption. It is in general assumed that the bonding of molecules to transition metals can be explained in terms of the interaction of the frontier HOMO and LUMO molecular orbitals with the d-orbitals. In such a picture the other molecular orbitals should remain essentially the same as in the free molecule. For the adsorption of the isoelectronic molecules CO and N{sub 2} this has led to the so called Blyholder model i.e., a synergetic {sigma} (HOMO) donor and {pi} (LUMO) backdonation bond. The authors results at the ALS show that such a picture is oversimplified. The direct observation and identification of the states related to the surface chemical bond is an experimental challenge. For noble and transition metal surfaces, the adsorption induced states overlap with the metal d valence band. Their signature is therefore often obscured by bulk substrate states. This complication has made it difficult for techniques such as photoemission and inverse photoemission to provide reliable information on the energy of chemisorption induced states and has left questions unanswered regarding the validity of the frontier orbitals concept. Here the authors show how x-ray emission spectroscopy (XES), in spite of its inherent bulk sensitivity, can be used to investigate adsorbed molecules. Due to the localization of the core-excited intermediate state, XE spectroscopy allows an atomic specific separation of the valence electronic states. Thus the molecular contributions to the surface measurements make it possible to determine the symmetry of the molecular states, i.e., the separation of {pi} and {sigma} type states. In all the authors can obtain an atomic view of the electronic states involved in the formation of the chemical bond to the surface.

  10. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige

    2000-01-01

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

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

    PubMed

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

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

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

    PubMed

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

    2012-10-19

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

  13. Atomic Structure and Fundamental Symmetry Measurements in a Thallium Atomic Beam

    NASA Astrophysics Data System (ADS)

    Majumder, P. K.; Nicholas, P. C.

    1998-05-01

    We have completed construction and testing of a new high-flux thallium atomic beam apparatus. Using a multiple slit oven source we achieve a favorable combination of throughput and modest Doppler narrowing. An in-vacuum chopper wheel provides ≈ 100 Hz modulation of the atomic beam and allows lock-in detection in the case of weak atomic beam absorption. Electric field plates allow precise application of ± 30 kV/cm fields in the interaction region. We will describe ongoing atomic beam spectroscopy of the 378 nm E1 transition, and a planned measurement of the Stark-induced amplitudes within the thallium 6P_1/2 - 6P_3/2 1283 nm M1 transition. We will also present the details of a new experimental proposal to search for time reversal-violating (T-odd, P-even) forces in thallium. In this new scheme, the 1283 nm M1 laser, tuned near the F=0arrowF'=1 transition, would be directed into high-finesse cavity which incorporates the atomic beam. In the presence of a longitudinal static electric field, E, a `TOPE' signature is revealed here by a cavity phase shift proportional to (hatk\\cdotE). We would search for a differential phase shift of counterpropagating (± hatk) laser beams correlated to electric field reversal. The cavity finesse both amplifies any TOPE effect and increases the precision with which it can be detected, while the differencing technique greatly reduces sensitivity to laser frequency or mechanical fluctuations.

  14. Chemical structure and intra-molecular effects on NMR-NQR tensors of harmine and harmaline alkaloids

    NASA Astrophysics Data System (ADS)

    Ahmadinejad, Neda; Tahan, Arezoo; Talebi Tari, Mostafa

    2016-02-01

    Density functional theory (DFT) methods were used to analyze the effects of molecular structure and ring currents on the NMR chemical shielding tensors and NQR frequencies of harmine and harmaline alkaloids in the gas phase. The results demonstrated that NMR tensors and NQR frequencies of 15N nuclei in these compounds depend on chemical environment and resonance interactions. Hence, their values are obviously different in the mentioned structures. The interpretation of natural bond orbital (NBO) data suggests that in harmine structure, the lone pair participation of N9 in π-system electron clouds causes to development of aromaticity nature in pyrrole ring. However, the chemical shielding around N9 atom in harmine structure is higher than in harmaline, while in harmaline structure, lone pair participation of N2 in π-system electron clouds causes to development of aromaticity nature in pyridine ring. Hence, chemical shielding around N2 atom in harmaline structure is higher than in harmine. It can be deduced that by increasing lone pair electrons contribution of nitrogen atoms in ring resonance interactions and aromaticity development, the values of NMR chemical shielding around them increase, while χ and q zz values of these nuclei decrease.

  15. Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

    PubMed

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  16. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    NASA Astrophysics Data System (ADS)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  17. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    SciTech Connect

    Grimme, Stefan Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  18. Novel chemical route for atomic layer deposition of MoS₂ thin film on SiO₂/Si substrate.

    PubMed

    Jin, Zhenyu; Shin, Seokhee; Kwon, Do Hyun; Han, Seung-Joo; Min, Yo-Sep

    2014-11-01

    Recently MoS₂ with a two-dimensional layered structure has attracted great attention as an emerging material for electronics and catalysis applications. Although atomic layer deposition (ALD) is well-known as a special modification of chemical vapor deposition in order to grow a thin film in a manner of layer-by-layer, there is little literature on ALD of MoS₂ due to a lack of suitable chemistry. Here we report MoS₂ growth by ALD using molybdenum hexacarbonyl and dimethyldisulfide as Mo and S precursors, respectively. MoS₂ can be directly grown on a SiO₂/Si substrate at 100 °C via the novel chemical route. Although the as-grown films are shown to be amorphous in X-ray diffraction analysis, they clearly show characteristic Raman modes (E(1)₂g and A₁g) of 2H-MoS₂ with a trigonal prismatic arrangement of S-Mo-S units. After annealing at 900 °C for 5 min under Ar atmosphere, the film is crystallized for MoS₂ layers to be aligned with its basal plane parallel to the substrate.

  19. Energetic Materials and Atomic Force Microscopy: Structure and Kinetics

    SciTech Connect

    Weeks, B.L.; Weese, R.K.; Zaug, J.M.

    2002-07-31

    Understanding the structure and composition of energetic materials at the sub-micron level is imperative for the fundamental studies of hot-spot formation and structural composition of energetic materials. Using in situ high-temperature AFM we have observed the solid-solid phase transition of Octahydro-1,3,5,7,-tetrazocine, HMX, in real time. Massive surface reconstruction occurs during the 1st-order transition. The temperature induced increase in void space and surface roughness observed in the delta phase polymorph of HMX serve to increase the growth rate and volume of shock initiated hot spots and possibly reaction sensitivity. HMX exists in four solid phase polymorphs, labeled {alpha}, {beta}, {chi}, and {delta}. The phase conversion of the {beta} phase to the {delta} phase involves a major disruption of the crystal lattice. The energy required to bring about this change is a measurable quantity. Multiple thermal analysis techniques carried out simultaneously are preferable because the results are directly comparable. Thermal methods are dynamic techniques, where heating or cooling is applied to a sample, unless isothermal conditions are employed. Thermogravimetic Analysis, TGA, can be used to quantify decomposition components in a substance while Differential Thermal Analysis, DTA, can be used to measure the heat flow or the specific heat capacity, with respect to time and temperature. The advantage of TGA/DTA analysis is that the measurement of weight loss and heat flow are taken simultaneously and the observed events are directly related with respect to time and temperature. TGA/DTA experiments were performed to help us take a different look at the chemical nature of HMX and aid us in understanding the void formation process.

  20. Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

    NASA Astrophysics Data System (ADS)

    Hay, Mark E.

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  1. Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

    PubMed Central

    Hay, Mark E.

    2012-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

  2. Marine chemical ecology: chemical signals and cues structure marine populations, communities, and ecosystems.

    PubMed

    Hay, Mark E

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  3. Observation of Metastable Structural Excitations and Concerted Atomic Motions on a Crystal Surface

    NASA Astrophysics Data System (ADS)

    Hwang, Ing-Shouh; Golovchenko, Jene

    1992-11-01

    The addition of a small number of lead atoms to a germanium(111) surface reduces the energy barrier for activated processes, and with a tunneling microscope it is possible to observe concerted atomic motions and metastable structures on this surface near room temperature. The formation and annihilation of these metastable structural surface excitations is associated with the shift in position of large numbers of germanium surface atoms along a specific row direction like beads on an abacus. The effect provides a mechanism for understanding the transport of atoms on a semiconductor surface.

  4. Study of the roles of chemical modifiers in determining boron using graphite furnace atomic absorption spectrometry and optimization of the temperature profile during atomization.

    PubMed

    Yamamoto, Yuhei; Shirasaki, Toshihiro; Yonetani, Akira; Imai, Shoji

    2015-01-01

    The measurement conditions for determining boron using graphite furnace-atomic absorption spectrometry (GF-AAS) were investigated. Differences in the boron absorbance profiles were found using three different commercially available GF-AAS instruments when the graphite atomizers in them were not tuned. The boron absorbances found with and without adjusting the graphite atomizers suggested that achieving an adequate absorbance for the determination of boron requires a sharp temperature profile that overshoots the target temperature during the atomization process. Chemical modifiers that could improve the boron absorbance without the need for using coating agents were tested. Calcium carbonate improved the boron absorbance but did not suppress variability in the peak height. Improvement of boron absorbance was comparatively less using iron nitrate or copper nitrate than using calcium carbonate, but variability in the peak height was clearly suppressed using iron nitrate or copper nitrate. The limit of detection was 0.0026 mg L(-1) when iron nitrate was used. It appears that iron nitrate is a useful new chemical modifier for the quick and simple determination of boron using GF-AAS.

  5. First-principles mobility calculations and atomic-scale interface roughness in nanoscale structures.

    PubMed

    Evans, M H; Zhang, X-G; Joannopoulos, J D; Pantelides, S T

    2005-09-01

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

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

    SciTech Connect

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

    2005-01-01

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

  7. 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

  8. 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.

  9. Chemical stabilization and improved thermal resilience of molecular arrangements: possible formation of a surface network of bonds by multiple pulse atomic layer deposition.

    PubMed

    de Pauli, Muriel; Matos, Matheus J S; Siles, Pablo F; Prado, Mariana C; Neves, Bernardo R A; Ferreira, Sukarno O; Mazzoni, Mário S C; Malachias, Angelo

    2014-08-14

    In this work, we make use of an atomic layer deposition (ALD) surface reaction based on trimethyl-aluminum (TMA) and water to modify O-H terminated self-assembled layers of octadecylphosphonic acid (OPA). The structural modifications were investigated by X-ray reflectivity, X-ray diffraction, and atomic force microscopy. We observed a significant improvement in the thermal stability of ALD-modified molecules, with the existence of a supramolecular packing structure up to 500 °C. Following the experimental observations, density functional theory (DFT) calculations indicate the possibility of formation of a covalent network with aluminum atoms connecting OPA molecules at terrace surfaces. Chemical stability is also achieved on top of such a composite surface, inhibiting further ALD oxide deposition. On the other hand, in the terrace edges, where the covalent array is discontinued, the chemical conditions allow for oxide growth. Analysis of the DFT results on band structure and density of states of modified OPA molecules suggests that besides the observed thermal resilience, the dielectric character of OPA layers is preserved. This new ALD-modified OPA composite is potentially suitable for applications such as dielectric layers in organic devices, where better thermal performance is required.

  10. Chemical stabilization and improved thermal resilience of molecular arrangements: possible formation of a surface network of bonds by multiple pulse atomic layer deposition.

