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Sample records for atomic structure chemical

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

    PubMed

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

    2015-08-12

    The properties of two-dimensional (2D) materials depend strongly on the chemical and electrochemical activity of their surfaces. MXene, one of the most recent additions to 2D materials, shows great promise as an energy storage material. In the present investigation, the chemical and structural properties of individual Ti3C2 MXene sheets with associated surface groups are investigated at the atomic level by aberration corrected STEM-EELS. The MXene sheets are shown to exhibit a nonuniform coverage of O-based surface groups which locally affect the chemistry. Additionally, native point defects which are proposed to affect the local surface chemistry, such as oxidized titanium adatoms (TiOx), are identified and found to be mobile. PMID:26177010

  2. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    NASA Astrophysics Data System (ADS)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from the questionnaires were formed from the combination of items found to measure different aspects of a specific topic area using a reliability analysis. Average scores for the subgroups were compared to results obtained by students on the diagnostic instrument targeting the same topic area. There were no significant differences of the scores on both of the diagnostic instruments between the levels of undergraduate chemistry students. There were, however, significant differences on certain items of the diagnostic instruments between upper and lower class students. Additionally, misconceptions were identified within all levels of these undergraduate students that corresponded to previous results reported in the literature. A significant relationship was found to exist between the scores obtained on the two diagnostic instruments, as well as strong correlations between specific items and the total scores of the instruments. Response to the expectations questionnaires revealed no differences between the chemical industry and chemical academia, but did provide information concerning the chemical community's expectations of undergraduate chemistry students. Results indicate that undergraduate students majoring in chemistry have conceptions that are inconsistent with currently accepted scientific views. The findings also support the hypothesis that an understanding of the general structure of the atom and the roles played by electrons in molecular bonding and structure is important to an understanding of chemical properties and behavior.

  3. Chemical structure of descriptors with an active hydrogen atom in certain bioregulators.

    PubMed

    Kurchii, B A

    1996-01-01

    The chemical structure of descriptors (D) for some plant growth regulators (PGR), herbicides, pesticides and drugs is described. The presence of an active hydrogen atom in molecules is an essential factor determining biological activity of chemicals. The results obtained from the study of dependence existing between the structure of a certain substance and its biological activity may be used in designing of novel compounds which possess in biological activity. PMID:8755094

  4. 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

  5. Atomic Scale Structure and Chemical Composition across Order-Disorder Interfaces

    NASA Astrophysics Data System (ADS)

    Srinivasan, R.; Banerjee, R.; Hwang, J. Y.; Viswanathan, G. B.; Tiley, J.; Dimiduk, D. M.; Fraser, H. L.

    2009-02-01

    Through a combination of aberration-corrected high-resolution scanning transmission electron microscopy and three-dimensional atom probe tomography, the true atomic-scale structure and change in chemical composition across the complex order-disorder interface in a metallic alloy has been determined. The study reveals the presence of two interfacial widths, one corresponding to an order-disorder transition, and the other to the compositional transition across the interface, raising fundamental questions regarding the definition of the interfacial width in such systems.

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

    NASA Astrophysics Data System (ADS)

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondr?ek, Martin; Jelnek, Pavel; Sugimoto, Yoshiaki

    2015-07-01

    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.

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

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondr?ek, Martin; Jelnek, 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

  8. 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.

  9. Effect of local atomic and electronic structures on thermoelectric properties of chemically substituted CoSi

    NASA Astrophysics Data System (ADS)

    Hsu, C. C.; Pao, C. W.; Chen, J. L.; Chen, C. L.; Dong, C. L.; Liu, Y. S.; Lee, J. F.; Chan, T. S.; Chang, C. L.; Kuo, Y. K.; Lue, C. S.

    2014-05-01

    We report the effects of Ge partial substitution for Si on local atomic and electronic structures of thermoelectric materials in binary compound cobalt monosilicides (\\text{CoSi}_{1-x}\\text{Ge}_{x}\\text{:}\\ 0 \\le x \\le 0.15 ). Correlations between local atomic/electronic structure and thermoelectric properties are investigated by means of X-ray absorption spectroscopy. The spectroscopic results indicate that as Ge is partially substituted onto Si sites at x \\le 0.05 , Co in CoSi1-xGex gains a certain amount of charge in its 3d orbitals. Contrarily, upon further replacing Si with Ge at x \\ge 0.05 , the Co 3d orbitals start to lose some of their charge. Notably, thermopower is strongly correlated with charge redistribution in the Co 3d orbital, and the observed charge transfer between Ge and Co is responsible for the variation of Co 3d occupancy number. In addition to Seebeck coefficient, which can be modified by tailoring the Co 3d states, local lattice disorder may also be beneficial in enhancing the thermoelectric properties. Extended X-ray absorption fine structure spectrum results further demonstrate that the lattice phonons can be enhanced by Ge doping, which results in the formation of the disordered Co-Co pair. Improvements in the thermoelectric properties are interpreted based on the variation of local atomic and electronic structure induced by lattice distortion through chemical substitution.

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

    NASA Astrophysics Data System (ADS)

    Tsaparlis, Georgios

    1997-08-01

    With the development during the past few decades of chemical education (and in general of science education) as a research discipline, the place of structural theories and concepts has undergone strong criticism. The main reason for this criticism is the difficulty students encounter in dealing with these concepts. An explanation of this difficulty occurs if one examines the relevant concepts from different perspectives of science education, some of which many researchers consider as conflicting theories. The perspectives employed in this paper are (i) the Piagetian developmental perspective, (ii) the Ausbelian theory of meaningful learning, (iii) the information processing theory, and (iv) the alternative conceptions movement. The implications for teaching and curriculums are discussed with respect to the following: (a) Atoms and molecules as structural units of matter; (b) classification of substances according to their electrical character; (c) teaching introductory chemistry in three cycles: macro, representational and submicro; (d) the historical method of teaching; and (e) the modern quantum mechanical structural theories.

  11. 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…

  12. 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

  13. 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)

  14. The atomic structure of a bare buffer layer on SiC(0001) chemically resolved.

    PubMed

    de Lima, Luis Henrique; Handschak, Dominique; Schnbohm, Frank; Landers, Richard; Westphal, Carsten; de Siervo, Abner

    2014-11-14

    A chemical-specific photoelectron diffraction structure determination of a carbon rich buffer layer on SiC is reported. In addition to the long-range ripple of this surface, a local buckling in the hexagonal sublattice, which breaks the local range order symmetry, was unraveled. PMID:25245167

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  16. Atomic-Scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-Ray Spectroscopy

    SciTech Connect

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

    2014-02-04

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

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

    PubMed Central

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

    2014-01-01

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

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

    DOE PAGESBeta

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

    2014-01-01

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) has relativelymore » 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

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

    SciTech Connect

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

    2012-09-12

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

  20. 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.

  1. 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.

  2. 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

    2014-01-01

    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. PMID:25404060

  3. Atom Interferometric Measurements of Atomic Structure

    NASA Astrophysics Data System (ADS)

    Cronin, Alex

    2014-05-01

    Measurements of atomic polarizability, tune-out wavelengths, and van der Waals potentials made with an atom interferometer all serve as benchmark tests for atomic structure calculations. We used a Pritchard-type atom interferometer with phase shifts caused by electric field gradients in order to measure electric polarizabilities of Na, K, and Rb atoms. We reported ratios of static polarizabilities ?Rb/?Na = 1.959(5) with 0.3 percent uncertainty. We studied atomic phase shifts due to laser light in order to measure a tune-out wavelength (where there is a root in dynamic polarizability) for potassium atoms of ?zero = 768.9712 nm with 1.5 pm uncertainty. Finally, we measured atom-surface interactions with 2 percent precision, which was sufficient to detect the impact of Rb atomic core electrons on van der Waals potentials. These serve as independent benchmarks for atomic structure calculations because polarizability depends on sums of oscillator strengths, tune-out wavelengths depend on ratios of oscillator strengths, and atom-surface van der Waals interactions depend on sums of oscillator strengths weighted by resonance frequencies. Advances in the atom interferometry measurement techniques used for these and next generation measurements will be discussed.

  4. 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.

  5. 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. PMID:26000963

  6. 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…

  7. 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

  8. Mapping chemical/structural order in double perovskite Sr2-xGdxMnTiO6 by atomic resolution electron microscopy

    NASA Astrophysics Data System (ADS)

    Alvarez, Inmaculada; Biskup, Neven; Lopez, Maria; Garcia-Hernandez, Mar; Veiga, Luisa; Varela, Maria; UCM Collaboration; ORNL Collaboration; CSIC Collaboration

    2013-03-01

    We report on visualizing the chemical and structural order of double perovskite Sr2-xGdxMnTiO6. The antisite disorder of Mn and Ti is detected even at atomic scale at all x, resulting in Mn-rich and Ti-rich regions. For x ?0.75, the majority of manganese ions are in Mn3+ state and are centered in Jahn-Teller distorted MnO6octahedra. The Fourier transformation of atomic resolution images along the [110] zone axis reveals a superstructure that corresponds to the tilting of oxygen octahedra and that doubles the unit cell along [001]c. This superstructure is spatially inhomogeneous and coincides with the regions where B-site ion (Mn/Ti) is displaced along the [110] direction. We discuss these findings in the frame of possible local ferroelectricity and in the light of strong electroresistance observed in Sr1.25Gd0.75MnTiO6. Research at ORNL supported by the U.S. DOE-BES, Materials Sciences and Engineering Division, and also by ORNL's ShaRE User Program (sponsored by DOE-BES). Research at UCM supported by the ERC Starting Investigator Award and MAT2010-20117.

  9. 3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  10. Morphology and atomic structure of hydrogen-terminated Si(110)-(1 1) surfaces prepared by a wet chemical process

    NASA Astrophysics Data System (ADS)

    Matsushita, Stephane Yu; Kawamoto, Erina; Haga, Kenya; Yamada, Taro; Suto, Shozo

    2015-02-01

    We have measured the macroscopic and microscopic surface morphology of hydrogen-terminated Si(110)-(1 1) [H:Si(110)-(1 1)] surfaces prepared by an improved wet chemical process. The observations were performed by high-resolution electron-energy-loss spectroscopy (HREELS), low-energy-electron diffraction (LEED), and scanning tunneling microscopy (STM). At macroscopic scale, it was found that the surface is a mono-hydride terminated surface with a two-dimensional p2mg space group, thus, being a well-defined H:Si(110)-(1 1) surface. At microscopic scale, elongated terraces were observed along the [1 1 bar0] direction reflecting surface anisotropy. The terraces extend in frames with sizes up to a few micrometers. We discussed the macroscopic and microscopic surface morphology by combining our LEED and STM results.

  11. 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 five or more figure accuracy, without prior knowledge of the sample. These elements were again listed in the table with no further information, is., no mass number or atomic weight value. For the elements, which have no stable or long-lived isotopes, the data on radioactive half-lives and relative atomic masses for the nuclides of interest have been evaluated. The values of the half-lives their uncertainties are listed. The uncertainties are given in the last digit quoted of the half-life vale and shown in parentheses. The criteria for consideration of entries in this Table continue to be the same as it has been for over fifty years. It is the same criteria, which are used for all data that are evaluated for inclusion in the Atomic Weight's Table. If a report of data is published in a peer-reviewed journal, that data is evaluated and considered for inclusion in the appropriate table of the biennial report of the Atomic Weights Commission. As better data might become available in the future, the information that is contained in either of the tables may be modified. The information contained in the Table of Radioactive Elements should enable the user to calculate the atomic weight for any sample of radioactive material, which might have a variety of isotopic compositions. The atomic mass values have been taken from the 2003 Atomic Mass Table. Most of these half-lives have already been documented in various sources.

  12. 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. PMID:26524121

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

    ERIC Educational Resources Information Center

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

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

  14. Development of a TEM to study in situ structural and chemical changes at an atomic level during gas-solid interactions at elevated temperatures.

    PubMed

    Sharma, R; Weiss, K

    1998-08-15

    A Philips (Eindhoven, The Netherlands) 430 (300 keV) high resolution transmission electron microscope has been modified for in situ study of gas-solid interactions at elevated temperatures. This microscope can be best described as a synthesis, processing, and characterization laboratory for nano-size materials. A differentially pumped environmental cell (E-cell), capable of handling up to 20 torr of gas pressure, is fitted in the objective lens pole-piece gap. Single-tilt or double-tilt heating holders can be used to heat the samples up to 1,300 degrees C and 850 degrees C, respectively. The system can handle any non-corrosive gases such as H2, O2, N2, NH3, CO, water vapor. Electron diffraction patterns are used to elucidate the reaction path and to identify stable and/or metastable phases formed. Time, temperature, and pressure resolved electron diffraction patterns can also be used to estimate the thermodynamical conditions for the onset of a reaction and the stability range of different phases observed during the process can also be determined. The high resolution imaging capabilities enable elucidation of the basic structural mechanisms involved at near atomic level. The TV rate camera/video recording system is used to measure the reaction rates (kinetics of the reaction). A post projector energy filter (Gatan Imaging Filter, GIF) is attached at the bottom of the microscope in order to filter the inelastic scattering from the gases/thick samples as well as to obtain energy filtered images (chemical maps). The GIF can also be used as a parallel electron energy loss spectrometer (PEELS) to obtain changes in the sample composition during the reactions. The changes in the near-edge structures of PEELS spectrum is used to monitor changes in bonding and/or chemical environment elements during reaction. The chemical maps obtained can also be used to identify preferred regions of gas reactions, e.g., grain boundaries or surfaces, etc. Various modifications of the microscope are described in detail, with suitable examples showing the performance. PMID:9779832

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  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 introduction to atomic structure. It covers single and many electron systems, how to set up a basis set of wavefunctions for a many electron system, LS coupling, single and multi-electron Hamiltonians, the elementary Hartree-Fock approximation and how variational methods are used to determine the ground state energy and wavefunctions. The computational methods used in the codes are outlined and there are exercises at the end of each chapter. For a number of candidate atomic configurations, explicit examples are given that illustrate the physics, the approximations and the computational methods involved, and which provide the reader with the opportunity to check that he is using the suite of codes correctly. Relativistic effects are covered as perturbations with Breit-Pauli Hamiltonians. Isotope and hyperfine level splitting are also covered. A summary chapter covers allowed and forbidden bound-bound transitions. It describes how to set up the matrix elements for transition operators, and the determination of selection rules and computational aspects of the methods for allowed and forbidden lines. The last chapter provides a brief introduction to continuum transitions, including how to compute the necessary wavefunctions to calculate photoionization or photodetachment and autoionization processes. Several appendices provide a summary of angular momentum theory, an introduction to the Dirac and Breit-Pauli theory for relativistic processes, and a description of the input parameters needed to run the programs. In summary, the book is an almost essential guide to anyone planning to use the Multi-Configuration Hartree-Fock suite of codes. With this guide, even someone not thoroughly familiar with the details of the subject or the codes should be able to use them to obtain energy levels, wavefunctions and transition rates for any atomic system of interest. This book serves as a model example for the general computational physics community of how to document an important suite of codes for a wide number of researchers and really make the suite usable to the general physics c

  17. 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. PMID:19928752

  18. 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

  19. Ring structures of atoms and molecules

    NASA Astrophysics Data System (ADS)

    Osmera, Pavel; Werner, Pavel; Osmera, Pavel

    2015-09-01

    Knowledge of structure rules of the atomic nucleus and the properties of vortex electromagnetic field allow us to create relatively precisely the structures of individual atoms and molecules. Properties of atoms are largely described by the structure of their electron shells. However, the standard model of atoms does not allow define this structure exactly. New theory VFRT (vortex-fractal-ring-theory) can solve this lack. Theory VFRT uses fractal ring structure of the electron, the proton and the neutron, and can describe the inner structure of atomic nuclei. Fractal descriptions of Nature are very promising. The atomic nucleus can be built from the ring protons and neutrons. This new theory assumes that the arrangement of electron shells arises from the structure of the atomic nucleus. Electrons are not in orbit around the atomic nucleus, but each electron levitates with the corresponding proton of the nucleus. The levitation bond between the electron and the proton is formed by an electromagnetic vortex structure. Theory VFRT expands understanding of nature through a new perspective on the evolution of lifeless nature using a vortex, fractal and ring substructures with self-organization, from quarks, electrons, protons and neutrons, atoms, molecules, to the structure of complex organic compounds.

  20. 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)

  1. 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)

  2. Atomic surface structure of graphene and its buffer layer on SiC(0001): A chemical-specific photoelectron diffraction approach

    NASA Astrophysics Data System (ADS)

    de Lima, L. H.; de Siervo, A.; Landers, R.; Viana, G. A.; Goncalves, A. M. B.; Lacerda, R. G.; Hberle, P.

    2013-02-01

    We report a chemically specific x-ray photoelectron diffraction (XPD) investigation using synchrotron radiation of the thermally induced growth of epitaxial graphene on the 6H-SiC(0001). The XPD results show that the buffer layer on the SiC(0001) surface is formed by two domain regions rotated by 60? with respect to each other. The experimental data supported by a comprehensive multiple scattering calculation approach indicates the existence of a long-range ripple due the (6363)R30? reconstruction, in addition to a local range buckling in the (0001) direction of the two sublattices that form the honeycomb structure of the buffer layer. This displacement supports the existence of an sp2-to-sp3 rehybridization in this layer. For the subsequent graphene layer this displacement is absent, which can explain several differences between the electronic structures of graphene and the buffer layer.

  3. 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.

  4. Evolution of atomic structure during nanoparticle formation.

    PubMed

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M ; Christensen, Mogens; Bjesen, 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. PMID:25075335

  5. Evolution of atomic structure during nanoparticle formation

    PubMed Central

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. .; Christensen, Mogens; Bjesen, 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

  6. Orientation dependences of atomic structures in chemically heterogeneous Cu{sub 50}Ta{sub 50}/Ta glass-crystal interfaces

    SciTech Connect

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

    2015-01-07

    Molecular dynamics simulations based on an angular-dependent potential were performed to examine the structural properties of chemically heterogeneous interfaces between amorphous Cu{sub 50}Ta{sub 50} and crystalline Ta. Several phenomena, namely, layering, crystallization, intermixing, and composition segregation, were observed in the Cu{sub 50}Ta{sub 50} region adjacent to the Ta layers. These interfacial behaviors are found to depend on the orientation of the underlying Ta substrate: Layering induced by Ta(110) extends the farthest into Cu{sub 50}Ta{sub 50}, crystallization in the Cu{sub 50}Ta{sub 50} region is most significant for interface against Ta(100), while inter-diffusion is most pronounced for Ta(111). It turns out that the induced layering behavior is dominated by the interlayer distances of the underlying Ta layers, while the degree of inter-diffusion is governed by the openness of the Ta crystalline layers. In addition, composition segregations are observed in all interface models, corresponding to the immiscible nature of the Cu-Ta system. Furthermore, Voronoi polyhedra ?0,5,2,6? and ?0,4,4,6? are found to be abundant in the vicinity of the interfaces for all models, whose presence is believed to facilitate the structural transition between amorphous and body centered cubic.

  7. 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., ? = 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

  8. 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)

  9. 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)

  10. 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 ? 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.