    PubMed

    de Pauli, Muriel; Matos, Matheus J S; Siles, Pablo F; Prado, Mariana C; Neves, Bernardo R A; Ferreira, Sukarno O; Mazzoni, Mário S C; Malachias, Angelo

    2014-08-14

    In this work, we make use of an atomic layer deposition (ALD) surface reaction based on trimethyl-aluminum (TMA) and water to modify O-H terminated self-assembled layers of octadecylphosphonic acid (OPA). The structural modifications were investigated by X-ray reflectivity, X-ray diffraction, and atomic force microscopy. We observed a significant improvement in the thermal stability of ALD-modified molecules, with the existence of a supramolecular packing structure up to 500 °C. Following the experimental observations, density functional theory (DFT) calculations indicate the possibility of formation of a covalent network with aluminum atoms connecting OPA molecules at terrace surfaces. Chemical stability is also achieved on top of such a composite surface, inhibiting further ALD oxide deposition. On the other hand, in the terrace edges, where the covalent array is discontinued, the chemical conditions allow for oxide growth. Analysis of the DFT results on band structure and density of states of modified OPA molecules suggests that besides the observed thermal resilience, the dielectric character of OPA layers is preserved. This new ALD-modified OPA composite is potentially suitable for applications such as dielectric layers in organic devices, where better thermal performance is required. PMID:25055162

  11. Structural, Nanomechanical and Nanotribological Characterization of Human Hair Using Atomic Force Microscopy and Nanoindentation

    NASA Astrophysics Data System (ADS)

    Bhushan, Bharat; Latorre, Carmen; Wei, Guohua

    Human hair is a nanocomposite biological fiber. Healthy, soft hair with good feel, shine, color and overall aesthetics is generally highly desirable. It is important to study hair care products such as shampoos and conditioners as well as damaging processes such as chemical dyeing and permanent wave treatments because they affect the maintenance and grooming process and therefore alter many hair properties. Nanoscale characterization of the cellular structure, the mechanical properties, as well as the morphological, frictional and adhesive properties (tribological properties) of hair is essential if we wish to evaluate and develop better cosmetic products, and crucial to advancing the understanding of biological and cosmetic science. The atomic/friction force microscope (AFM/FFM) and nanoindenter have recently become important tools for studying the micro/nanoscale properties of human hair. In this chapter, we present a comprehensive review of structural, mechanical, and tribological properties of various hair and skin as a function of ethnicity, damage, conditioning treatment, and various environments. Various cellular structures of human hair and fine sublamellar structures of the cuticle are identified and studied. Nanomechanical properties such as hardness, elastic modulus, creep and scratch resistance are discussed. Nanotribological properties such as roughness, friction, and adhesion are presented, as well as investigations of conditioner distribution, thickness and binding interactions.

  12. Chain-branching control of the atomic structure of alkanethiol-based gold-sulfur interfaces.

    PubMed

    Wang, Yun; Chi, Qijin; Zhang, Jingdong; Hush, Noel S; Reimers, Jeffrey R; Ulstrup, Jens

    2011-09-28

    Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the α carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.

  13. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  14. [Relationship between chemical structure and sweetness. XIV. Analogs of aspartame].

    PubMed

    De Nardo, M

    1977-07-01

    Several analogs structurally related to aspartame were prepared in order to establish if chemical modifications of the molecule might improve sweetness. None of these analogs exhibited any sweet taste; on the contrary in most cases they were bitter.

  15. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    PubMed

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, the scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics. Such link groups (amines, methylsuflides, pyridines, etc.) maintain a stable lone pair configuration that selectively bonds to specific, undercoordinated transition metal atoms available following rupture of a metal point contact in the STM-BJ experiments. This basic chemical principle rationalizes the observation of highly reproducible conductance signatures. Subsequently, the method has been extended to probe a variety of physical phenomena ranging from basic I-V characteristics to more complex properties such as thermopower and electrochemical response. By adapting the technique to a conducting cantilever atomic force microscope (AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale junctions as they

  16. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    PubMed

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, the scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics. Such link groups (amines, methylsuflides, pyridines, etc.) maintain a stable lone pair configuration that selectively bonds to specific, undercoordinated transition metal atoms available following rupture of a metal point contact in the STM-BJ experiments. This basic chemical principle rationalizes the observation of highly reproducible conductance signatures. Subsequently, the method has been extended to probe a variety of physical phenomena ranging from basic I-V characteristics to more complex properties such as thermopower and electrochemical response. By adapting the technique to a conducting cantilever atomic force microscope (AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale junctions as they

  17. Atomic-Scale Structure and Local Chemistry of CoFeB-MgO Magnetic Tunnel Junctions.

    PubMed

    Wang, Zhongchang; Saito, Mitsuhiro; McKenna, Keith P; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi

    2016-03-01

    Magnetic tunnel junctions (MTJs) constitute a promising building block for future nonvolatile memories and logic circuits. Despite their pivotal role, spatially resolving and chemically identifying each individual stacking layer remains challenging due to spatially localized features that complicate characterizations limiting understanding of the physics of MTJs. Here, we combine advanced electron microscopy, spectroscopy, and first-principles calculations to obtain a direct structural and chemical imaging of the atomically confined layers in a CoFeB-MgO MTJ, and clarify atom diffusion and interface structures in the MTJ following annealing. The combined techniques demonstrate that B diffuses out of CoFeB electrodes into Ta interstitial sites rather than MgO after annealing, and CoFe bonds atomically to MgO grains with an epitaxial orientation relationship by forming Fe(Co)-O bonds, yet without incorporation of CoFe in MgO. These findings afford a comprehensive perspective on structure and chemistry of MTJs, helping to develop high-performance spintronic devices by atomistic design.

  18. An exploratory study of high school students' conceptions of atomic and cellular structure and the relationship between atoms and cells

    NASA Astrophysics Data System (ADS)

    Roland, Elizabeth Anne Edwards

    Constructivist learning theory is based upon the tenets that students come to learning experiences with prior knowledge and experiences that the learner will choose from to make sense of the present situation. This leads to a mixture of understandings among students. This study proposed to reveal students' understanding of atomic structure and cell structure as well as the relationships between atoms and cells. High school students from one private school participated in a paper-and-pencil test to uncover conceptual understanding and content knowledge of atoms and cells. The 120 participants were from grades: 9 (13m, 15f), 10 (9m, 20f), 11 (21m, 17f), and 12 (17m, 8f). All 120 students took the paper-and-pencil test and 16 students (4 per grade) participated in a follow-up interview. Drawings were analyzed by individual characteristics then using groups of characteristics models classes were formed. Open-ended questions were scored holistically by rubric scores and then deconstructed into individual content statements. A limited number of findings follow. Students were more likely to draw a Bohr model. Freshmen were less likely to indicate living materials contained atoms and more likely to indicate forms of energy contained atoms. As students progressed through high school, details included in cells decreased. Students failed to recognize that the sum of the products from cell division will be larger than the original cell due to the two growth periods included in the division cycle. Students were often able to provide the correct yes or no answer to are atoms and cells similar, different, or related but the follow-up answers often included non-scientific conceptions. Recommendations include implementing instructional strategies that promote long-term retention of conceptual understanding and the underlying content knowledge. Design evaluation methods to monitor student understanding throughout a unit of study that go beyond traditional closed-ended questions

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

    PubMed

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

    2015-04-28

    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 ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα 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. PMID:25933773

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

    SciTech Connect

    Zhang, Hao; Zhong, Cheng; Wang, Xiaodong; Cao, Qingping; Jiang, Jian-Zhong E-mail: jack.douglas@nist.gov; Douglas, Jack F. E-mail: jack.douglas@nist.gov; Zhang, Dongxian

    2015-04-28

    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 ΔG{sub a} with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τ{sub α} 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.

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

    PubMed

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

    2015-04-28

    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 ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα 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.

  2. Earth's interdependent thermal, structural, and chemical evolution

    NASA Astrophysics Data System (ADS)

    Hofmeister, A.; Criss, R. E.

    2012-12-01

    The popular view that 30-55% of Earth's global power is primordial, with deep layers emanating significant power, rests on misunderstandings and models that omit magmatism and outgassing. These processes link Earth's chemical and thermal evolution, while creating layers, mainly because magmas transport latent heat and radioactive isotopes rapidly upwards. We link chemistry to heat flow, measured and theoretical, to understand the interior layering and workings. Quasi-steady state conditions describe most of Earth's history: (1) Accretion was cold and was not a source of deep heat. (2) Friction during core formation cannot have greatly heated the interior (thermodynamics plus buoyancy). (3) Conduction is the governing microscopic mechanism in the deep Earth. (4) Using well-constrained values of thermal conductivity (k), we find that homogeneously distributed radionuclides provide extremely high internal temperature (T) under radial symmetry. Moreover, for any given global power, sequestering heat producing elements into the upper mantle reduces Earth's central temperature by a factor of 10 from a homogeneous distribution. Hence, (5) core formation was a major cooling event. From modern determinations of k(T) we provide a reference conductive geotherm. Present-day global power of 30 TW from heat flux measurements and sequestering of heat producing elements in the upper mantle and transition zone, produces nearly isothermal T = 5300 K below 670 km, which equals experimentally determined freezing of pure Fe0 at the inner core boundary. Core freezing buffers the interior temperatures, while the Sun constrains the surface temperature, providing steady state conditions: Earth's deep interior is isothermal due to these constraints, low flux and high k. Our geotherms point to a stagnant lower mantle and convection above 670 km. Rotational flattening cracks the brittle lithosphere, providing paths for buoyant magmas to ascend. Release of latent heat augments the conductive

  3. 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.

  4. Structure-dependent response of a chemiluminescence nitrogen detector for organic compounds with adjacent nitrogen atoms connected by a single bond.

    PubMed

    Yan, Bing; Zhao, Jiang; Leopold, Kyle; Zhang, Bin; Jiang, Guibin

    2007-01-15

    High-throughput screening (HTS) of chemical libraries is indispensable for drug discovery research. However, the HTS data quality for lead discovery, lead optimization, and quantitative structure activity relationship studies has been severely compromised due to the uncertain compound concentrations in screening plates. In order to address this issue, we compared various high-throughput technologies for quantification of compounds in microtiter plate format without the need for authentic compounds as standards and identified the chemiluminescence nitrogen detector (CLND) as the method of choice at the present time. However, the structure dependence of this detector has not been well studied. A proposed rule suggested that the only exception to equimolar response is for compounds that contain adjacent nitrogen atoms. The response should be zero when the adjacent nitrogen atoms are connected by a double bond and 0.5 when they are connected by a single bond. In this investigation, we studied a broad range of compounds with isolated and adjacent nitrogen atoms. We confirmed that compounds with isolated nitrogen atoms produce an equimolar response with a 15-20% variation depending on structures and compounds with adjacent nitrogen atoms connected by a double bond giving nearly zero response. We discovered that the CLND response for compounds containing adjacent nitrogen atoms that are connected with a single bond is highly structure dependent. Substitutions on the nitrogen atoms or nearby in the molecule can increase the CLND response to approach a value higher than the predicted value 0.5 (maximal value 0.82/nitrogen atom). Without substitution, much lower values than predicted (minimal value 0.0-0.08/nitrogen atom) are obtained. Therefore, the prediction of response of 0.5/nitrogen atom for compounds with adjacent nitrogen atoms connected by a single bond should be abandoned. Compounds with similar structures should be used to generate calibration curves for

  5. 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).

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

    PubMed Central

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

    2013-01-01

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

  7. Atomic and Electronic Structure of Polar Oxide Interfaces

    SciTech Connect

    Gajdardziska-Josifovska, Marija

    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.

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

    NASA Astrophysics Data System (ADS)

    Langhoff, Peter; Mills, Jeffrey; Boatz, Jerry

    2016-05-01

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

  9. Atomic spectral methods for molecular electronic structure calculations.

    PubMed

    Langhoff, P W; Boatz, J A; Hinde, R J; Sheehy, J A

    2004-11-15

    Theoretical methods are reported for ab initio calculations of the adiabatic (Born-Oppenheimer) electronic wave functions and potential energy surfaces of molecules and other atomic aggregates. An outer product of complete sets of atomic eigenstates familiar from perturbation-theoretical treatments of long-range interactions is employed as a representational basis without prior enforcement of aggregate wave function antisymmetry. The nature and attributes of this atomic spectral-product basis are indicated, completeness proofs for representation of antisymmetric states provided, convergence of Schrodinger eigenstates in the basis established, and strategies for computational implemention of the theory described. A diabaticlike Hamiltonian matrix representative is obtained, which is additive in atomic-energy and pairwise-atomic interaction-energy matrices, providing a basis for molecular calculations in terms of the (Coulombic) interactions of the atomic constituents. The spectral-product basis is shown to contain the totally antisymmetric irreducible representation of the symmetric group of aggregate electron coordinate permutations once and only once, but to also span other (non-Pauli) symmetric group representations known to contain unphysical discrete states and associated continua in which the physically significant Schrodinger eigenstates are generally embedded. These unphysical representations are avoided by isolating the physical block of the Hamiltonian matrix with a unitary transformation obtained from the metric matrix of the explicitly antisymmetrized spectral-product basis. A formal proof of convergence is given in the limit of spectral closure to wave functions and energy surfaces obtained employing conventional prior antisymmetrization, but determined without repeated calculations of Hamiltonian matrix elements as integrals over explicitly antisymmetric aggregate basis states. Computational implementations of the theory employ efficient recursive

  10. X-ray crystal structure analyses and atomic charges of color former and developer. I. Color developers

    NASA Astrophysics Data System (ADS)

    Okada, Kenji

    1996-07-01

    The crystal and molecular structures of 2,2-bis(4-hydroxyphenyl)propane (Bisphenol A, BPA) ( 1), benzyl 4-hydroxybenzoate ( 2), 1,7-bis(4-hydroxyphenylthio)-3,5-dioxaheptane ( 3) and 4-hydroxyphenyl 4-isopropoxyphenyl sulfone ( 4) have been determined by X-ray crystal structure analysis. Theoretical calculations of the steric hindrance and semiempirical quantum chemical calculations to determine the color characteristics have been carried out. It is clear that the energy barriers for the variation of the orientation of phenol group in 1 to 4 are due to steric hindrance caused by the other moiety and the peak profiles are due to repulsive interactions of the other moiety. Net atomic charges on the hydrogen of the OH group are larger than those on the other atoms in the molecules. This high electron charge of the para orientation will cause the different thermosensitivity and stabilization.