  11. Chemical structure and dynamics: Annual report 1993

    SciTech Connect

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  12. Iodine Atoms Structured in (SN)x

    NASA Astrophysics Data System (ADS)

    Isoda, Seiji; Kawaguchi, Akiyoshi; Uemura, Akio; Katayama, Ken-ichi

    1985-05-01

    Electron diffraction pattern of iodinated (SN)x shows that iodine atoms are structured as a chain along the molecular axis of (SN)x. High resolution electron micrograph and its optical transform show that the crystalline lattice is severely distorted by iodination, but the (\\bar{1}02) plane is comparatively stable for iodine invasion. Iodine atoms are considered to be settled on the (\\bar{1}02) plane, where iodine atoms are structured as iodine chains and the two iodine chains tend to pair.

  13. Atomic and Electronic Structures of Zr Atomic Chains

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Shou; Li, Ai-Yu; Zhu, Zi-Zhong

    2004-09-01

    The atomic, binding and electronic structures of very thin Zr chains are studied by the first-principles density-functional method. The present calculations reveal that zirconium can form planar chains in zigzag, dimer and ladder structures. The zigzag geometry has two minima. The most stable geometry is the zigzag one with a unit cell rather close to equilateral triangles with four nearest neighbours. The other stable zigzag structure has a wide bond angle and allows for two nearest neighbours. An intermediary structure has the ladder geometry and is formed by two strands. The dimer structure is also found to be more stable than the truly linear chain. All these planar geometries are more favourable energetically than the linear chain. We also show that by going from Zr bulk to a Zr chain, the characters of bonding do not change significantly.

  14. New hexagonal structure for silicon atoms

    NASA Astrophysics Data System (ADS)

    Naji, S.; Belhaj, A.; Labrim, H.; Benyoussef, A.; El Kenz, A.

    2012-11-01

    Motivated by recent experimental and theoretical works on silicene and its derived materials and based on the exceptional Lie algebra G2 we propose a new hexagonal symmetry producing the (√3 × √3)R30° superstructure for silicon atoms. The principal hexagonal unit cell contains twelve atoms instead of the usual structure involving only six ones and it is associated with the G2 root system. In this silicon atom configuration appears two hexagons of unequal side length at angle 30°. This atomic structure can be tessellated to exhibit two superstructures (1 × 1) and (√3 × √3)R30° on the same atomic sheet. To test this double hexagonal structure, we perform a numerical study using Ab-initio calculations based on FPLO9.00-34 code. We observe that the usual silicon electronic properties and the lattice parameters of planar geometry are modified. In particular, the corresponding material becomes a conductor rather than zero gaped semi-conductor arising in single hexagonal structure. Although the calculation is done for silicon atoms, we expect that this structure could be adapted to all two dimensional materials having a single hexagonal flat geometry.

  15. 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.

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

    PubMed

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

    2014-01-01

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

  17. 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.

  18. 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)

  19. Quartet structure in atomic nuclei

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  20. Organic structure determination using atomic-resolution scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Gross, Leo; Mohn, Fabian; Moll, Nikolaj; Meyer, Gerhard; Ebel, Rainer; Abdel-Mageed, Wael M.; Jaspars, Marcel

    2010-10-01

    Nature offers a huge and only partially explored variety of small molecules with potential pharmaceutical applications. Commonly used characterization methods for natural products include spectroscopic techniques such as nuclear magnetic resonance spectroscopy and mass spectrometry. In some cases, however, these techniques do not succeed in the unambiguous determination of the chemical structure of unknown compounds. To validate the usefulness of scanning probe microscopy as an adjunct to the other tools available for organic structure analysis, we used the natural product cephalandole A, which had previously been misassigned, and later corrected. Our results, corroborated by density functional theory, demonstrate that direct imaging of an organic compound with atomic-resolution force microscopy facilitates the accurate determination of its chemical structure. We anticipate that our method may be developed further towards molecular imaging with chemical sensitivity, and will become generally useful in solving certain classes of natural product structures.

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

    SciTech Connect

    Dmowski, W.; Egami, T.; Swider-Lyons, K.; Dai, Sheng; Overbury, Steven {Steve} H

    2007-01-01

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

  2. Structure validation in chemical crystallography

    PubMed Central

    Spek, Anthony L.

    2009-01-01

    Automated structure validation was introduced in chemical crystallography about 12?years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

  3. 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.

  4. Molecular structures derived from deterministic theory of atomic structure

    SciTech Connect

    Lu, K.U.

    1996-07-01

    Based on the deterministic theory of the atomic structure, details of the electronic orbits and electronic configurations of H, He, Li, Be, B, C, N, O, and P atoms are calculated. The bond angles of water, benzene, Adenine, Thymine, Uracil, Guanine, and Cytosine are deduced. {copyright} {ital 1996 American Institute of Physics.}

  5. Atomic structure of Beta-tantalum nanocrystallites.

    PubMed

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

    2005-12-01

    The structural properties of beta-phase tantalum nanocrystallites prepared by room temperature magnetron sputter deposition on amorphous carbon substrates are investigated at atomic resolution. For these purposes spherical aberration-corrected high-resolution transmission electron microscopy is applied in tandem with the numerical retrieval of the exit-plane wavefunction as obtained from a through-focus series of experimental micrographs. We demonstrate that recent improvements in the resolving power of electron microscopes enable the imaging of the atomic structure of beta-tantalum with column spacings of solely 0.127 nm with directly interpretable contrast features. For the first time ever, we substantiate the existence of grain boundaries of 30 degrees tilt type in beta-Ta whose formation may be well explained by atomic agglomeration processes taking place during sputter deposition. PMID:17481332

  6. 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.

  7. Gas-phase ion/molecule isotope-exchange reactions: methodology for counting hydrogen atoms in specific organic structural environments by chemical ionization mass spectrometry

    SciTech Connect

    Hunt, D.F.; Sethi, S.K.

    1980-11-05

    Ion/molecule reactions are described which facilitate exchange of hydrogens for deuteriums in a variety of different chemical environments. Aromatic hydrogens in alkylbenzenes, oxygenated benzenes, m-toluidine, m-phenylenediamine, thiophene, and several polycyclic aromatic hydrocarbons and metallocenes are exchanged under positive ion CI conditions by using either D/sub 2/O, EtOD, or ND/sub 3/ as the reagent gas. Aromatic hydrogens, benzylic hydrogens, and hydrogens on carbon adjacent to carbonyl groups suffer exchange under negative ion CI conditions in ND/sub 3/, D/sub 2/O, and EtOD, respectively. A possible mechanism for the exchange process is discussed. 1 figure, 2 tables.

  8. Likelihood of atomatom 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 ? 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 ?-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 CH?Cl and OH?O are the preferred interactions in compounds containing both O and Cl. PMID:25995842

  9. 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.

  10. 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.

  11. Chemically induced magnetism in atomically precise gold clusters.

    PubMed

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

    2014-03-12

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

  12. Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765) structures: their long c axis and composite crystals, chemical twinning, and atomic site preferences.

    PubMed

    Schmidt, Joshua Teal; Lee, Stephen; Fredrickson, Daniel C; Conrad, Matthias; Sun, Junliang; Harbrecht, Bernd

    2007-01-01

    We present single-crystal studies of Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765), synchrotron powder studies of Pd(1-x)Cd(x), 0.755> or =x> or =0.800, and LDA-DFT and extended Hckel (eH) calculations on these or related phases. The two single-crystal structures have a, b, and c axis lengths of 9.9013(7), 14.0033(10), 37.063(24) and 9.9251(3), 14.0212(7), 60.181(3) A, respectively and they crystallize in the space groups Ccme and F2mm, respectively (solved as (3+1)-dimensional crystals their most convenient superspace group is Xmmm(00gamma)s00). The structures have two different structural components each with their own separate axis parameters. Powder data shows that the ratio of these separate axes (S/L) varies from 1.615 to 1.64, values near the golden mean (1.618). For Pd(0.213)Cd(0.787), different Pd and Cd site occupancies lead to variation in the R factor from 2.6-3.6 %. The site occupancy pattern with the lowest R factor (among the 26 820 variants studied) is the exact site occupancy pattern predicted by LDA-DFT parameterized eH Mulliken charge populations. The phases can be understood through a chemical twinning principle found in gamma-brass, the parent structure for the above phases (a relation with the MgCu(2) Laves phase is also noted). This twinning principle can be used to account for Cd and Pd site preferences. At the same time there is a clean separation among the Cd and Pd atoms for the two separate chain types at height b=0 and 1/2. These results indicate that Cd:Pd stoichiometry plays a role in phase stability. PMID:17091515

  13. Unraveling the Molecular Structures of Asphaltenes by Atomic Force Microscopy.

    PubMed

    Schuler, Bruno; Meyer, Gerhard; Pea, Diego; Mullins, Oliver C; Gross, Leo

    2015-08-12

    Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomic-resolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices. PMID:26170086

  14. 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.