  11. Adsorption process, atomic geometry, electronic structure and stability of Si(001)/Te surface

    NASA Astrophysics Data System (ADS)

    Miwa, R. H.; Ferraz, A. C.

    2000-03-01

    The adsorption process, atomic geometry, electronic structure and energetics of a Si(001) surface covered by Te atoms have been studied using first-principles total-energy calculations. Our findings indicate that the Te atoms adsorb in the 'bridge' site on the surface Si dimer bond, in agreement with recent experimental results. We have also verified that the Si dimers (underneath adsorbed Te atoms) do not dissociate. The subsequent atomic exchange between the adsorbed Te atom and the surface Si atom, giving rise to an interdiffusion process of Te atoms towards Si substrate, is not an exothermic process. We have considered a number of possible coverages of Te atoms on Si(001) surface and our results indicate that for a coverage of one monolayer (1 ML), the Si(001)/Te-(1×1) surface represents the energetically more stable configuration. For a coverage of 2/3 ML, we have verified the formation of TeSiTe mixed trimers, in a (3×1) reconstructed surface. At 1/3 ML coverage, we have obtained the formation of Si dimers with a single Te atom at the surface, in a (3×1) reconstruction. Finally, for a coverage of 1/2 ML, we have obtained the formation of SiTe mixed dimers, in a (2×1) reconstructed surface, but the calculated formation energy indicates that this atomic configuration is not energetically favourable.

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

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

  13. EXAFS Measurements and Reverse Monte Carlo Modeling of Atomic Structure in Amorphous Ni80P20 Alloys

    SciTech Connect

    Luo,W.; Ma, E.

    2008-01-01

    This paper presents a full account of the EXAFS measurements and reverse Monte Carlo (RMC) modeling of the atomic arrangements and short-to-medium range structure in an amorphous Ni-P alloy, expanding on the description included in our recent publication. The atomic packing is analyzed from the standpoint of solute atoms. The short-to-medium range structure is discussed based on single-solute-centered quasi-equivalent clusters that form due to strong chemical short-range ordering, and the topological order is described in terms of both intra-cluster and inter-cluster dense packing for efficient filling of space. This analysis is also conducted for amorphous Ni80P20 prepared via different processing routes, to observe if the polyamorphism suggested in literature for amorphous Ni-P can be confirmed from the local structure perspective. The structural differences between the proposed polymorphs are apparently subtle and a full resolution of this issue is found to be beyond the capabilities of our EXAFS/RMC modeling approach. The amorphous structural features uncovered are also compared briefly with those observed before in amorphous alloy systems with positive heat of mixing.

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

    DOEpatents

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

    2004-07-13

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

  15. Atomic layer deposition and chemical vapor deposition precursor selection method application to strontium and barium precursors.

    PubMed

    Holme, Timothy P; Prinz, Fritz B

    2007-08-23

    A new selection method for atomic layer deposition (ALD) or chemical vapor deposition (CVD) precursors is proposed and tested. Density functional theory was used to simulate Sr and Ba precursors, and several precursors were selected and used to grow films via ALD as test cases for the precursor selection method. The precursors studied were M(x)2 (M = Sr, Ba; x = tetramethylheptanedionate (tmhd), acetylacetonate (acac), hexafluoroacetylacetonate (hfac), cyclopentadienyl (H(5)C(5)), pentamethylcyclopentadienyl (Me(5)C(5)), n-propyltetramethylcyclopentadienyl (PrMe(4)C(5)), tris(isopropylcyclopentadienyl) (Pr(3)(i)H(2)C(5)), tris(isopropylcyclopentadienyl)(THF) (Pr(3)(i)H(2)C(5))(OC(4)H(8)), tris(isopropylcyclopentadienyl)(THF)2 (Pr(3)(i)H(2)C(5))(OC(4)H(8))2, tris(tert-butylcyclopentadienyl) (Bu(3)(t)H(2)C(5)), tris(tert-butylcyclopentadienyl)(THF) (Bu(3)(t)H(2)C(5))(OC(4)H(8)), heptafluoro-2,2-dimethyl-3,5-octanedionate (fod)). The energy required to break bonds between the metal atom and the ligands was calculated to find which precursors react most readily. In the case of tmhd and Cp precursors, the energy required to break bonds in the precursor ligand was studied to evaluate the most likely mechanism of carbon incorporation into the film. Trends for Ba and Sr followed each other closely, reflecting the similar chemistry among alkaline earth metals. The diketonate precursors have stronger bonds to the metals than the Cp precursors, but weaker bonds within the ligand, explaining the carbon contamination found in experimentally grown films. Atomic layer deposition of SrO was tested with Sr(tmhd)2 and Sr(PrMe(4)Cp)2 and oxygen, ozone, and water as oxygen sources. No deposition was measured with tmhd precursors, and SrO films were deposited with PrMe(4)Cp with a source temperature of 200 degrees C and at substrate temperatures between 250 and 350 degrees C with growth rates increasing for oxygen sources in this order: O2 < H2O < O2 + H2O. The experimental results

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

    PubMed

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

    2014-01-28

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

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

    PubMed

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

    2012-05-01

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

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

    PubMed

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

    2011-01-20

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

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

    PubMed

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

    2013-01-01

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

  20. 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)

  1. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.

    PubMed

    Li, Yunqi; Roy, Ambrish; Zhang, Yang

    2009-08-20

    Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.

  2. Possible atomic structures responsible for the sub-bandgap absorption of chalcogen-hyperdoped silicon

    SciTech Connect

    Wang, Ke-Fan; Shao, Hezhu; Liu, Kong; Qu, Shengchun E-mail: wangyx@henu.edu.cn; Wang, Zhanguo; Wang, Yuanxu E-mail: wangyx@henu.edu.cn

    2015-09-14

    Single-crystal silicon was hyperdoped with sulfur, selenium, and tellurium using ion implantation and nanosecond laser melting. The hyperdoping of such chalcogen elements led to strong and wide sub-bandgap light absorption. Annealing the hyperdoped silicon, even at low temperatures (such as 200–400 °C), led to attenuation of the sub-bandgap absorption. To explain the attenuation process, we modeled it as chemical decomposition reaction from an optically absorbing structure to a non-absorbing structure. Attenuation of the experimental absorption coefficient was fit using the Arrhenius equation. From the fitted data, we extracted the reaction activation energies of S-, Se-, and T-hyperdoped silicon as 0.338 ± 0.029 eV, 0.471 ± 0.040 eV, and 0.357 ± 0.028 eV, respectively. We discuss these activation energies in terms of the bond energies of chalcogen–Si metastable bonds, and suggest that several high-energy interstitial sites, rather than substitutional sites, are candidates for the atomic structures that are responsible for the strong sub-bandgap absorption of chalcogen hyperdoped silicon.

  3. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

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

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

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

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

    ERIC Educational Resources Information Center

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

    2002-01-01

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

  6. [Erytrocyte membrane change due to the chemical treatment studied with atomic force microscopy].

    PubMed

    Targosz-Korecka, Marta; Sułowicz, Władysław; Czuba, Paweł; Szymoński, Marek; Miklaszewska, Monika; Pietrzyk, Jacek A; Rumian, Roman; Krawentek, Lidia

    2009-01-01

    The influence of some selected pharmacological compounds on the structure of human erythrocytes (red blood cells, RBCs) has been studied by means of an atomic force microscopy (AFM). The imaging has been done both in the air environment on the fixed cells, and in the liquid (physiological conditions). It was shown that RBCs are very sensitive to osmotic changes in the solution. Increased NaCl concentration in the solution to a value higher than 0.9% leads to the characteristic changes of the erythrocyte from a discoid-like shape to a very irregular one, the so-called "echinocyte", with a lot of ledges. After exposition on nifedipin the modification of the erythrocyte surface morphology was observed. Based on the contact and non-contact AFMs study the consecutive stages of RBCs surface modification were observed. Scanning electron microscopy pictures of erythrocytes were presented for comparison. PMID:20514900

  7. The atomic and electronic structure of nitrogen- and boron-doped phosphorene.

    PubMed

    Boukhvalov, Danil W

    2015-10-28

    First principles modeling of nitrogen- and boron-doped phosphorene demonstrates the tendency toward the formation of highly ordered structures. Nitrogen doping leads to the formation of -N-P-P-P-N- lines. Further transformation into -P-N-P-N- lines across the chains of phosphorene occurs with increasing band gap and increasing nitrogen concentration, which coincides with the decreasing chemical activity of N-doped phosphorene. In contrast to the case of nitrogen, boron atoms prefer to form -B-B- pairs with the further formation of -P-P-B-B-P-P- patterns along the phosphorene chains. The low concentration of boron dopants converts the phosphorene from a semiconductor into a semimetal with the simultaneous enhancement of its chemical activity. Co-doping of phosphorene by both boron and nitrogen starts from the formation of -B-N- pairs, which provides flat bands and further transformation of these pairs into hexagonal BN lines and ribbons across the phosphorene chains.

  8. 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.

  9. Forgotten topological index of chemical structure in drugs.

    PubMed

    Gao, Wei; Siddiqui, Muhammad Kamran; Imran, Muhammad; Jamil, Muhammad Kamran; Farahani, Mohammad Reza

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs. PMID:27275112

  10. Chemical composition in relation with biomass ash structure

    NASA Astrophysics Data System (ADS)

    Holubcik, Michal; Jandacka, Jozef

    2014-08-01

    Biomass combustion can be more complicated like combustion of fossil fuels because it is necessary to solve problems with lower ash melting temperature. It can cause a lot of problems during combustion process. Chemical composition of biomass ash has great impact on sinters and slags creation in ash because it affects structure of heated ash. In this paper was solved relation between chemical composition and structure of heated ash from three types of biomass (spruce wood, miscanthus giganteus and wheat straw). Amount of SiO2, CaO, MgO, Al2O3 and K2O was determined. Structure of heated ash was optically determined after heating to 1000 °C or 1200 °C. Results demonstrated that chemical composition has strong effect on structure and color of heated ash.

  11. Increase in the power of lasing on atomic and ion transitions in chemical elements

    SciTech Connect

    Klimkin, V M; Sokovikov, V G

    2007-02-28

    A method for increasing the power of pulsed lasing on atomic and ion transitions in chemical elements obtained by the conversion of the UV radiation of excimer lasers in cells with metal vapours is studied. A part of UV radiation transmitted through a cell with metal vapour is used for pumping a dye solution in such a way that the cell converter with metal vapour represents a master oscillator, while the dye cell represents an amplifier. The study is performed by the example of amplification of weak spectral components of radiation from a XeCl* laser converted in mercury and barium vapours. In the amplifying stage the longitudinal pumping of the dye is used and a scheme for suppressing self-excitation is employed. It is found by selecting dyes that the alcohol solution of uranin is nearly optimal for amplification of the 546.1-nm laser line of mercury, while the best results in amplification of the 533-nm and 648.2-nm laser lines of barium were obtained by using alcohol solutions of rhodamine 6G and oxazine 17, respectively. The power of the 546.1-nm mercury line was increased by an order of magnitude, while the power of the 533-nm and 648.2-nm lines of barium - almost by a factor of twenty-five. (lasers)

  12. Reaction of atomically clean aluminum and chemically modified aluminum with alkyl halides

    SciTech Connect

    Chen, J.G.; Beebe, T.P. Jr.; Crowell, J.E.; Yates, J.T. Jr.

    1987-03-18

    The interaction of methyl halides with an atomically clean A(111) surface has been investigated using high-resolution electron energy loss spectroscopy (EELS), Auger electron spectroscopy (AES), and temperature programmed desorption (TPD). CH/sub 3/I adsorbs on A(111) both molecularly and dissociatively at 150 K; adsorbed CH/sub 3/I decomposes to CH/sub (a)/ and I/sub (a)/ in the temperature range of 250-450 K. No surface reaction of CH/sub 3/Cl or CH/sub 3/Br with clean or chemically modified Al(111) was observed, and a reactive sticking coefficient of < 10/sup -5/ was estimated in the temperature range of 135-500 K (CH/sub 3/Cl) or at 150 K (CH/sub 3/Br). Reasons for the reactivity differences of the methyl halides toward the Al(111) surface are discussed. These findings on Al, and their implication in Grignard reaction mechanisms, are compared with recent studies by another group on a Mg surface.