  15. A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL).

    PubMed

    Trepalin, Sergei V; Yarkov, Alexander V; Pletnev, Igor V; Gakh, Andrei A

    2006-01-01

    A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI). PMID:17962754

  16. Chemical reactions of excited nitrogen atoms for short wavelength chemical lasers. Final technical report

    SciTech Connect

    Not Available

    1989-12-15

    Accomplishments of this program include the following: (1) Scalable, chemical generation of oxygen atoms by reaction of fluorine atoms and water vapor. (2) Production of nitrogen atom densities of 1 {times} 10{sup 1}5 cm{sup {minus}3} with 5% electrical efficiency by injecting trace amounts of fluorine into microwave discharged nitrogen. (3) Production of cyanide radicals by reaction of high densities of N atoms with cyanogen. (4) Production of carbon atoms by reaction of nitrogen atoms with cyanogen or with fluorine atoms and hydrogen cyanide. (5) Confirmation that the reaction of carbon atoms and carbonyl sulfide produces CS(a{sup 3} {Pi}{sub r}), as predicted by conservation of electron spin and orbital angular momenta and as proposed by others under another SWCL program. (6) Production of cyanide radicals by injection of cyanogen halides into active nitrogen and use as spectroscopic calibration source. (7) Demonstration that sodium atoms react with cyanogen chloride, bromide and iodide and with cyanuric trifluoride to produce cyanide radicals. (8) Demonstration of the potential utility of the fluorine atom plus ammonia reaction system in the production of NF(b{sup l}{Sigma}{sup +}) via N({sup 2}D) + F{sub 2}.

  17. Statistical thermodynamics and atomic structure of metallic glasses

    NASA Astrophysics Data System (ADS)

    Lass, Eric Andrew

    The purpose of this research is to develop an improved atomic scale understanding of the thermodynamic and kinetic behavior of a metallic glass. A realistic link between the macroscopic and atomic behavior of a metallic glass has not yet been achieved. The most widespread model describing the amorphous state, borrowed from the description of liquids, is the free volume model. It is primarily phenomenological, and does not explain the observed properties of a metallic glass in many aspects. This is because the idea of free volume in a metallic glass is fundamentally flawed in several respects. For example, unlike in the liquid phase, atomic mobility is limited in a glass, and requires thermal activation. Recently, structural models have been developed based on the idea of efficient atomic packing. While geometric these models successfully describe atomic structure, the underlying governing principles, thermodynamics, are mitigated or often neglected. The model described in this work takes advantage of the short-range atomic order inherent in metallic glasses. Developed around the central atoms model (CAM), it uses a statistical thermodynamic approach, and can more accurately describe the amorphous state on the atomic level. Each atom is considered to be surrounded by a "cage" of nearest-neighbors (NNs). In an ideal metallic glass, these cages are described by geometrically preferred configurations. The enthalpy of each possible NN cage is calculated from the energy of a cluster of two, three, or four atoms. The structure and thermodynamics of the metallic glass are dependent on the probability distributions of NN cages. Defects, termed bond deficiencies (BDs), are introduced into the model, and are analogous to vacancies in a crystalline material, except they occupy less volume, and cost less energy to create. These defects are considered to be thermodynamically stable, and provide the primary vehicle of atomic transport. CAM is applied to ideal and defect-containing binary, ternary, and quaternary Zr-and Fe-based metallic glass forming systems. In binary alloys, strong chemical short-range ordering (CSRO) effects are observed, occurring most prominently at compositions which experimentally show the best glass formability (GFA). Partial coordination numbers calculated using CAM correlate well with those determined by neutron and x-ray scattering experiments. Experimentally, Cu-Zr binary glasses exhibit a well-defined glass transition temperature, Tg, while Ni-Zr glasses do not. CAM suggests that the local atomic structure around Cu and Ni atoms is responsible for this difference. Fe-P alloys are shown to have a greater degree of Fe-Fe metallic bonding than Fe-B alloys, possibly elucidating the increased ductility in Fe-based glasses containing P. When BDs are included in CAM, the defect concentration surrounding one particular species in a system is observed to reach a constant value at Tg. Compositional changes in the values of T g predicted by CAM are in excellent agreement with those determined experimentally for both Cu- and Ni-Zr alloys. Using a combination of atomic structural differences and thermodynamic stability of the various phases, an understanding is gained of the difference between glass-forming and non-glass-forming systems. Similarly promising results are observed in ternary metallic glasses. CAM shows the CSRO around Cu atoms in ternary Cu-Zr-Al and Cu-Zr-Ti alloys reaches a maximum near compositions with high GFA. Similar to the binary system, the Zr BD concentration reaches a critical level at experimentally observed Tgs. The use of three-body atomic bonding energies is beneficial in describing ternary interactions in metallic glasses, compared to pair-wise bonding used in other models. Fe-(Mo)-B-P alloys exhibit increased glass stability over their binary counterparts. Replacing 1 at% Fe with Mo in Fe-B-P alloys shows increased stability of the amorphous phase, brought on by the creation of a strong network of Mo-metalloid bonding.

  18. Atomic structure evolution in bulk metallic glass under compressive stress

    NASA Astrophysics Data System (ADS)

    Wang, G.; Mattern, N.; Pauly, S.; Bednar?ik, J.; Eckert, J.

    2009-12-01

    The structural behavior of Cu64.5Zr35.5 bulk metallic glass under compressive stress was investigated by means of in situ high energy x-ray synchrotron diffraction. The topological and chemical short-range order of the glass changes reversible upon loading within the elastic range. The number density of Cu-(Zr,Cu) and Zr-Zr nearest neighbor atomic pairs becomes oriented along the loading direction. The macroscopic stress state is reflected by the medium-range order. The determination of the components of the strain tensor from the shift of the positions of the nearest neighbor distances is not possible due to the structure changes.

  19. Atomic-scale chemical quantification of oxide interfaces using energy-dispersive X-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Lu, Ping; Xiong, Jie; Van Benthem, Mark; Jia, Quanxi

    2013-04-01

    Atomic-scale quantification of chemical composition across oxide interfaces is important for understanding physical properties of epitaxial oxide nanostructures. Energy-dispersive X-ray spectroscopy (EDS) in an aberration-corrected scanning transmission electron microscope was used to quantify chemical composition across the interface of ferromagnetic La0.7Sr0.3MnO3 and antiferromagnetic BiFeO3 quantum structure. This research demonstrates that chemical composition at atomic columns can be quantified by Gaussian peak-fitting of EDS compositional profiles across the interface. Cation diffusion was observed at both A- and B-sublattice sites; and asymmetric chemical profiles exist across the interface, consistent with the previous studies.

  20. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grgoire 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.

  1. Structural Stabilities and Electronic Structures of Ga Atomic Chains

    NASA Astrophysics Data System (ADS)

    Wu, Shun-qing; Chen, Guo-zhen; Zhu, Zi-zhong

    2006-06-01

    The structural stabilities and electronic structures of Ga atomic chains are studied by the first-principles plane wave pseudopotential method based on the density functional theory. The present calculations show that gallium can form planar chains in linear-, zigzag- and ladder-form one-dimensional structures. The most stable one among the studied structures is the zigzag chain with a unit cell rather close to equilateral triangles with four nearest neighbors, and all the other structures are metastable. The relative structural stability, the energy bands and the charge densities are discussed based on the ab initio calculations and the Jahn-Teller effect.

  2. Diamagnetic shifts in atomic hyperfine structure

    SciTech Connect

    Lipson, S.J.

    1986-01-01

    A series of precision measurements of the hyperfine structure of the 5/sup 2/S/sub 1/2/ ground state of two isotopes of atomic rubidium in magnetic fields of up to 8 T was made using a laser optical-pumping technique. Observed departures from the predictions of the Breit-Rabi formula include the first measurement of a magnetically induced quadrupole hyperfine shift. A field dependence of the effective value of the nuclear-to-electronic g-factor ratio g/sub I//g/sub J/ was revealed, and the previous observation of a diamagnetic shift in dipole hyperfine structure in /sup 85/Rb was confirmed and extended to /sup 87/Rb. In order to distinguish among these effects, all of the ..delta..m/sub I/ = +/- 1 nuclear Zeeman transitions in both /sup 85/Rb and /sup 87/Rb were measured at each field. Four evacuated, wax-coated sample cells were used, containing natural isotopic abundance rubidium vapor. Perturbation theory is used to examine the effects of an external magnetic field on the ground-state hyperfine structure of an alkali atom. A Hamiltonian is developed and evaluated to yield a modified Breit-Rabi formula which provides an excellent fit to the experimental data. Approximate calculations performed using this model are in good agreement with the dipole and quadruple results. The shift in the g-factor ratio, on the other hand, is much larger than predicted.

  3. 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)

  4. Atomic structure and hierarchical assembly of a cross-? amyloid fibril.

    PubMed

    Fitzpatrick, Anthony W P; Debelouchina, Galia T; Bayro, Marvin J; Clare, Daniel K; Caporini, Marc A; Bajaj, Vikram S; Jaroniec, Christopher P; Wang, Luchun; Ladizhansky, Vladimir; Mller, Shirley A; MacPhee, Cait E; Waudby, Christopher A; Mott, Helen R; De Simone, Alfonso; Knowles, Tuomas P J; Saibil, Helen R; Vendruscolo, Michele; Orlova, Elena V; Griffin, Robert G; Dobson, Christopher M

    2013-04-01

    The cross-? amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of ?-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-? amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 ) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent ?-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. PMID:23513222

  5. 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.

  6. 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*. PMID:15740205

  7. Electronic structure of super heavy atoms revisited

    NASA Astrophysics Data System (ADS)

    Gitman, D. M.; Levin, A. D.; Tyutin, I. V.; Voronov, B. L.

    2013-03-01

    The electronic structure of an atom with Z ⩽ Zc = 137 can be described by the Dirac equation with the Coulomb field of a point charge Ze. It was believed that the Dirac equation with Z > Zc poses difficulties because the formula for the lower energy level of the Dirac Hamiltonian formally gives imaginary eigenvalues. But a strict mathematical consideration shows that difficulties with the electronic spectrum for Z > Zc do not arise if the Dirac Hamiltonian is correctly defined as a self-adjoint operator. In this paper, we briefly summarize the main physical results of that consideration in a form suitable for physicists with some additional new details and numerical calculations of the electronic spectra.

  8. 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.

  9. 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.