  13. Determination of cadmium in water samples by fast pyrolysis-chemical vapor generation atomic fluorescence spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Jingya; Fang, Jinliang; Duan, Xuchuan

    2016-08-01

    A pyrolysis-vapor generation procedure to determine cadmium by atomic fluorescence spectrometry has been established. Under fast pyrolysis, cadmium ion can be reduced to volatile cadmium species by sodium formate. The presence of thiourea enhanced the efficiency of cadmium vapor generation and eliminated the interference of copper. The possible mechanism of vapor generation of cadmium was discussed. The optimization of the parameters for pyrolysis-chemical vapor generation, including pyrolysis temperature, amount of sodium formate, concentration of hydrochloric acid, and carrier argon flow rate were carried out. Under the optimized conditions, the absolute and concentration detection limits were 0.38 ng and 2.2 ng ml- 1, respectively, assuming that 0.17 ml of sample was injected. The generation efficiency of was 28-37%. The method was successfully applied to determine trace amounts of cadmium in two certified reference materials of Environmental Water (GSB07-1185-2000 and GSBZ 50009-88). The results were in good agreement with the certified reference values.

  14. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    PubMed

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  15. Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.

    PubMed

    Ismer, Jochen; Rose, Alexander S; Tiemann, Johanna K S; Goede, Andrean; Rother, Kristian; Hildebrand, Peter W

    2013-01-01

    Voronoia4RNA (http://proteinformatics.charite.de/voronoia4rna/) is a structural database storing precalculated atomic volumes, atomic packing densities (PDs) and coordinates of internal cavities for currently 1869 RNAs and RNA-protein complexes. Atomic PDs are a measure for van der Waals interactions. Regions of low PD, containing water-sized internal cavities, refer to local structure flexibility or compressibility. RNA molecules build up the skeleton of large molecular machineries such as ribosomes or form smaller flexible structures such as riboswitches. The wealth of structural data on RNAs and their complexes allows setting up representative data sets and analysis of their structural features. We calculated atomic PDs from atomic volumes determined by the Voronoi cell method and internal cavities analytically by Delaunay triangulation. Reference internal PD values were derived from a non-redundant sub-data set of buried atoms. Comparison of internal PD values shows that RNA is more tightly packed than proteins. Finally, the relation between structure size, resolution and internal PD of the Voronoia4RNA entries is discussed. RNA, protein structures and their complexes can be visualized by the Jmol-based viewer Provi. Variations in PD are depicted by a color code. Internal cavities are represented by their molecular boundaries or schematically as balls.

  16. Magneto-structural relationships for radical cation and neutral pyridinophane structures with intrabridgehead nitrogen atoms. An integrated experimental and quantum mechanical study.

    PubMed

    Williams, Ffrancon; Chen, Guo-Fei; Mattar, Saba M; Scudder, Paul H; Trieber, Dwight A; Saven, Jeffery G; Whritenour, David C; Cimino, Paola; Barone, Vincenzo

    2009-07-01

    An integrated experimental and computational approach was used to compare the properties of representative molecules containing intrabridgehead nitrogen atoms with those of the corresponding radical cations issuing from one-electron oxidation with the aim of unraveling the characteristics of the three-electron sigma-bonds formed in the open-shell species. From a quantitative point of view, last-generation density functional methods coupled with proper basis sets and, when needed, continuum models for describing bulk solvent effects confirm their reliability for the computation of structures and magnetic properties of organic free radicals. From an interpretative point of view, different hybridizations of nitrogen atoms tuned by their chemical environment lead to markedly different magnetic properties that represent reliable and sensitive probes of structural and electronic characteristics.

  17. Spectacular enhancement of thermoelectric phenomena in chemically synthesized graphene nanoribbons with substitution atoms.

    PubMed

    Zberecki, K; Swirkowicz, R; Wierzbicki, M; Barnaś, J

    2016-07-21

    We analyze theoretically the transport and thermoelectric properties of graphene nanoribbons of a specific geometry, which have been synthesized recently from polymers [Cai, et al., Nature, 2011, 466, 470]. When such nanoribbons are modified at one of the two edges by Al or N substitutions, they acquire a ferromagnetic moment localized at the modified edge. We present numerical results on the electronic structure and thermoelectric properties (including also spin thermoelectricity) of the modified nanoribbons. The results show that such nanoribbons can display large thermoelectric efficiency in certain regions of chemical potential, where the corresponding electric and spin figures of merit achieve unusually large values. The enhancement of thermoelectric efficiency follows from a reduced phonon heat conductance of the nanoribbons and from their peculiar electronic band structure. Thus, such nanoribbons are promising for practical applications in nanoelectronic and spintronic devices. PMID:27331357

  18. Spectacular enhancement of thermoelectric phenomena in chemically synthesized graphene nanoribbons with substitution atoms.

    PubMed

    Zberecki, K; Swirkowicz, R; Wierzbicki, M; Barnaś, J

    2016-07-21

    We analyze theoretically the transport and thermoelectric properties of graphene nanoribbons of a specific geometry, which have been synthesized recently from polymers [Cai, et al., Nature, 2011, 466, 470]. When such nanoribbons are modified at one of the two edges by Al or N substitutions, they acquire a ferromagnetic moment localized at the modified edge. We present numerical results on the electronic structure and thermoelectric properties (including also spin thermoelectricity) of the modified nanoribbons. The results show that such nanoribbons can display large thermoelectric efficiency in certain regions of chemical potential, where the corresponding electric and spin figures of merit achieve unusually large values. The enhancement of thermoelectric efficiency follows from a reduced phonon heat conductance of the nanoribbons and from their peculiar electronic band structure. Thus, such nanoribbons are promising for practical applications in nanoelectronic and spintronic devices.

  19. 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).

  20. Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

    ERIC Educational Resources Information Center

    Akaygun, Sevil

    2016-01-01

    Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

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

    SciTech Connect

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

    2013-08-01

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

  2. Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions.

    PubMed

    Volkmann, Niels

    2012-02-01

    A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  4. STM study of the atomic structure of the icosahedral Al-Cu-Fe fivefold surface

    NASA Astrophysics Data System (ADS)

    Cai, T.; Fournée, V.; Lograsso, T.; Ross, A.; Thiel, P. A.

    2002-04-01

    We use scanning tunneling microscopy (STM) to investigate the atomic structure of the icosahedral (i-) Al-Cu-Fe fivefold surface in ultra high vacuum (UHV). Studies show that large, atomically flat terraces feature many ten-petal ``flowers'' with internal structure. The observed flower patterns can be associated with features on Al rich dense atomic planes generated from two-dimensional cuts of bulk models based on x-ray and neutron diffraction experiments. The results confirm that the fivefold surface of i-Al-Cu-Fe corresponds to a bulk-terminated plane.

  5. Atomic Structure of Highly Strained BiFeO3 Thin Films

    SciTech Connect

    Rossell, M.D.; Erni, R.; Prange, Micah P; Idrobo Tapia, Juan C; Luo, Weidong; Zeches, R J; Pantelides, Sokrates T; Ramesh, R

    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.

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

    PubMed

    Aguado, Andrés; López, José M

    2010-09-01

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

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

    PubMed

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

    2015-08-19

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

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

    PubMed Central

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

    2015-01-01

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

  9. Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.

    PubMed

    Serrano, Jorge; Moros, Javier; Laserna, J Javier

    2015-03-01

    Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule. PMID:25668318

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

    PubMed

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

    2015-08-12

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

  11. Chemical Structure-Related Drug-Like Criteria of Global Approved Drugs.

    PubMed

    Mao, Fei; Ni, Wei; Xu, Xiang; Wang, Hui; Wang, Jing; Ji, Min; Li, Jian

    2016-01-12

    The chemical structure of a drug determines its physicochemical properties, further determines its ADME/Tox properties, and ultimately affects its pharmacological activity. Medicinal chemists can regulate the pharmacological activity of drug molecules by modifying their structure. Ring systems and functional groups are important components of a drug. The proportion of non-hydrocarbon atoms among non-hydrogen atoms reflects the heavy atoms proportion of a drug. The three factors have considerable potential for the assessment of the drug-like properties of organic molecules. However, to the best of our knowledge, there have been no studies to systematically analyze the simultaneous effects of the number of aromatic and non-aromatic rings, the number of some special functional groups and the proportion of heavy atoms on the drug-like properties of an organic molecule. To this end, the numbers of aromatic and non-aromatic rings, the numbers of some special functional groups and the heavy atoms proportion of 6891 global approved small drugs have been comprehensively analyzed. We first uncovered three important structure-related criteria closely related to drug-likeness, namely: (1) the best numbers of aromatic and non-aromatic rings are 2 and 1, respectively; (2) the best functional groups of candidate drugs are usually -OH, -COOR and -COOH in turn, but not -CONHOH, -SH, -CHO and -SO3H. In addition, the -F functional group is beneficial to CNS drugs, and -NH2 functional group is beneficial to anti-infective drugs and anti-cancer drugs; (3) the best R value intervals of candidate drugs are in the range of 0.05-0.50 (preferably 0.10-0.35), and R value of the candidate CNS drugs should be as small as possible in this interval. We envision that the three chemical structure-related criteria may be applicable in a prospective manner for the identification of novel candidate drugs and will provide a theoretical foundation for designing new chemical entities with good drug

  12. Role of preferential weak hybridization between the surface-state of a metal and the oxygen atom in the chemical adsorption mechanism.

    PubMed

    Kim, Yong Su; Jeon, Sang Ho; Bostwick, Aaron; Rotenberg, Eli; Ross, Philip N; Walter, Andrew L; Chang, Young Jun; Stamenkovic, Vojislav R; Markovic, Nenad M; Noh, Tae Won; Han, Seungwu; Mun, Bongjin Simon

    2013-11-21

    We report on the chemical adsorption mechanism of atomic oxygen on the Pt(111) surface using angle-resolved-photoemission spectroscopy (ARPES) and density functional calculations. The detailed band structure of Pt(111) from ARPES reveals that most of the bands near the Fermi level are surface-states. By comparing band maps of Pt and O/Pt, we identify that dxz (dyz) and dz(2) orbitals are strongly correlated in the surface-states around the symmetry point M and K, respectively. Additionally, we demonstrate that the s- or p-orbital of oxygen atoms hybridizes preferentially with the dxz (dyz) orbital near the M symmetry point. This weak hybridization occurs with minimal charge transfer. PMID:24097254

  13. Quantum Chemical Insight into the LiF Interlayer Effects in Organic Electronics: Reactions between Al Atom and LiF Clusters.

    PubMed

    Wu, Shui-Xing; Kan, Yu-He; Li, Hai-Bin; Zhao, Liang; Wu, Yong; Su, Zhong-Min

    2015-08-01

    It is well known that the aluminum cathode performs dramatically better when a thin lithium fluoride (LiF) layer inserted in organic electronic devices. The doping effect induced by the librated Li atom via the chemical reactions producing AlF3 as byproduct was previously proposed as one of possible mechanisms. However, the underlying mechanism discussion is quite complicated and not fully understood so far, although the LiF interlayer is widely used. In this paper, we perform theoretical calculations to consider the reactions between an aluminum atom and distinct LiF clusters. The reaction pathways of the Al-(LiF)n (n = 2, 4, 16) systems were discovered and the energetics were theoretically evaluated. The release of Li atom and the formation of AlF3 were found in two different chemical reaction routes. The undissociated Al-(LiF)n systems have chances to change to some structures with loosely bound electrons. Our findings about the interacted Al-(LiF)n systems reveal new insights into the LiF interlayer effects in organic electronics applications.

  14. Resolving the structure of Ti3C2Tx MXenes through multilevel structural modeling of the atomic pair distribution function

    DOE PAGES

    Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; Naguib, Michael; Gogotsi, Yury

    2015-12-08

    MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and a great promise in energy storage and many other applications. However, a complex surface chemistry and small coherence length has been an obstacle in some applications of MXenes, also limiting accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti3C2Tx MXenes (T standsmore » for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. The true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed third-generation structure model we present. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical and functional properties of Ti3C2-based MXenes. Furthermore, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical and other properties. We suggest that the multi-level structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.« less

  15. Measuring the Effect of Fuel Chemical Structure on Particulate and Gaseous Emissions using Isotope Tracing

    SciTech Connect

    Buchholz, B A; Mueller, C J; Martin, G C; Upatnicks, A; Dibble, R W; Cheng, S

    2003-09-11

    Using accelerator mass spectrometry (AMS), a technique initially developed for radiocarbon dating and recently applied to internal combustion engines, carbon atoms within specific fuel molecules can be labeled and followed in particulate or gaseous emissions. In addition to examining the effect of fuel chemical structure on emissions, the specific source of carbon for PM can be identified if an isotope label exists in the appropriate fuel source. Existing work has focused on diesel engines, but the samples (soot collected on quartz filters or combustion gases captured in bombs or bags) are readily collected from large industrial combustors as well.

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

    NASA Astrophysics Data System (ADS)

    Barton, Jeffrey Thomas

    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 films with excellent properties and unparalleled precision. This work describes the development of novel CVD and ALD processes to deposit a variety of materials. Hafnium oxide and zirconium oxide show promise as replacements for SiO 2 as gate dielectrics in future-generation transistors. These high-k materials would provide sufficient capacitance with layers thick enough to avoid leakage from tunneling. An ALD method is presented here for depositing conformal hafnium oxide from tetrakis-(diethylamido)hafnium and oxygen gas. A CVD method for depositing zirconium oxide from tetrakis-(dialkylamido)zirconium and either oxygen gas or water vapor is also described. The use of copper for interconnects in integrated circuits requires improved diffusion barrier materials, given its high diffusivity compared to the previously-used aluminum and tungsten. Tungsten nitride has a low resistivity among barrier materials, and can be deposited in amorphous films that are effective diffusion barriers in layers as thin as a few nanometers. Here we demonstrate CVD and plasma-enhanced CVD methods to deposit tungsten nitride films from bis-(dialkylamido)bis-( tert-butylimido)tungsten precursors and ammonia gas. Recent findings had shown uniform copper growth on tantalum silicate films, without the dewetting that usually occurs on oxide surfaces. Tantalum and tungsten silicates were deposited by a CVD reaction from the reaction of either tris-(diethylamido)ethylimido tantalum or bis-(ethylmethylamido)-bis-( tert-butylimido)tungsten with tris-(tert-butoxy)silanol. The ability of evaporated

  17. 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.

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

    SciTech Connect

    Oliver, Paul; Hibbert, Alan

    2011-05-11

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

  19. Simple Nuclear Structure in Cd-129111 from Atomic Isomer Shifts

    NASA Astrophysics Data System (ADS)

    Yordanov, D. T.; Balabanski, D. L.; Bissell, M. L.; Blaum, K.; Budinčević, I.; Cheal, B.; Flanagan, K.; Frömmgen, N.; Georgiev, G.; Geppert, Ch.; Hammen, M.; Kowalska, M.; Kreim, K.; Krieger, A.; Meng, J.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Rajabali, M. M.; Papuga, J.; Schmidt, S.; Zhao, P. W.

    2016-01-01

    Isomer shifts have been determined in 111-129>Cd by high-resolution laser spectroscopy at CERN-ISOLDE. The corresponding mean square charge-radii changes, from the 1 /2+ and the 3 /2+ ground states to the 11 /2- isomers, have been found to follow a distinct parabolic dependence as a function of the atomic mass number. Since the isomers have been previously associated with simplicity due to the linear mass dependence of their quadrupole moments, the regularity of the isomer shifts suggests a higher order of symmetry affecting the ground states in addition. A comprehensive description assuming nuclear deformation is found to accurately reproduce the radii differences in conjunction with the known quadrupole moments. This intuitive interpretation is supported by covariant density functional theory.

  20. Chemical Vapor Deposition Synthesized Atomically Thin Molybdenum Disulfide with Optoelectronic-Grade Crystalline Quality.

    PubMed

    Bilgin, Ismail; Liu, Fangze; Vargas, Anthony; Winchester, Andrew; Man, Michael K L; Upmanyu, Moneesh; Dani, Keshav M; Gupta, Gautam; Talapatra, Saikat; Mohite, Aditya D; Kar, Swastik

    2015-09-22

    The ability to synthesize high-quality samples over large areas and at low cost is one of the biggest challenges during the developmental stage of any novel material. While chemical vapor deposition (CVD) methods provide a promising low-cost route for CMOS compatible, large-scale growth of materials, it often falls short of the high-quality demands in nanoelectronics and optoelectronics. We present large-scale CVD synthesis of single- and few-layered MoS2 using direct vapor-phase sulfurization of MoO2, which enables us to obtain extremely high-quality single-crystal monolayer MoS2 samples with field-effect mobility exceeding 30 cm(2)/(V s) in monolayers. These samples can be readily synthesized on a variety of substrates, and demonstrate a high-degree of optoelectronic uniformity in Raman and photoluminescence mapping over entire crystals with areas exceeding hundreds of square micrometers. Because of their high crystalline quality, Raman spectroscopy on these samples reveal a range of multiphonon processes through peaks with equal or better clarity compared to past reports on mechanically exfoliated samples. This enables us to investigate the layer thickness and substrate dependence of the extremely weak phonon processes at 285 and 487 cm(-1) in 2D-MoS2. The ultrahigh, optoelectronic-grade crystalline quality of these samples could be further established through photocurrent spectroscopy, which clearly reveal excitonic states at room temperature, a feat that has been previously demonstrated only on samples which were fabricated by micro-mechanical exfoliation and then artificially suspended across trenches. Our method reflects a big step in the development of atomically thin, 2D-MoS2 for scalable, high-quality optoelectronics. PMID:26256639

  1. Chemical Vapor Deposition Synthesized Atomically Thin Molybdenum Disulfide with Optoelectronic-Grade Crystalline Quality.

    PubMed

    Bilgin, Ismail; Liu, Fangze; Vargas, Anthony; Winchester, Andrew; Man, Michael K L; Upmanyu, Moneesh; Dani, Keshav M; Gupta, Gautam; Talapatra, Saikat; Mohite, Aditya D; Kar, Swastik

    2015-09-22

    The ability to synthesize high-quality samples over large areas and at low cost is one of the biggest challenges during the developmental stage of any novel material. While chemical vapor deposition (CVD) methods provide a promising low-cost route for CMOS compatible, large-scale growth of materials, it often falls short of the high-quality demands in nanoelectronics and optoelectronics. We present large-scale CVD synthesis of single- and few-layered MoS2 using direct vapor-phase sulfurization of MoO2, which enables us to obtain extremely high-quality single-crystal monolayer MoS2 samples with field-effect mobility exceeding 30 cm(2)/(V s) in monolayers. These samples can be readily synthesized on a variety of substrates, and demonstrate a high-degree of optoelectronic uniformity in Raman and photoluminescence mapping over entire crystals with areas exceeding hundreds of square micrometers. Because of their high crystalline quality, Raman spectroscopy on these samples reveal a range of multiphonon processes through peaks with equal or better clarity compared to past reports on mechanically exfoliated samples. This enables us to investigate the layer thickness and substrate dependence of the extremely weak phonon processes at 285 and 487 cm(-1) in 2D-MoS2. The ultrahigh, optoelectronic-grade crystalline quality of these samples could be further established through photocurrent spectroscopy, which clearly reveal excitonic states at room temperature, a feat that has been previously demonstrated only on samples which were fabricated by micro-mechanical exfoliation and then artificially suspended across trenches. Our method reflects a big step in the development of atomically thin, 2D-MoS2 for scalable, high-quality optoelectronics.

  2. Atomic structure and dynamic behaviour of truly one-dimensional ionic chains inside carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Senga, Ryosuke; Komsa, Hannu-Pekka; Liu, Zheng; Hirose-Takai, Kaori; Krasheninnikov, Arkady V.; Suenaga, Kazu

    2014-11-01

    Materials with reduced dimensionality have attracted much interest in various fields of fundamental and applied science. True one-dimensional (1D) crystals with single-atom thickness have been realized only for few elemental metals (Au, Ag) or carbon, all of which showed very short lifetimes under ambient conditions. We demonstrate here a successful synthesis of stable 1D ionic crystals in which two chemical elements, one being a cation and the other an anion, align alternately inside carbon nanotubes. Unusual dynamical behaviours for different atoms in the 1D lattice are experimentally corroborated and suggest substantial interactions of the atoms with the nanotube sheath. Our theoretical studies indicate that the 1D ionic crystals have optical properties distinct from those of their bulk counterparts and that the properties can be engineered by introducing atomic defects into the chains.

  3. Atomic Models of Strong Solids Interfaces Viewed as Composite Structures

    NASA Astrophysics Data System (ADS)

    Staffell, I.; Shang, J. L.; Kendall, K.

    2014-02-01

    This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.

  4. Element-resolved atomic structure imaging of rocksalt Ge2Sb2Te5 phase-change material

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Zhang, Wei; Shen, Zhenju; Chen, Yongjin; Li, Jixue; Zhang, Shengbai; Zhang, Ze; Wuttig, Matthias; Mazzarello, Riccardo; Ma, Evan; Han, Xiaodong

    2016-05-01

    Disorder-induced electron localization and metal-insulator transitions (MITs) have been a very active research field starting from the seminal paper by Anderson half a century ago. However, pure Anderson insulators are very difficult to identify due to ubiquitous electron-correlation effects. Recently, an MIT has been observed in electrical transport measurements on the crystalline state of phase-change GeSbTe compounds, which appears to be exclusively disorder driven. Subsequent density functional theory simulations have identified vacancy disorder to localize electrons at the Fermi level. Here, we report a direct atomic scale chemical identification experiment on the rocksalt structure obtained upon crystallization of amorphous Ge2Sb2Te5. Our results confirm the two-sublattice structure resolving the distribution of chemical species and demonstrate the existence of atomic disorder on the Ge/Sb/vacancy sublattice. Moreover, we identify a gradual vacancy ordering process upon further annealing. These findings not only provide a structural underpinning of the observed Anderson localization but also have implications for the development of novel multi-level data storage within the crystalline phases.

  5. 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.

  6. Chemical ordering of Co and Ni in a W-(AlCoNi) crystalline approximant related to Al-Co-Ni decagonal quasicrystals studied by atomic resolution energy-dispersive X-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Yasuhara, Akira; Hiraga, Kenji

    2015-01-01

    A W-(AlCoNi) crystalline approximant, which is closely related to Al-Co-Ni decagonal quasicrystals, in an Al72.5Co20Ni7.5 alloy has been studied by atomic resolution energy-dispersive X-ray spectroscopy (EDS), in an instrument attached to a spherical aberration (Cs)-corrected scanning transmission electron microscope. On high-resolution EDS maps of Co and Ni elements, obtained by integrating many sets of EDS data taken from undamaged areas, chemical ordering of Co and Ni is clearly detected. In the structure of the W-(AlCoNi) phase, consisting of arrangements of transition-metal (TM) atoms located at vertices of pentagonal tilings and pentagonal arrangements of mixed sites (MSs) of TM and Al atoms, Co atoms occupy the TM atom positions with the pentagonal tiling and Ni is enriched in part of the pentagonal arrangements of MSs.

  7. 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.

  8. The role of radial nodes of atomic orbitals for chemical bonding and the periodic table.

    PubMed

    Kaupp, Martin

    2007-01-15

    The role of radial nodes, or of their absence, in valence orbitals for chemical bonding and periodic trends is discussed from a unified viewpoint. In particular, we emphasize the special role of the absence of a radial node whenever a shell with angular quantum number l is occupied for the first time (lack of "primogenic repulsion"), as with the 1s, 2p, 3d, and 4f shells. Although the consequences of the very compact 2p shell (e.g. good isovalent hybridization, multiple bonding, high electronegativity, lone-pair repulsion, octet rule) are relatively well known, it seems that some of the aspects of the very compact 3d shell in transition-metal chemistry are less well appreciated, e.g., the often weakened and stretched bonds at equilibrium structure, the frequently colored complexes, and the importance of nondynamical electron-correlation effects in bonding.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  11. Determination of bismuth in environmental samples by slurry sampling graphite furnace atomic absorption spectrometry using combined chemical modifiers.

    PubMed

    Dobrowolski, Ryszard; Dobrzyńska, Joanna; Gawrońska, 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(NO₃)₂ 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.

  12. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    PubMed

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  13. 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…

  14. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  15. Iron Isotope Fractionation Reveals Structural Change upon Microbial and Chemical Reduction of Nontronite NAu-1

    NASA Astrophysics Data System (ADS)

    Liu, K.; Wu, L.; Shi, B.; Smeaton, C. M.; Li, W.; Beard, B. L.; Johnson, C.; Roden, E. E.; Van Cappellen, P.