  10. 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 constraints. In approaching this challenge, we have developed a scheme for allocating the grid pressures to contacts inspired by the Hirshfeld charge analysis. Here, each voxel is allocated to the contact between the two atoms whose free atom electron densities show the largest values at that position. In this way, the differing sizes of atoms are naturally included in the division of space without resorting to empirical radii. The use of the improved DFT-CP method is illustrated through analyses of the applicability of radius ratio arguments to Laves phase structures and the structural preferences of AB5 intermetallics between the CaCu5 and AuBe5 structure types. PMID:26588306

  11. Application of magnetic atom induced bound states in superconducting gap for chemical identification of single magnetic atoms

    NASA Astrophysics Data System (ADS)

    Ji, Shuai-Hua; Zhang, Tong; Fu, Ying-Shuang; Chen, Xi; Jia, Jin-Feng; Xue, Qi-Kun; Ma, Xu-Cun

    2010-02-01

    Elemental identification at single atom level has been achieved with a low temperature scanning tunneling microscope. Magnetic atoms (Mn or Cr) adsorbed on a superconducting Pb substrate induce a set of well-defined resonance states inside the superconductor gap in scanning tunneling spectroscopy. We show that these localized characteristic bound states could serve as fingerprint for chemical identification of the corresponding atoms, similar to atomic/molecular spectra widely used in optical spectrometry. The experiment demonstrates a technique for element-resolved spectroscopy with simultaneous atomic-level spatial resolution. The influence of magnetic impurity concentration on the bound states has also been investigated.

  12. An atomic structure of human ?-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 ?-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 ?-secretase at 3.4 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 ?-secretase function. PMID:26280335

  13. 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.

  14. 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.

  15. 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.

  16. 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 (?), C 1s core-level shifts, resonance substituent parameters (?R), Lewis structures, and oxidation states of transition-metal complexes. PMID:26583402

  17. Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis.

    PubMed

    Erlacher, Matthias D; Chirkova, Anna; Voegele, Paul; Polacek, Norbert

    2011-05-01

    The protocol describes the site-specific chemical modification of 23S rRNA of Thermus aquaticus ribosomes. The centerpiece of this 'atomic mutagenesis' approach is the site-specific incorporation of non-natural nucleoside analogs into 23S rRNA in the context of the entire 70S ribosome. This technique exhaustively makes use of the available crystallographic structures of the ribosome for designing detailed biochemical experiments aiming at unraveling molecular insights of ribosomal functions. The generation of chemically engineered ribosomes carrying a particular non-natural 23S rRNA residue at the site of interest, a procedure that typically takes less than 2 d, allows the study of translation at the molecular level and goes far beyond the limits of standard mutagenesis approaches. This methodology, in combination with the presented tests for ribosomal functions adapted to chemically engineered ribosomes, allows unprecedented molecular insight into the mechanisms of protein biosynthesis. PMID:21527916

  18. Atomic resolution chemical bond analysis of oxygen in La2CuO4

    NASA Astrophysics Data System (ADS)

    Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

    2013-08-01

    The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

  19. 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.

  20. 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 BhatiaThornton numbernumber 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 ZrO 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 ZrO 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

  1. 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

  2. Topological Properties of Atomic Lead Film with Honeycomb Structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

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

    PubMed

    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

  4. 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

  5. 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)

  6. [Sunscreens--chemical structure and application].

    PubMed

    Klimowicz, Adam; Bielecka-Grzela, Stanisława; Czuba, Ewelina; Zejmo, Maria

    2007-01-01

    In the paper chemical structures and classification of active ingredients of sunscreens as physical or chemical filters are presented. Adequately selected to skin phototype sunscreen protects body against sunburn and prolonged sunlight exposure skin changes, induced by harmful ultraviolet radiation. PMID:18561604

  7. Linear complexions: Confined chemical and structural states at dislocations.

    PubMed

    Kuzmina, M; Herbig, M; Ponge, D; Sandlbes, S; Raabe, D

    2015-09-01

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states. PMID:26339026

  8. Linear complexions: Confined chemical and structural states at dislocations

    NASA Astrophysics Data System (ADS)

    Kuzmina, M.; Herbig, M.; Ponge, D.; Sandlbes, S.; Raabe, D.

    2015-09-01

    For 5000 years, metals have been mankinds most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  9. 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.

  10. 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 practical method that allows, on one hand, assignment of the observed spectroscopic features to precise structural pathways followed by the photoelectron within the mica structure and, on the other hand, clarification of the amount of electronic interactions and forces acting onto the individual atoms at the various structural sites.

  11. 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.

  12. 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 Mssbauer 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.

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

    NASA Astrophysics Data System (ADS)

    Kraj?, 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 responsible for the "dark stars" in the STM images. Since both are molecular adsorption sites, our study predicts that these characteristic features should be affected by CO adsorption.

  14. 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.

  15. 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.

  16. 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

  17. Atomic structures and oxygen dynamics of CeO2 grain boundaries.

    PubMed

    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

  18. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, AunPt38-n (0 ? n ? 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold's. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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…

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

    ERIC Educational Resources Information Center

    Moreno, Luis F.; Hincapi, Gina; Alzate, Mara 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

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

    ERIC Educational Resources Information Center

    Eilks, Ingo; Leerhoff, Gabriele

    2001-01-01

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

  7. 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.

  8. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  9. Relating Dynamic Properties to Atomic Structure in Metallic Glasses

    SciTech Connect

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

    2012-07-18

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

  10. Hydrogen plasma and atomic oxygen treatments of diamond: Chemical versus morphological effects

    SciTech Connect

    Shpilman, Z.; Gouzman, I.; Grossman, E.; Akhvlediani, R.; Hoffman, A.

    2008-06-09

    Chemical bonding and morphology of chemical vapor deposited diamond films were studied using high resolution electron energy loss spectroscopy and atomic force microscopy, following hydrogen plasma and atomic oxygen exposures. The hydrogen plasma exposure resulted in preferential etching of nondiamond carbon phases, selective etching of diamond facets, and termination of the diamond surfaces by sp{sup 3}-C-H species. Exposure to atomic oxygen, on the other hand, produced significant chemical changes resulting in oxidized hydrocarbon ill defined top layer, while the morphology of the surface remained almost unchanged.

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  15. Gas atomized chemical reservoir ODS ferritic stainless steels

    SciTech Connect

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

    2010-06-27

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

  16. Structural and Chemical Dynamics of Pyridinic-Nitrogen Defects in Graphene.

    PubMed

    Lin, Yung-Chang; Teng, Po-Yuan; Yeh, Chao-Hui; Koshino, Masanori; Chiu, Po-Wen; Suenaga, Kazu

    2015-11-11

    High density and controllable nitrogen doping in graphene is a critical issue to realize high performance graphene-based devices. In this paper, we demonstrate an efficient method to selectively produce graphitic-N and pyridinic-N defects in graphene by using the mixture plasma of ozone and nitrogen. The atomic structure, electronic structure, and dynamic behavior of these nitrogen defects are systematically studied at the atomic level by using a scanning transmission electron microscopy. The pyridinic-N exhibits higher chemical activity and tends to trap a series of transition metal atoms (Mg, Al, Ca, Ti, Cr, Mn, and Fe) as individual atoms. PMID:26488153

  17. Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

    NASA Astrophysics Data System (ADS)

    McBriarty, Martin E.

    Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

  18. 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,…

  19. 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,

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

    PubMed Central

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

    2015-01-01

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

  1. Quantum chemical studies of protein structure

    PubMed Central

    Oldfield, Eric

    2004-01-01

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

  2. 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.

  3. 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

  4. 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…

  5. Atomic-level structure and structure-property relationship in metallic glass

    NASA Astrophysics Data System (ADS)

    Cheng, Yongqiang

    One of the key tasks in material science is to understand the structure and structure-property relationship. The recently emerging bulk metallic glasses (BMGs) have demonstrated unique properties, especially intriguing mechanical properties such as their high strength and high propensity to localize deformation in shear bands. However, a comprehensive understanding of the structure of BMGs has been hindered by the complexity of these amorphous materials. Even more challenging is the structure-property correlation, which has been well established in crystals but has been seriously lacking for BMGs. This thesis presents a systematic study of the atomic-level structures of two representative BMGs, Cu-Zr and Cu-Zr-Al. The interpenetrating Cu-centered icosahedral clusters have been identified to be the primary structural feature. The fraction of icosahedra increases with increasing Cu or Al contents, and with decreasing cooling rate. The effect of Al in improving the icosahedral order is two-fold: the geometric effect due to the atomic-size mismatch and the chemical effect originated from the Cu-Al bond shortening. The resolved structure is used to study the structure-property relationship. The full icosahedra are found to be responsible for the dynamical slowdown of the supercooled liquid, which underlies the non-Arrhenius behavior, and explains the composition dependence of glass transition temperature, glass forming ability, and the room temperature strength. By simulated deformation, the initiation of plasticity and tendency for strain localization are also investigated. The full icosahedra are found to be the most rigid and resistant cluster with solid-like character, while the unstable clusters with liquid-like character serve as the fertile sites for initiating shear transformations. In addition, the elastic moduli are calculated and analyzed, and the origins of the different configurational dependence of shear modulus (G) and bulk modulus ( B) are explained. The Poisson's ratio, which scales with G/B, is then taken as a dimensionless indicator of the internal structural state. Combining the structure-plasticity and structure-elasticity relationships, the common structural origin of the elasticity-plasticity correlation is identified. More general implications are discussed by separating the effects of structural order and constituent elements (alloy composition), leading to a map that may guide the search for plastic BMGs.

  6. 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.

  7. Chemical mapping of mammalian cells by atom probe tomography

    PubMed Central

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

    2012-01-01

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

  8. Chemical profiling of silicon nitride structures

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  10. Relativistic many-body theory of atomic structures

    SciTech Connect

    Cheng, K.T.

    1983-01-01

    The main objective of this program is to improve our understanding of the effect of relativity and electron correlations on atomic processes. Current efforts include hyperfine structure (hfs) studies using the multiconfiguration Dirac-Fock (MCDF) technique. Atomic hfs are known to be sensitive to relativity and electron correlations, and provide important tests of relativistic atomic many-body theories. Preliminary results on the hfs of the 4f/sup 12/ /sup 3/H ground state of /sub 68/Er/sup 167/ are shown and are in good agreement with experiment. This shows that the MCDF technique can be an efficient and powerful method for atomic hfs studies. Further tests of this method are in progress. We are also studying the absorption spectra for Xe-like ions in the region of 4d ..-->.. nf, epsilonf transitions.

  11. 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).

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Osmera, Pavel

    2010-06-01

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

  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. 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. PMID:26955850

  17. Determination of the fine structure constant from atom interferometry

    NASA Astrophysics Data System (ADS)

    Guellati, Saida

    2012-06-01

    We report a new measurement of the atomic recoil using atom interferometry and Bloch oscillations (BO) in a vertical accelerated optical lattice. Such a measurement yields to a determination of h/mRb (mRb is the mass of Rubidium atom) which can be used to obtain a value of the fine structure constant following the equation: 2?=2R?cmRbmehmRb where the Rydberg constant R? and the mass ratio mRb/me are precisely known. The key idea to precisely determine the recoil velocity, is to transfer to the atoms as many recoils as possible and to measure their velocity variation. For this purpose we use an atomic interferometer consisting in two pairs of ?/2 pulses combined with Bloch oscillations. The first pair selects an atomic sub recoil velocity Ramsey pattern from an ultra cold Rb atoms sample. We then accelerate the atoms and give to the selected atoms up to 1000 recoils by means of Bloch oscillations. The final velocity distribution is measured by scanning the frequency of the second pair of ?/2 pulses. Following this scheme, we have performed in 2010 a measurement of ? with an uncertainty of 6.6 x10-10. Our final result is: 1/?= 137.035 999 037 (91). Using this determination, we obtain a theoretical value of the electron anomaly ae=0.001 159 652 181 13(84) which is in agreement with the experimental measurement of Gabrielse (ae=0.001 159 652 180 73(28)). The comparison of these values provides the most stringent test of the QED. Moreover, the precision is large enough to verify for the first time the muonic and hadronic contributions to this anomaly.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  19. Highly scalable, atomically thin WSe2 grown via metal-organic chemical vapor deposition.

    PubMed

    Eichfeld, Sarah M; Hossain, Lorraine; Lin, Yu-Chuan; Piasecki, Aleksander F; Kupp, Benjamin; Birdwell, A Glen; Burke, Robert A; Lu, Ning; Peng, Xin; Li, Jie; Azcatl, Angelica; McDonnell, Stephen; Wallace, Robert M; Kim, Moon J; Mayer, Theresa S; Redwing, Joan M; Robinson, Joshua A

    2015-02-24

    Tungsten diselenide (WSe2) is a two-dimensional material that is of interest for next-generation electronic and optoelectronic devices due to its direct bandgap of 1.65 eV in the monolayer form and excellent transport properties. However, technologies based on this 2D material cannot be realized without a scalable synthesis process. Here, we demonstrate the first scalable synthesis of large-area, mono and few-layer WSe2 via metal-organic chemical vapor deposition using tungsten hexacarbonyl (W(CO)6) and dimethylselenium ((CH3)2Se). In addition to being intrinsically scalable, this technique allows for the precise control of the vapor-phase chemistry, which is unobtainable using more traditional oxide vaporization routes. We show that temperature, pressure, Se:W ratio, and substrate choice have a strong impact on the ensuing atomic layer structure, with optimized conditions yielding >8 μm size domains. Raman spectroscopy, atomic force microscopy (AFM), and cross-sectional transmission electron microscopy (TEM) confirm crystalline monoto-multilayer WSe2 is achievable. Finally, TEM and vertical current/voltage transport provide evidence that a pristine van der Waals gap exists in WSe2/graphene heterostructures. PMID:25625184

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  2. Various atomic structures of monolayer silicene fabricated on Ag(111)

    NASA Astrophysics Data System (ADS)

    Liu, Zhi-Long; Wang, Mei-Xiao; Xu, Jin-Peng; Ge, Jian-Feng; Le Lay, Guy; Vogt, Patrick; Qian, Dong; Gao, Chun-Lei; Liu, Canhua; Jia, Jin-Feng

    2014-07-01

    Silicene, a monolayer of silicon atoms arranged in honeycomb lattices, can be synthesized on the Ag(111) surface, where it forms several superstructures with different buckling patterns and periodicity. Using scanning tunneling microscopy (STM), we obtained high-resolution images of silicene grown on Ag(111) and revealed its five phases, i.e., 4 4 - ?, 4 4 - ?, \\sqrt{13}\\times \\sqrt{13} - ?, \\sqrt{13}\\times \\sqrt{13} - ? and \\sqrt{13}\\times \\sqrt{13} - ?, some observed for the first time. For each of the phases, we have determined its atomic structure by comparing the atomic-resolution STM images with theoretical simulation results previously reported. We thus eliminate the contradictions of previous studies on the structural models of various silicene phases supported by the Ag(111) surface.

  3. 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

    2016-01-01

    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

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

    SciTech Connect

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

    2013-12-07

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

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Solid state 93Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. 93Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni60Nb35Sn5 has been found to be 100 ppm lower than that of Ni60Nb35Zr5 MG, which is correlated with their intrinsic fracture toughness. The evolution of 93Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.

  7. 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.

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

    SciTech Connect

    Not Available

    1981-03-01

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

  9. 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. PMID:26538495

  10. Understanding chemical expansion in perovskite-structured oxides.

    PubMed

    Marrocchelli, Dario; Perry, Nicola H; Bishop, Sean R

    2015-04-21

    In this work, chemical expansion in perovskite oxides was characterized in detail, motivated, inter alia, by a desire to understand the lower chemical expansion coefficients observed for perovskites in comparison to fluorite-structured oxides. Changes in lattice parameter and in local atomic arrangements taking place during compositional changes of perovskites, i.e., stoichiometric expansion, were investigated by developing an empirical model and through molecular dynamics and density functional theory atomistic simulations. An accurate empirical expression for predicting lattice constants of perovskites was developed, using a similar approach to previous reports. From this equation, analytical expressions relating chemical expansion coefficients to separate contributions from the cation and anion sublattices, assuming Shannon ionic radii, were developed and used to isolate the effective radius of an oxygen vacancy, rV. Using both experimental and simulated chemical expansion coefficient data, rV for a variety of perovskite compositions was estimated, and trends in rV were studied. In most cases, rV was slightly smaller than or similar to the radius of an oxide ion, but larger than in the fluorite structured materials. This result was in good agreement with the atomistic simulations, showing contractive relaxations of the closest oxide ions towards the oxygen vacancy. The results indicate that the smaller chemical expansion coefficients of perovskites vs. fluorites are largely due to the smaller change in cation radii in perovskites, given that the contraction around the oxygen vacancy appears to be less in this structure. Limitations of applicability for the model are discussed. PMID:25785684

  11. Emergent Chemical Mapping at Atomic-Column Resolution by Energy-Dispersive X-Ray Spectroscopy in an Aberration-Corrected Electron Microscope

    NASA Astrophysics Data System (ADS)

    Chu, M.-W.; Liou, S. C.; Chang, C.-P.; Choa, F.-S.; Chen, C. H.

    2010-05-01

    Chemical mapping at atomic-column resolution by energy-dispersive x-ray spectroscopy in a spherical aberration-corrected scanning transmission electron microscope (STEM) has been demonstrated for the 1.47- dumbbell structure in InGaAs. The structural imaging and the chemical information in the two-dimensional map are directly correlated. Comparisons with the other existing mapping techniques of STEM in conjunction with electron energy-loss spectroscopy were discussed from aspects of ionization interactions.

  12. 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.

  13. Atomic Structure and Properties of Extended Defects in Silicon

    SciTech Connect

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

    1998-10-15

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

  14. Local atomic structure of Ca-Mg-Zn metallic glasses

    NASA Astrophysics Data System (ADS)

    Senkov, O. N.; Miracle, D. B.; Barney, E. R.; Hannon, A. C.; Cheng, Y. Q.; Ma, E.

    2010-09-01

    The amorphous structure of four Ca60MgXZn40-X ( X=10 , 15, 20, and 25at.% ) ternary metallic glasses (MGs) has been investigated by neutron and x-ray diffraction, using Reverse Monte Carlo modeling to simulate the results. A critical analysis of the resultant models, corroborated by ab initio molecular-dynamics simulations, indicate that the glass structure for this system can be described as a mixture of Mg- and Zn-centered clusters, with Ca dominating in the first coordination shell of these clusters. A coordination number (CN) of 10 [with about 7 Ca and 3 (Mg+Zn) atoms] is most common for the Zn-centered clusters. CN=11 and 12 [with about 7-8 Ca and 4 (Mg+Zn) atoms] are most common for Mg-centered clusters. Fivefold bond configurations (pentagonal pyramids) dominate (60%) in the first coordination shell of the clusters, suggesting dense atomic packing. Bond-angle distributions suggest near-equilateral triangles and pentagonal bipyramids to be the most common nearest atom configurations. This is the systematic characterization of the structure of Ca-Mg-Zn MGs, a category of bulk MGs with interesting properties and intriguing applications. It is also the experimental verification of the principle of efficient packing of solute-centered clusters in ternary MGs.