    2015-12-01

    Iron (Fe) isotope fractionations were determined during reduction of structural Fe(III) in nontronite NAu-1 biologically by Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA and chemically by dithionite. ~10% reduction was achieved in biological reactors, with similar reduction extents obtained by dithionite. We hypothesize that two stages occurred in our reactors. Firstly, reduction started from edge sites of clays and the produced Fe(II) partially remained in situ and partially was released into solution. Next aqueous Fe(II) adsorbed onto basal planes. The basal sorbed Fe(II) then undergoes electron transfer and atom exchange (ETAE) with octahedral Fe(III) in clays, with the most negative fractionation factor Δ56Febasal Fe(II)-structural Fe(III)of -1.7‰ when basal sorption reached a threshold value. Secondly, when the most reactive Fe(III) was exhausted, bioreduction significantly slowed down and chemical reduction was able to achieve 24% due to diffusion of small size dithionite. Importantly, no ETAE occurred between basal Fe(II) and structural Fe(III) due to blockage of pathways by collapsed clay layers. This two-stage process in our reduction experiments is distinctive from abiotic exchange experiments by mixing aqueous Fe(II) and NAu-1, where no structural change of clay would block ETAE between basal Fe(II) and structural Fe(III). The separation of reduction sites (clay edges) and sorption sites (basal planes) is unique to clay minerals with layered structure. In contrast, reduction and sorption occur on the same sites on the surfaces of Fe oxyhydroxides, where reduction does not induce structure change. Thus, the Fe isotope fractionations are the same for reduction and abiotic exchange experiments for Fe oxides. Our study reveals important changes in electron transfer and atom exchange pathways upon reduction of clay minerals by dissimilatory Fe reducing bacteria, which is prevalent in anoxic soils and sediments.

  16. Local atomic structure in equilibrium and supercooled liquid Zr(75.5)Pd(24.5).

    PubMed

    Mauro, N A; Fu, W; Bendert, J C; Cheng, Y Q; Ma, E; Kelton, K F

    2012-07-28

    Atomic structures were obtained in equilibrium and supercooled eutectic Zr(75.5)Pd(24.5) liquids by in situ high-energy synchrotron diffraction measurements using the beamline electrostatic levitation (BESL) technique, which provides a high-vacuum, containerless, environment. Reverse Monte Carlo fits to the x-ray static structure factors, constrained using partial pair correlation functions obtained from ab initio molecular dynamics simulations, indicate the presence of medium-range order (MRO) in the form of a strong tendency for Pd-Pd (solute-solute) avoidance. This order persists over the entire temperature range studied, from 170 °C above the equilibrium liquidus temperature to 263 °C below it. Further, a quantitative analysis of the atomic structures obtained indicates a modest degree of icosahedral-like local order around Pd atoms, with the clusters showing an increased tendency for face-sharing to form more extended structures with decreasing temperature. PMID:22852625

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-09-21

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

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

    PubMed

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

    2016-01-01

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

  20. First-principles calculation of atomic forces and structural distortions in strongly correlated materials.

    PubMed

    Leonov, I; Anisimov, V I; Vollhardt, D

    2014-04-11

    We introduce a novel computational approach for the investigation of complex correlated electron materials which makes it possible to evaluate interatomic forces and, thereby, determine atomic displacements and structural transformations induced by electronic correlations. It combines ab initio band structure and dynamical mean-field theory and is implemented with the linear-response formalism regarding atomic displacements. We apply this new technique to explore structural transitions of prototypical correlated systems such as elemental hydrogen, SrVO3, and KCuF3. PMID:24765993

  1. Atomic structure of interface states in silicon heterojunction solar cells.

    PubMed

    George, B M; Behrends, J; Schnegg, A; Schulze, T F; Fehr, M; Korte, L; Rech, B; Lips, K; Rohrmüller, M; Rauls, E; Schmidt, W G; Gerstmann, U

    2013-03-29

    Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism.

  2. Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy

    NASA Technical Reports Server (NTRS)

    Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.

    1991-01-01

    Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.

  3. The atomic and electronic structure of oxygen polyvacancies in anatase

    NASA Astrophysics Data System (ADS)

    Perevalov, T. V.; Islamov, D. R.; Saraev, A. A.

    2016-06-01

    We investigate oxygen-deficient anatase using quantum-chemical simulation within the density functional theory and X-ray photoelectron spectroscopy. It is demonstrated that etching of anatase with argon ions with an energy of 2.4 keV results in the formation of oxygen vacancies and polyvacancies at a concentration of approximately 1020 cm-3 in the crystal. It was found that the most energetically favorable spatial configuration of an oxygen polyvacancy is a three-dimensional chain in crystallographic direction [100] or [010]. The ability of oxygen polyvacancy in the form of a chain to act as a conductive filament and to participate in the resistive switching is discussed.

  4. Ultrathin film of nickel on the Cu (100) surface: Atomic structure and phonons

    SciTech Connect

    Borisova, Svetlana D. E-mail: rusina@ispms.tsc.ru Rusina, Galina G. E-mail: rusina@ispms.tsc.ru

    2014-11-14

    We investigated the structural and vibrational properties of the Cu (100) surface covered with ultrathin (1-5 ML) Ni films using interaction potential from the embedded atom method. The surface relaxation, dispersion relation and polarization of vibrational modes are discussed. Our calculated structural parameters are in good agreement with experimental results. The obtained vibrational frequencies compare well with the available experimental data.

  5. 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.

  6. Ultracold Chemical Reactions of a Single Rydberg Atom in a Dense Gas

    NASA Astrophysics Data System (ADS)

    Schlagmüller, Michael; Liebisch, Tara Cubel; Engel, Felix; Kleinbach, Kathrin S.; Böttcher, Fabian; Hermann, Udo; Westphal, Karl M.; Gaj, Anita; Löw, Robert; Hofferberth, Sebastian; Pfau, Tilman; Pérez-Ríos, Jesús; Greene, Chris H.

    2016-07-01

    Within a dense environment (ρ ≈1014 atoms /cm3 ) at ultracold temperatures (T <1 μ K ), a single atom excited to a Rydberg state acts as a reaction center for surrounding neutral atoms. At these temperatures, almost all neutral atoms within the Rydberg orbit are bound to the Rydberg core and interact with the Rydberg atom. We have studied the reaction rate and products for n S 87Rb Rydberg states, and we mainly observe a state change of the Rydberg electron to a high orbital angular momentum l , with the released energy being converted into kinetic energy of the Rydberg atom. Unexpectedly, the measurements show a threshold behavior at n ≈100 for the inelastic collision time leading to increased lifetimes of the Rydberg state independent of the densities investigated. Even at very high densities (ρ ≈4.8 ×1014 cm-3 ), the lifetime of a Rydberg atom exceeds 10 μ s at n >140 compared to 1 μ s at n =90 . In addition, a second observed reaction mechanism, namely, Rb2+ molecule formation, was studied. Both reaction products are equally probable for n =40 , but the fraction of Rb2+ created drops to below 10% for n ≥90 .

  7. 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.

  8. Weighted voting-based consensus clustering for chemical structure databases.

    PubMed

    Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

  9. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

  10. First-principles studies of BN sheets with absorbed transition metal single atoms or dimers: stabilities, electronic structures, and magnetic properties.

    PubMed

    Ma, Dongwei; Lu, Zhansheng; Ju, Weiwei; Tang, Yanan

    2012-04-11

    BN sheets with absorbed transition metal (TM) single atoms, including Fe, Co, and Ni, and their dimers have been investigated by using a first-principles method within the generalized gradient approximation. All of the TM atoms studied are found to be chemically adsorbed on BN sheets. Upon adsorption, the binding energies of the Fe and Co single atoms are modest and almost independent of the adsorption sites, indicating the high mobility of the adatoms and isolated particles to be easily formed on the surface. However, Ni atoms are found to bind tightly to BN sheets and may adopt a layer-by-layer growth mode. The Fe, Co, and Ni dimers tend to lie (nearly) perpendicular to the BN plane. Due to the wide band gap of the pure BN sheet, the electronic structures of the BN sheets with TM adatoms are determined primarily by the distribution of TM electronic states around the Fermi level. Very interesting spin gapless semiconductors or half-metals can be obtained in the studied systems. The magnetism of the TM atoms is preserved well on the BN sheet, very close to that of the corresponding free atoms and often weakly dependent on the adsorption sites. The present results indicate that BN sheets with adsorbed TM atoms have potential applications in fields such as spintronics and magnetic data storage due to the special spin-polarized electronic structures and magnetic properties they possess.

  11. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E.

    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.

  12. A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions

    NASA Astrophysics Data System (ADS)

    Hawthorne, Frank C.

    2012-11-01

    Here, I describe a theoretical approach to the structure and chemical composition of minerals based on their bond topology. This approach allows consideration of many aspects of minerals and mineral behaviour that cannot be addressed by current theoretical methods. It consists of combining the bond topology of the structure with aspects of graph theory and bond-valence theory (both long range and short range), and using the moments approach to the electronic energy density-of-states to interpret topological aspects of crystal structures. The structure hierarchy hypothesis states that higher bond-valence polyhedra polymerize to form the (usually anionic) structural unit, the excess charge of which is balanced by the interstitial complex (usually consisting of large low-valence cations and (H2O) groups). This hypothesis may be justified within the framework of bond topology and bond-valence theory, and may be used to hierarchically classify oxysalt minerals. It is the weak interaction between the structural unit and the interstitial complex that controls the stability of the structural arrangement. The principle of correspondence of Lewis acidity-basicity states that stable structures will form when the Lewis-acid strength of the interstitial complex closely matches the Lewis-base strength of the structural unit, and allows us to examine the factors that control the chemical composition and aspects of the structural arrangements of minerals. It also provides a connection between a structure, the speciation of its constituents in aqueous solution and its mechanism of crystallization. The moments approach to the electronic energy density-of-states provides a link between the bond topology of a structure and its thermodynamic properties, as indicated by correlations between average anion coordination number and reduced enthalpy of formation from the oxides for [6]Mg{/m [4]}Si n O( m+2 n) and MgSO4(H2O) n .

  13. 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

  14. Electronic structure and nuclear magnetic resonance chemical shift of solids and surfaces

    NASA Astrophysics Data System (ADS)

    Pfrommer, Bernd Georg

    Several different topics related to the electronic structure of solids and surfaces are discussed in this thesis. With the quasi-Newton algorithm for relaxing crystal structures and a new ab initio method to compute nuclear magnetic resonance (NMR) chemical shifts, numerical methods are developed and implemented to efficiently compute properties related to the electronic structure. These techniques are then applied to a range of different materials. The quasi-Newton method is used to study the recently discovered high-pressure R8 phase of silicon, and the fcc-hcp high-pressure structural phase transition of xenon. Using the pressure-induced magnetic phase transition of a model atomic hydrogen crystal as a test system, the accuracy of density functional theory in both the generalized gradient approximation (GGA) and the local spin density approximation (LSDA) is compared to variational quantum Monte Carlo (VQMC) calculations (1). Finally, for the first time, the NMR chemical shift of extended systems such as amorphous carbon and the hydrogenated diamond (111) surface are calculated from first principles. 1. In the first chapter, a model body-centered cubic (bcc) atomic hydrogen solid is studied using density functional theory in LSDA and GGA. 2. How a quasi-Newton method can be used to simultaneously relax the internal coordinates and lattice parameters of crystals under pressure is the subject of the second chapter. 3. Chapter three presents a detailed ab initio study of the electronic and structural properties of the recently discovered R8 phase of silicon. 4. In chapter four, the fcc-hcp high pressure structural phase transition of xenon is calculated. 5. Chapter five describes a theory for the ab initio computation of the NMR chemical shift in extended systems, using periodic boundary conditions. 6. In chapter six, the NMR chemical shift spectra of diamond, CVD diamond, and diamond-like amorphous carbon are computed from first principles. 7. Unexpected features

  15. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    DOE PAGES

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

  16. Structure of magnetic resonance in 87Rb atoms

    NASA Astrophysics Data System (ADS)

    Kozlov, A. N.; Zibrov, S. A.; Zibrov, A. A.; Yudin, V. I.; Taichenachev, A. V.; Yakovlev, V. P.; Tsygankov, E. A.; Zibrov, A. S.; Vassiliev, V. V.; Velichansky, V. L.

    2016-05-01

    Magnetic resonance at the F g = 1 rightleftarrows F e = 1 transition of the D 1 line in 87Rb has been studied with pumping and detection by linearly polarized radiation and detection at the double frequency of the radiofrequency field. The intervals of allowed values of the static and alternating magnetic fields in which magnetic resonance has a single maximum have been found. The structure appearing beyond these intervals has been explained. It has been shown that the quadratic Zeeman shift is responsible for the three-peak structure of resonance; the radiofrequency shift results in the appearance of additional extrema in resonance, which can be used to determine the relaxation constant Γ2. The possibility of application in magnetometry has been discussed.

  17. Electron spectra and structure of atomic and molecular clusters

    SciTech Connect

    Dehmer, Patricia M.

    1980-01-01

    Changes in electronic structure that occur during the stepwise transition from gas phase monomers to large clusters which resemble the condensed phase were studied. This basic information on weakly bound clusters is critical to the understanding of such phenomena as nucleation, aerosol formation, catalysis, and gas-to-particle conversion, yet there exist almost no experimental data on neutral particle energy levels or binding energies as a function of cluster size. (GHT)

  18. Flow injection-chemical vapor generation atomic fluorescence spectrometry hyphenated system for organic mercury determination: A step forward

    NASA Astrophysics Data System (ADS)

    Angeli, Valeria; Biagi, Simona; Ghimenti, Silvia; Onor, Massimo; D'Ulivo, Alessandro; Bramanti, Emilia

    2011-11-01

    Monomethylmercury and ethylmercury were determined on line using flow injection-chemical vapor generation atomic fluorescence spectrometry without neither requiring a pre-treatment with chemical oxidants, nor UV/MW additional post column interface, nor organic solvents, nor complexing agents, such as cysteine. Inorganic mercury, monomethylmercury and ethylmercury were detected by atomic fluorescence spectrometry in an Ar/H 2 miniaturized flame after sodium borohydride reduction to Hg 0, monomethylmercury hydride and ethylmercury hydride, respectively. The effect of mercury complexing agent such as cysteine, ethylendiaminotetracetic acid and HCl with respect to water and Ar/H 2 microflame was investigated. The behavior of inorganic mercury, monomethylmercury and ethylmercury and their cysteine-complexes was also studied by continuous flow-chemical vapor generation atomic fluorescence spectrometry in order to characterize the reduction reaction with tetrahydroborate. When complexed with cysteine, inorganic mercury, monomethylmercury and ethylmercury cannot be separately quantified varying tetrahydroborate concentration due to a lack of selectivity, and their speciation requires a pre-separation stage (e.g. a chromatographic separation). If not complexed with cysteine, monomethylmercury and ethylmercury cannot be separated, as well, but their sum can be quantified separately with respect to inorganic mercury choosing a suitable concentration of tetrahydroborate (e.g. 10 - 5 mol L - 1 ), thus allowing the organic/inorganic mercury speciation. The detection limits of the flow injection-chemical vapor generation atomic fluorescence spectrometry method were about 45 nmol L - 1 (as mercury) for all the species considered, a relative standard deviation ranging between 1.8 and 2.9% and a linear dynamic range between 0.1 and 5 μmol L - 1 were obtained. Recoveries of monomethylmercury and ethylmercury with respect to inorganic mercury were never less than 91%. Flow injection-chemical

  19. 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.

  20. 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.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    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.

  1. New horizons in chemical propulsion. [processes using free radicals, atomic hydrogen, excited species, etc

    NASA Technical Reports Server (NTRS)

    Cohen, W.

    1973-01-01

    After a review of the work of the late-Fifties on free radicals for propulsion, it is concluded that atomic hydrogen would provide a potentially large increase in specific impulse. Work conducted to find an approach for isolating atomic hydrogen is considered. Other possibilities for obtaining propellants of greatly increased capability might be connected with the technology for the generation of activated states of gases, metallic hydrogen, fuels obtained from other planets, and laser transfer of energy.

  2. 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.

  3. The effect of different chemical agents on human enamel: an atomic force and scanning electron microscopy study

    NASA Astrophysics Data System (ADS)

    Rominu, Roxana O.; Rominu, Mihai; Negrutiu, Meda Lavinia; Sinescu, Cosmin; Pop, Daniela; Petrescu, Emanuela

    2010-12-01

    PURPOSE: The goal of our study was to investigate the changes in enamel surface roughess induced by the application of different chemical substances by atomic force microscopy and scanning electron microscopy. METHOD: Five sound human first upper premolar teeth were chosen for the study. The buccal surface of each tooth was treated with a different chemical agent as follows: Sample 1 - 38% phosphoric acid etching (30s) , sample 2 - no surface treatment (control sample), 3 - bleaching with 37.5 % hydrogen peroxide (according to the manufacturer's instructions), 4 - conditioning with a self-etching primer (15 s), 5 - 9.6 % hydrofluoric acid etching (30s). All samples were investigated by atomic force microscopy in a non-contact mode and by scanning electron microscopy. Several images were obtained for each sample, showing evident differences regarding enamel surface morphology. The mean surface roughness and the mean square roughness were calculated and compared. RESULTS: All chemical substances led to an increased surface roughness. Phosphoric acid led to the highest roughness while the control sample showed the lowest. Hydrofluoric acid also led to an increase in surface roughness but its effects have yet to be investigated due to its potential toxicity. CONCLUSIONS: By treating the human enamel with the above mentioned chemical compounds a negative microretentive surface is obtained, with a morphology depending on the applied substance.

  4. 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 π 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.

  5. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling

    NASA Astrophysics Data System (ADS)

    Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

    2012-10-01

    Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.

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

    SciTech Connect

    Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; Cullen, David; Dass, Amala

    2015-04-03

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

  7. 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

  8. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    NASA Astrophysics Data System (ADS)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  9. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    PubMed Central

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  10. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures.

    PubMed

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-25

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  11. Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.

    PubMed

    Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

    2014-05-23

    The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding.

  12. Applications of the Cambridge Structural Database in chemical education.

    PubMed

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  13. Applications of the Cambridge Structural Database in chemical education.

    PubMed

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  14. Computational analysis of RNA structures with chemical probing data.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-06-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.

  15. 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

  16. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up.

    PubMed

    Hoelz, André; Glavy, Joseph S; Beck, Martin

    2016-07-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  17. 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 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα 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 13Cα. The orientations of the 13Cα 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 α-helical versus β-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 13Cα 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 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å 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-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

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

    SciTech Connect

    Pennycook, S.J.; Chisholm, M.F.; Nellist, P.D.; Browning, N.D.; Wallis, D.J.; Dickey, E.C.

    1996-12-31

    It is over 100 y since Lord Rayleigh first showed the differences between coherent and incoherent imaging in the light microscope, pointing out the advantages of the latter for resolution and image interpretation. The annular detector in the high-resolution STEM provides the same advantages for electrons, allowing incoherent imaging at atomic resolution, with image contrast strongly dependent on atomic number (Z). Since incoherent imaging has no phase problem, these Z-contrast images may be directly inverted to given the (projected) atomic positions. A maximum entropy method avoids false detail associated with direct deconvolution, and gives atomic coordinates to an accuracy of {+-}0.1{Angstrom}. Electron energy loss spectroscopy can provide valuable complementary information on light element bonding and the presence of impurities in specific atomic planes selected from the image. Together, these techniques have revealed some surprisingly complex interfacial structures. For surface studies, the 1.3{Angstrom} probe of the VG Microscopes HB603U STEM provides sufficient penetration and contrast to image single Pt and Rh atoms on {gamma}-alumina supports. Such images reveal preferred atomic configurations and allow possible surface adsorption sites to be deduced.

  19. Atomic Resolution Crystal Structure of NAD+-Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1

    PubMed Central

    Shabalin, I.G.; Polyakov, K.M.; Tishkov, V.I.

    2009-01-01

    The crystal structure of the ternary complex of NAD+-dependent formate dehydrogenase from the methylotrophic bacterium Moraxella sp. C-1 with the cofactor (NAD+) and the inhibitor (azide ion) was established at 1.1 A resolution. The complex mimics the structure of the transition state of the enzymatic reaction. The structure was refined with anisotropic displacitalicents parameters for non-hydrogen atoms to a R factor of 13.4%. Most of the nitrogen, oxygen, and carbon atoms were distinguished based on the analysis of the titalicperature factors and electron density peaks, with the result that side-chain rotamers of histidine residues and most of asparagine and glutamine residues were unambiguously determined. A comparative analysis of the structure of the ternary complex determined at the atomic resolution and the structure of this complex at 1.95 A resolution was performed. In the atomic resolution structure, the covalent bonds in the nicotinamide group are somewhat changed in agreitalicent with the results of quantum mechanical calculations, providing evidence that the cofactor acquires a bipolar form in the transition state of the enzymatic reaction. PMID:22649619

  20. Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures.

    PubMed

    Flatow, Daniel; Leelananda, Sumudu P; Skliros, Aris; Kloczkowski, Andrzej; Jernigan, Robert L

    2014-01-01

    Computing volumes and surface areas of molecular structures is generally considered to be a solved problem, however, comparisons presented in this review show that different ways of computing surface areas and volumes can yield dramatically different values. Volumes and surface areas are the most basic geometric properties of structures, and estimating these becomes especially important for large scale simulations when individual components are being assembled in protein complexes or drugs being fitted into proteins. Good approximations of volumes and surfaces are derived from Delaunay tessellations, but these values can differ significantly from those from the rolling ball approach of Lee and Richards (3V webserver). The origin of these differences lies in the extended parts and the less well packed parts of the proteins, which are ignored in some approaches. Even though surface areas and volumes from the two approaches differ significantly, their correlations are high. Atomic models have been compared, and the poorly packed regions of proteins are found to be most different between the two approaches. The Delaunay complexes have been explored for both fully atomic and for coarse-grained representations of proteins based on only C(α) atoms. The scaling relationships between the fully atomic models and the coarse-grained model representations of proteins are reported, and the lines fit yield simple relationships for the surface areas and volumes as a function of the number of protein residues and the number of heavy atoms. Further, the atomic and coarse-grained values are strongly correlated and simple relationships are reported.

  1. Spatially localized structures and oscillons in atomic Bose-Einstein condensates confined in optical lattices

    NASA Astrophysics Data System (ADS)

    Charukhchyan, M. V.; Sedov, E. S.; Arakelian, S. M.; Alodjants, A. P.

    2014-06-01

    We consider the problem of formation of small-amplitude spatially localized oscillatory structures for atomic Bose-Einstein condensates confined in two- and three-dimensional optical lattices, respectively. Our approach is based on applying the regions with different signs of atomic effective masses where an atomic system exhibits effective hyperbolic dispersion within the first Brillouin zone. By using the kp method we have demonstrated mapping of the initial Gross-Pitaevskii equation on nonlinear Klein-Gordon and/or Ginzburg-Landau-Higgs equations, which is inherent in matter fields within ϕ4-field theories. Formation of breatherlike oscillating localized states—atomic oscillons—as well as kink-shaped states have been predicted in this case. Apart from classical field theories atomic field oscillons occurring in finite lattice structures possess a critical number of particles for their formation. The obtained results pave the way to simulating some analogues of fundamental cosmological processes occurring during our Universe's evolution and to modeling nonlinear hyperbolic metamaterials with condensed matter (atomic) systems.

  2. Extended x-ray absorption fine structure studies of the atomic structure of nanoparticles in different metallic matrices.

    PubMed

    Baker, S H; Roy, M; Gurman, S J; Binns, C

    2009-05-01

    It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.

  3. Constructing Atomic-Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR RDCs

    PubMed Central

    Stelzer, Andrew C.; Frank, Aaron T.; Bailor, Maximillian H.; Andricioaei, Ioan; Al-Hashimi, Hashim M.