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

    SciTech Connect

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

    2012-09-17

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

  16. 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.

  17. Effective charges of the valence shells on atoms of A15 chemical compounds

    NASA Astrophysics Data System (ADS)

    Kodess, B. N.; Massalimov, I. A.

    1983-08-01

    X-ray diffraction data are used to calculate the charges of the valence shells of Si and V in V 3Si. The subsequent integration of the deformation density (? def ( limit?) = ? exp( limit?) - ? at( limit?) indicates that the charges on Si atoms decrease and on V atoms increase in comparison with the charges on free atoms. The magnitude of charge transfer are compared to the results of self-consistent band structure calculation. The observed increase of charge for atom V may be associated with the compression of the 3d-shells of V in V 3Si.

  18. 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.

  19. 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.

  20. Stable atomic structure of NiTi austenite

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2014-08-01

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

  1. Degradation of High-k/Interface Layer Structures by H Atoms and Interface Engineering with O Atom Manipulation

    NASA Astrophysics Data System (ADS)

    Kato, K.; Hirano, I.; Matsushita, D.; Nakasaki, Y.; Mitani, Y.

    2011-12-01

    With regard to the growing numbers of H atoms in high-k/SiO2/Si systems, it is revealed through first principles calculations that degradation of high-k/interface layer structures has been found to occur from the interface layers by H atoms, even if the interface defects are terminated with H atoms by forming gas annealing. O termination is proposed to prevent this degradation. The effects of H and O atoms are verified by experimental analyses.

  2. 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.

  3. 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

  4. Modeling Protein Structure at Near Atomic Resolutions With Gorgon

    PubMed Central

    Baker, Matthew L.; Abeysinghe, Sasakthi S.; Schuh, Stephen; Coleman, Ross A.; Abrams, Austin; Marsh, Michael P.; Hryc, Corey F.; Ruths, Troy; Chiu, Wah; Ju, Tao

    2011-01-01

    Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. PMID:21296162

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

    PubMed

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

    2016-01-01

    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 moir 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

  6. Insight into Amyloid Structure Using Chemical Probes

    PubMed Central

    Reinke, Ashley A.; Gestwicki, Jason E.

    2011-01-01

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

  7. 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.

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

    PubMed Central

    2013-01-01

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

  9. 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.

  10. Atomic-resolution chemical mapping using energy-dispersive x-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    D'Alfonso, A. J.; Freitag, B.; Klenov, D.; Allen, L. J.

    2010-03-01

    We demonstrate atomic-resolution chemical mapping using energy-dispersive x-ray spectroscopy in scanning transmission electron microscopy. Theoretical simulations of the imaging process demonstrate that these images are directly interpretable. This is due to the fact that the effective ionization interaction is local and this is an incoherent mode of imaging.

  11. 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. PMID:24206242

  12. 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.

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

    PubMed Central

    March, Norman H.; Parr, Robert G.

    1980-01-01

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

  14. 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 relatively short length scales, with moderate increases in dissolved solutes over as little as 1km along the course of a river crossing a debris fan within the catchment. We hypothesise that debris fans and associated hyporheic regimes act as a filter of sorts, with the solute output from these sources being driven by dissolution and reprecipitation depending on the residence time of water within the vadose zone. This is controlled primarily by the prevailing seasonal weather: groundwater reservoirs are rapidly flushed during heavy precipitation associated with typhoons and tropical storms. In view of an expected increase of typhoon activity in the region, we propose that long-term monitoring of hydrological and chemical fluxes from mixed bedrock-alluvial mountain catchments can contribute to understanding of the impact of climate variability and change on Earth's carbon cycle.

  15. Berry-like phases in structured atoms and molecules

    SciTech Connect

    Meyer, Edmund R.; Cornell, Eric A.; Bohn, John L.; Leanhardt, Aaron E.

    2009-12-15

    Quantum mechanical phases arising from a periodically varying Hamiltonian are considered. These phases are derived from the eigenvalues of a stationary, 'dressed' Hamiltonian that is able to treat internal atomic or molecular structure in addition to the time variation. In the limit of an adiabatic time variation, the usual Berry phase is recovered. For more rapid variation, nonadiabatic corrections to the Berry phase are recovered in perturbation theory, and their explicit dependence on internal structure emerges. Simple demonstrations of this formalism are given, to particles containing interacting spins, and to molecules in electric fields.

  16. 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.

  17. Chemical Erosion of Diamond-Coated Graphite under Low-Energy Hydrogen Atom Irradiation

    NASA Astrophysics Data System (ADS)

    Takeguchi, Yuji; Kyo, Masaaki; Uesugi, Yoshihiko; Tanaka, Yasunori; Masuzaki, Suguru

    We experimentally investigate chemical erosion of polycrystalline graphite targets coated with boron-doped diamond (BDD) using an induction plasma containing low-energy, high-atomic-hydrogen flux. Chemical erosion is drastically suppressed by diamond coating the graphite target. The chemical sputtering yield for the BDD layer is about two orders of magnitude lower than that for the graphite target. After exposure in low-temperature hydrogen plasmas, however, the surface morphology of the BDD target is significantly modified. The polycrystalline diamond is eroded near the grain boundary, and many pits with diamond-like shapes are observed on the crystal surface. X-ray photoelectron spectroscopy and Raman spectroscopy reveal that the hydrogen atoms penetrate into the BDD target to a depth of at least 20 nm.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

    Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

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

    SciTech Connect

    Akazawa, Housei

    2012-03-15

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

  1. InChI - the worldwide chemical structure identifier standard

    PubMed Central

    2013-01-01

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

  2. InChI - the worldwide chemical structure identifier standard.

    PubMed

    Heller, Stephen; McNaught, Alan; Stein, Stephen; Tchekhovskoi, Dmitrii; Pletnev, Igor

    2013-01-01

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

  3. 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. PMID:25307942

  4. 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.

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

    DOE PAGESBeta

    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 Structure of Trichomonas vaginalis Surface Lipoglycan

    PubMed Central

    Ryan, Christopher M.; Mehlert, Angela; Richardson, Julia M.; Ferguson, Michael A. J.; Johnson, Patricia J.

    2011-01-01

    The extracellular parasite Trichomonas vaginalis contains a surface glycoconjugate that appears to mediate parasite-host cell interaction via binding to human galectin-1. This glycoconjugate also elicits cytokine production from human vaginal epithelial cells, implicating its role in modulation of host immune responses. We have analyzed the structure of this glycoconjugate, previously described to contain the sugars rhamnose (Rha), N-acetylglucosamine (GlcNAc), galactose (Gal), xylose (Xyl), N-acetylgalactosamine (GalNAc), and glucose (Glc), using gas chromatograph mass spectrometry (GC-MS), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF), electrospray MS/MS, and nuclear magnetic resonance (NMR), combined with chemical and enzymatic digestions. Our data reveal a complex structure, named T. vaginalis lipoglycan (TvLG), that differs markedly from Leishmania lipophosphoglycan and Entamoeba lipopeptidophosphoglycan and is devoid of phosphosaccharide repeats. TvLG is composed of an ?13 linked polyrhamnose core, where Rha residues are substituted at the 2-position with either ?-Xyl or chains of, on average, five N-acetyllactosamine (-3Gal?14GlcNAc?1-) (LacNAc) units and occasionally lacto-N-biose (-3Gal?1-3GlcNAc?1-) (LNB). These chains are themselves periodically substituted at the Gal residues with Xyl-Rha. These structural analyses led us to test the role of the poly-LacNAc/LNB chains in parasite binding to host cells. We found that reduction of poly-LacNAc/LNB chains decreased the ability of TvLG to compete parasite binding to host cells. In summary, our data provide a new model for the structure of TvLG, composed of a polyrhamnose backbone with branches of Xyl and poly-LacNAc/LNB. Furthermore, the poly-LacNAc side chains are shown to be involved in parasite-host cell interaction. PMID:21900246

  7. Quantitative metallography of structural materials with the atomic force microscope

    SciTech Connect

    Goeken, M.; Vehoff, H.

    1996-10-15

    The atomic force microscopy (AFM) is now a well-established technique for imaging surface topography with high resolution and can be used to study the microstructure of structural materials in a nanometer range. On multiphase materials a contrast in the topographic AFM images is obtained from small height differences between the different phases. Accordingly investigations of microstructures that are prepared to have small height differences between the phases can be done. The AFM needs no vacuum, large specimen areas compared to the small areas in thinned TEM foils can be analyzed. This reduces the costs of the measurements significantly. In addition it is advantageous that all measurements are stored as data files in the computer and therefore quantitative evaluations of the topographic data can be performed directly. The microstructures of different crystalline alloys were investigated with the atomic force microscope. The examples include superalloys (Waspaloy, CMSX-6), martensitic transformed surfaces (NiAlCo), and steels (microalloyed steel, perlitic carbon steel).

  8. 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.

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

    PubMed

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

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (?)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9- resolution. The structure reveals the long-sought-after catalytic ?-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  10. 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 ?-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet29. Although atomic structures of PA prepores are available1014, 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- resolution. The structure reveals the long-sought-after catalytic ?-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700

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

    PubMed

    Berns, Veronica M; Fredrickson, Daniel C

    2014-10-01

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

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

    SciTech Connect

    Atuchin, V.V. . E-mail: atuchin@thermo.isp.nsc.ru; Alekseeva, O.A.; Kesler, V.G.; Pokrovsky, L.D.; Sorokina, N.I.; Voronkova, V.I.

    2006-08-15

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

  13. 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.

  14. Computer simulation of bulk and surface chemical diffusion of light atoms in metals

    SciTech Connect

    Murch, G.E.