    2012-01-01

    A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned 13C/15N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions. PMID:19699798

  4. Atomic calligraphy: the direct writing of nanoscale structures using a microelectromechanical system.

    PubMed

    Imboden, Matthias; Han, Han; Chang, Jackson; Pardo, Flavio; Bolle, Cristian A; Lowell, Evan; Bishop, David J

    2013-07-10

    We present a microelectromechanical system (MEMS) based method for the resist-free patterning of nanostructures. Using a focused ion beam to customize larger MEMS machines, we fabricate apertures with features less than 50 nm in diameter on plates that can be moved with nanometer precision over an area greater than 20 × 20 μm(2). Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter positioned micrometers above the aperture enables high speed control of not only where but also when atoms are deposited. With this shutter, different-sized apertures can be opened and closed selectively for nanostructure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms. PMID:23782403

  5. Predicting modes of toxic action from chemical structure: an overview.

    PubMed

    Bradbury, S P

    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 consequence, there has been an evolution of QSAR development and application from that of a chemical-class perspective to one that is more consistent with assumptions regarding modes of toxic action. The assessment of a compound's likely mode of toxic action is critical for a correct QSAR selection; incorrect mode of action-based QSAR selections can result in 10- to 1000-fold errors in toxicity predictions. The establishment of toxicologically-credible techniques to assess mode of toxic action from chemical structure requires toxicodynamic knowledge bases that are clearly defined with regard to exposure regimes and biological models/endpoints and based on compounds that adequately span the diversity of chemicals anticipated for future applications. With such knowledge bases classification systems, including rule-based experts systems, have been established for use in predictive aquatic toxicology applications. PMID:8790641

  6. Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and Its Precursors on Metal Surfaces

    SciTech Connect

    Flynn, George W

    2015-02-16

    Executive Summary of Final Report for Award DE-FG02-88ER13937 Project Title: Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and its Precursors on Metal Surfaces Applicant/Institution: Columbia University Principal Investigator: George W. Flynn Objectives: The objectives of this project were to reveal the mechanisms and reaction processes that solid carbon materials undergo when combining with gases such as oxygen, water vapor and hydrocarbons. This research was focused on fundamental chemical events taking place on single carbon sheets of graphene, a two-dimensional, polycyclic carbon material that possesses remarkable chemical and electronic properties. Ultimately, this work is related to the role of these materials in mediating the formation of polycyclic aromatic hydrocarbons (PAH’s), their reactions at interfaces, and the growth of soot particles. Our intent has been to contribute to a fundamental understanding of carbon chemistry and the mechanisms that control the formation of PAH’s, which eventually lead to the growth of undesirable particulates. We expect increased understanding of these basic chemical mechanisms to spur development of techniques for more efficient combustion of fossil fuels and to lead to a concomitant reduction in the production of undesirable solid carbon material. Project Description: Our work treated specifically the surface chemistry aspects of carbon reactions by using proximal probe (atomic scale imaging) techniques to study model systems of graphene that have many features in common with soot forming reactions of importance in combustion flames. Scanning tunneling microscopy (STM) is the main probe technique that we used to study the interfacial structure and chemistry of graphene, mainly because of its ability to elucidate surface structure and dynamics with molecular or even atomic resolution. Scanning tunneling spectroscopy (STS), which measures the local density of quantum states over a single

  7. Organohelium compounds: structures, stabilities and chemical bonding analyses.

    PubMed

    Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

    2014-02-24

    This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology. PMID:24488791

  8. Atomic structure, alloying behavior, and magnetism in small Fe-Pt clusters

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Kumar, Vijay

    2015-09-01

    We report results of the atomic structure, alloying behavior, and magnetism in F emP tn(m +n =2 -10 ) clusters using projector augmented wave (PAW) pseudopotential method and spin-polarized generalized gradient approximation (GGA) for the exchange-correlation energy. These results are compared with those obtained by using HCTH exchange-correlation functional and LANL2DZ basis set in the Gaussian program and the overall trends are found to be similar. As in bulk Fe-Pt alloys, clusters with equal composition of Fe and Pt have the largest binding energy and the largest heat of nanoalloy formation for a given number of atoms in the cluster. There are some deviations due to the different symmetries in clusters and in cases where the total number of atoms is odd. The lowest energy isomers tend to maximize bonds between unlike atoms with Fe (Pt) atoms occupying high (low) coordination sites in the core (surface) of the cluster. The binding energy, heat of formation, and the second order difference of the total energy show F e2P t2 , F e4P t4 , and F e4P t6 clusters to be the most stable ones among the different clusters we have studied. The magnetic moments on Fe atoms are high in Pt-rich clusters as well as in small Fe-rich clusters and decrease as the aggregation of Fe atoms and the cluster size increases. The maximum value of the magnetic moments on Fe atoms is ˜3.8 μB , whereas for Pt atoms it is 1 μB. These are quite high compared with the values for bulk Fe as well as bulk FePt and F e3Pt phases while bulk Pt is nonmagnetic. There is significant charge transfer from those Fe atoms that interact directly with Pt atoms. We discuss the hybridization between the electronic states of Pt and Fe atoms as well as the variation in the magnetic moments on Fe and Pt atoms. Our results provide insight into the understanding of the nanoalloy behavior of Fe-Pt and we hope that this would help to design Fe based nanoalloys and their assemblies with high magnetic moments for

  9. 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.

  10. Mapping chemical disorder and ferroelectric distortions in the double perovskite compound Sr 2-x Gd x MnTiO6 by atomic resolution electron microscopy and spectroscopy.

    PubMed

    Biškup, Neven; Álvarez-Serrano, Inmaculada; Veiga, Maria; Rivera-Calzada, Alberto; Garcia-Hernandez, Mar; Pennycook, Stephen J; Varela, Maria

    2014-06-01

    In this work we report a study of the chemical and structural order of the double perovskite compound Sr 2-x Gd x MnTiO6 for compositions x=0, 0.25, 0.5, 0.75, and 1. A noticeable disorder at the B-site in the Mn and Ti sublattice is detected at the atomic scale by electron energy-loss spectroscopy for all x values, resulting in Mn-rich and Ti-rich regions. For x ≥ 0.75, the cubic unit cell doubles and lowers its symmetry because of structural rearrangements associated with a giant ferroelectric displacement of the perovskite B-site cation. We discuss this finding in the light of the large electroresistance observed in Sr 2-x Gd x MnTiO6, x ≥ 0.75.

  11. 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.

  12. Breit–Pauli atomic structure calculations for Fe XI

    SciTech Connect

    Aggarwal, Sunny Singh, Jagjit; Mohan, Man

    2013-11-15

    Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many of the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.

  13. Importance of the structural zinc atom for the stability of yeast alcohol dehydrogenase.

    PubMed Central

    Magonet, E; Hayen, P; Delforge, D; Delaive, E; Remacle, J

    1992-01-01

    Yeast alcohol dehydrogenase is a tetrameric enzyme containing zinc. Initially we confirmed the presence of two zinc atoms per subunit. Incubation of the enzyme with increasing concentrations of dithiothreitol, a method for partial chelation, allowed first the reduction of four disulphide bridges per enzyme, but eventually was sufficient to chelate the structural zinc atom without having any effect on the zinc located in the active site. The enzyme activity was not affected but the enzyme became very sensitive to heat denaturation. Chelation by EDTA was also performed. Given its location at an external position in the globular protein, protected in each subunit by one disulphide bridge, the results establish that the second zinc atom present on each enzymic subunit plays a prominent conformational role, probably by stabilizing the tertiary structure of yeast alcohol dehydrogenase. Recovery experiments were performed by incubation of the native enzyme, or the dithiothreitol-treated enzyme, with a small amount of Zn2+. A stabilization effect was found when the structural zinc was re-incorporated after its removal by dithiothreitol. In all cases a large increase in activity was also observed, which was much greater than that expected based on the amount of re-incorporated zinc atom, suggesting the re-activation of some inactive commercial enzyme which had lost some of its original catalytic zinc atoms. PMID:1445195

  14. Chemical compatibility of structural materials in alkali metals

    SciTech Connect

    Natesan, K.; Rink, D.L.; Haglund, R.

    1995-04-01

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments.

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

    SciTech Connect

    Schnohr, C. S.

    2015-09-15

    Compound semiconductor alloys such as In{sub x}Ga{sub 1−x}As, GaAs{sub x}P{sub 1−x}, or CuIn{sub x}Ga{sub 1−x}Se{sub 2} are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI{sub 2} chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family.

  16. Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Nieuwkoop, Andrew J.; Wylie, Benjamin J.; Franks, W. Trent; Shah, Gautam J.; Rienstra, Chad M.

    2009-09-01

    We show that quantitative internuclear N15-C13 distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of C13 sites in the β1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-C13 or 2-C13-glycerol as the C13 source. Quantitative dipolar trajectories are extracted from two-dimensional N15-C13 planes, in which ˜750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one C13 and several N15 each), yielding quantitative precision as good as 0.1 Å for ˜350 sites, better than 0.3 Å for another 150, and ˜1.0 Å for 150 distances in the range of 5-8 Å. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25±0.09 Å), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79±0.03 Å). Moreover, side chain heavy atoms are well restrained (0.76±0.06 Å total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure.

  17. Multiple doping structures of the rare-earth atoms in β-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

    2015-07-14

    The critical doping structures of rare-earth atoms in the promising β-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 β-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.

  18. Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms.

    PubMed

    Zhang, Lei; Sob, M; Wu, Zhe; Zhang, Ying; Lu, Guang-Hong

    2014-02-26

    We present a comprehensive study of the relationship between the ferromagnetism and the structural properties of Fe systems from three-dimensional ones to isolated atoms based on the spin-density functional theory. We have found a relation between the magnetic moment and the volume of the Voronoi polyhedron, determining, in most cases, the value of the total magnetic moment as a function of this volume with an average accuracy of ±0.28 μ(B) and of the 3d magnetic moment with an average accuracy of ±0.07 μ(B) when the atomic volume is larger than 22 ų. It is demonstrated that this approach is applicable for many three-dimensional systems, including high-symmetry structures of perfect body-centered cubic (bcc), face-centered cubic (fcc), hexagonal close-packed (hcp), double hexagonal close-packed (dhcp), and simple cubic (sc) crystals, as well as for lower-symmetry ones, for example atoms near a grain boundary (GB) or a surface, around a vacancy or in a linear chain (for low-dimensional cases, we provide a generalized definition of the Voronoi polyhedron). Also, we extend the validity of the Stoner model to low-dimensional structures, such as atomic chains, free-standing monolayers and surfaces, determining the Stoner parameter for these systems. The ratio of the 3d-exchange splitting to the magnetic moment, corresponding to the Stoner parameter, is found to be I(3d) = (0.998 ± 0.006) eV /μ(B) for magnetic moments up to 3.0 μ(B). Further, the 3d exchange splitting changes nearly linearly in the region of higher magnetic moments (3.0-4.0 μ(B)) and the corresponding Stoner exchange parameter equals I(h)(3d) = (0.272 ± 0.006) eV /μ(B). The existence of these two regions reflects the fact that, with increasing Voronoi volume, the 3d bands separate first and, consequently, the 3d magnetic moment increases. When the Voronoi volume is sufficiently large (≥22 ų), the separation of the 3d bands is complete and the magnetic moment reaches a value of 3.0

  19. Composition and conductance distributions of single GeSi quantum rings studied by conductive atomic force microscopy combined with selective chemical etching

    NASA Astrophysics Data System (ADS)

    Lv, Y.; Cui, J.; Jiang, Z. M.; Yang, X. J.

    2013-02-01

    Atomic force microscopy imaging combined with selective chemical etching is employed to quantitatively investigate three-dimensional (3D) composition distributions of single GeSi quantum rings (QRs). In addition, the 3D quantitative composition distributions and the corresponding conductance distributions are simultaneously obtained on the same single GeSi QRs by conductive atomic force microscopy combined with selective chemical etching, allowing us to investigate the correlations between the conductance and composition distributions of single QRs. The results show that the QRs’ central holes have higher Ge content, but exhibit lower conductance, indicating that the QRs’ conductance distribution is not consistent with their composition distribution. By comparing the topography, composition and conductance profiles of the same single QRs before and after different etching processes, it is found that the conductance distributions of GeSi QRs do not vary with the change of composition distribution. Instead, the QRs’ conductance distributions are found to be consistent with their topographic shapes, which can be supposed to be due to the shape determined electronic structures.

  20. Composition and conductance distributions of single GeSi quantum rings studied by conductive atomic force microscopy combined with selective chemical etching.

    PubMed

    Lv, Y; Cui, J; Jiang, Z M; Yang, X J

    2013-02-15

    Atomic force microscopy imaging combined with selective chemical etching is employed to quantitatively investigate three-dimensional (3D) composition distributions of single GeSi quantum rings (QRs). In addition, the 3D quantitative composition distributions and the corresponding conductance distributions are simultaneously obtained on the same single GeSi QRs by conductive atomic force microscopy combined with selective chemical etching, allowing us to investigate the correlations between the conductance and composition distributions of single QRs. The results show that the QRs' central holes have higher Ge content, but exhibit lower conductance, indicating that the QRs' conductance distribution is not consistent with their composition distribution. By comparing the topography, composition and conductance profiles of the same single QRs before and after different etching processes, it is found that the conductance distributions of GeSi QRs do not vary with the change of composition distribution. Instead, the QRs' conductance distributions are found to be consistent with their topographic shapes, which can be supposed to be due to the shape determined electronic structures.