    1981-01-01

    The lattice gas as a model for interstitial solid solution and adsorption systems is reviewed with emphasis on the generation of ordered structures. Then, as a prelude to the main discourse on chemical diffusion, the tracer diffusion coefficient is discussed in conjunction with the presentation of Monte Carlo results. Next, chemical diffusion is treated in detail with emphasis on the Danken equation. Monte Carlo results are then presented for the chemical diffusion coefficient. The large maximum in the chemical diffusivity observed within the ordered phase is traced back to the very strong driving force provided by the chemical potential derivative.

  15. Ordering of carbon atoms in boron carbide structure

    SciTech Connect

    Ponomarev, V. I. Kovalev, I. D.; Konovalikhin, S. V.; Vershinnikov, V. I.

    2013-05-15

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

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

    NASA Astrophysics Data System (ADS)

    Sabater, Carlos; Caturla, Mara Jos; Palacios, Juan Jos; Untiedt, Carlos

    2013-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

    From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics has been generated by the application of concepts from wave optics to matter waves. An example is the contribution by Franke-Arnold et al. The authors investigate the coherence properties of two trapped cold atoms using concepts developed in wave optics. Nevertheless, novel features appear in this system due to the quantum statistics - as atoms may be bosons or fermions - and due to interactions. Matter waves find a spectacular manifestation in Bose-Einstein condensates (BECs) of cold dilute atomic gases. Several concepts of wave optics, like the laser, have been discussed in relation to BECs, and the .eld of atom optics with BECs is rapidly developing. The similarity between the theoretical description of a weakly interacting BEC with that of a non-linear optical system has motivated a series of experiments that led to the observation of, e.g., solitons, vortices and vortex crystallization in matter waves. In this context, the paper by Josopait et al. describes the dynamics of a Bose-Einstein condensate containing a vortex. The vortex stability is discussed as a function of the interparticle interaction, which can be tuned using Feshbach resonances, and the dynamics of the BEC reflected by an atomic mirror is investigated. Non-linear optics merges with atomic physics also in a relatively new research area which aims at quantum non-linear optics with cold atomic gases. Labeyrie et al. use a dense, laser-cooled atomic gas as a non-linear medium for light propagation, and discuss the conditions for observing optical patterns in the transmitted beam. Pattern formation in non-linear optical media is one of the numerous forms of self-organization that these systems display, including also turbulence and optical solitons. With respects to other physical systems, where these phenomena are commonly observed, optical systems are however special: at optical frequencies thermal .uctuations are negligible and do not hide the presence of quantum .uctuations, even at room temperature. Remarkably, the interplay between non-linearity and quantum noise leads to novel phenomena, including optical patterns driven by quantum noise, quantum images, non-classical spatio-temporal correlations, and spatial quantum entanglement. Quantum images are an example of spatial structures dominated by quantum noise, where the structure is absent at a classical level and only proper correlation functions of quantum fluctuations reveal the presence of a regular spatial order. Hoyuelos et al. describe an example of such an image, which is formed in the cross section of the light emitted by an optical parametric oscillator, close to but below the threshold for a square pattern formation. The optical parametric oscillator is also studied in the paper by Rabbiosi et al. which describes the onset of a spatial structure consisting of arrays of localized peaks (cavity solitons) in the transverse cross section of the signal beam. This represents an example of a "disorder to order" transition mediated by quantum noise, where the ordered arrays of solitons are selected among the many possible stable states, only thanks to the presence of quantum noise. As the study of the dynamics of quantum .uctuations in spatially extended systems is a nontraditional subject in quantum optics, alternative techniques of theoretical analysis are needed. The paper by Zambrini et al. proposes an approach based on the use of phase-space representations, in particular of the Q-function with its associated nonlinear Langevin equations. This method provides a full description of the transition from a quantum image to a classical structure through a modulation instability. The Q-representation is also used in a different physical system, the dynamics of the electrons in a driven Helium atom, in the paper by Schlagheck and Buchleitner. Here the authors investigate the quantum manifestations of order and disorder in the motion of the electrons, identifying correspondences between features of the classical phase space and the quantum dynamics. In optical patterns the structure and stability are critically determined by the type of non-linearity of the medium where light propagates, and by the cavity geometry. In atom optics, spatial atomic patterns can be created by light potentials, in particular by arrangements of suitably polarized laser beams which form an optical lattice. The atoms experience mechanical forces arising from the gradient of the light potential. Depending on the tuning of the lasers with respect to the driven atomic transition, these light forces can have a strong or negligible dissipative component, leading to incoherent or coherent motional dynamics. Atomic motion in optical lattices is experimentally investigated in the contributions by Carminati et al. and Jersblad et al. The first article investigates motion-induced resonances in a three-dimensional optical lattice which are observed through pumpprobe laser spectroscopy. The latter contribution studies the effect of the lattice geometry on the atomic steady-state by measuring velocity distributions. The creation of more complex light structures is the subject of the paper by Ellmann et al., where the realization of a double optical lattice is discussed. Such lattices may open up the possibility of coherent manipulation of the atoms in the individual potential wells. An alternative way to structure atoms spatially is discussed by Grabowski and Pfau: here, a regular arrangement of magnetic and magneto-optical traps for ultracold atoms above a surface is described and experimentally observed, where the lattice con.guration is determined by the direction of currents in wire segments beneath the surface. In a different physical systems, semiconductor quantum dots, Jacak et al. study the coupling of arti.cial atoms with the collective excitations of the bulk material in which they are embedded, and investigate coherent and incoherent effects due to this interaction. The presence of correlations at the quantum level leads naturally to the issue of entanglement. This is an exclusive feature of the quantum world, which represents a valuable resource for quantum information processing and for high-precision measurements. The de.nition and criteria for measuring entanglement have been traditionally formulated within the Hilbert-space formalism (the quantum state formalism). However, quantum structures are intrinsically multi-mode systems, for which the Hilbert-space approach is often unpractical and cumbersome. More appealing are the "classical looking" phase space descriptions, where it is hence of great importance to reformulate concepts such as entanglement or Bell inequalities. The paper by Santos addresses the general problem of characterizing the entanglement properties of an electromagnetic field in the language of Q-representation. Entanglement involving the spatial modes of the electromagnetic field carrying orbital angular momentum provides new degrees of freedom and could play an important role in the field of quantum information, since such non-classical states enable the possibility of multichannel communications. The paper by Barbosa discusses quantum states of twin photons produced by parametric down-conversion and entangled in polarization and orbital angular momentum. The issue of entanglement is intrinsically connected to decoherence, and to the transition from the quantum to the classical world. In particular, massive systems are characterized by strong interactions with the environment, and at room temperature they usually exhibit classical behaviour. In this context, the paper by Karlsson discusses the decay of quantum correlations of protons and positive muons in condensed matter, a system characterized by strong coupling to the environment, and proposes experiments where such quantum correlations could be measured. Mancini et al. investigate macroscopic manifestations of quantum features, presenting a proposal for entangling the macroscopic oscillation modes of two cavity mirrors by coupling them to an optical cavity mode. This kind of continuous-variable quantum entanglement may find applications in highprecision measurements, like in atomic force microscopy or gravity wave detection. The question of entanglement for high-precision measurements is also addressed by the paper of Yurtsever et al. which discusses entanglement between matter waves, and proposes the use of entangled atom pairs for a highly sensitive quantum gravity gradiometer. Besides their fundamental interest as a manifestation of quantum .uctuations, spatial quantum correlations in optical beams find their most natural and promising applications in the field of image processing and, more in general, of parallel processing of information. This has opened a new chapter of quantum optics that has been given the name "quantum imaging". In this context, one of the .rst achievements have been the so-called entangled two-photon imaging experiments. This is a technique that exploits the quantum entanglement of a two-photon state to retrieve information about a remote object. In the typical set-up, one photon out of a pair produced by spontaneous parametric down-conversion is used to probe an object, while the other provides a reference. The image of the object emerges in the coincidence counting rate registered as a function of the second photon position. The paper by Shih offers an extensive review of fundamental aspects linked to the entangled two-photon imaging phenomena. It illustrates how quantum imaging techniques may improve classical spatial resolution and presents some of their potential applications for lithography and other microsystem fabrication technologies. A different view on the problem is offered by the paper of Tan et al., which reformulates the two-photon quantum imaging theory from the point of view of retrodictive quantum theory. Since long, quantum noise has been known to represent a limit in high-precision optical measurements. In this context, the contribution by Eschner discusses a single trapped atom probing an optical field and shows that the quantum noise in the atomic motion poses the ultimate limit to the achievable resolution. Recently, it was recognized that quantum noise affects also our ability to resolve an optical image or to detect a small displacement of an optical beam. Properly synthesized multi-mode quantum states are able to circumvent the quantum noise limit and to improve our resolution capabilities in measuring beam displacements. The paper by Barnett et al. shows the similarities between longitudinal phase shifts and transverse beam displacements measurements. Like in interferometry, the sensitivity in the transverse displacement measurement is ultimately limited by the quantum nature of light and can be improved by the use of specific non classical states. The problem of realizing a multi-mode squeezed state is addressed by the paper of Petsas et al. It discusses a realistic implementation of parametric down-conversion in a confocal cavity, able to produce a significant amount of squeezing in small portions of the signal beam cross section. Quantum imaging with macroscopic light beams is a rather new subject of investigation, which represents a non-trivial challenge from the point of view of experimental implementations. One of the main problems is posed by detectors, which should be able to resolve the spatial features of the detected beam with a sensitivity in the photon number measurement beyond the shot noise level. The calibrated CCD camera developed by Jiang et al. makes it possible to get rid of electronic noise or spatial inhomogeneities, a.ecting most of the spatially resolved detectors, and allows the retrieval of spatial shot noise in its full dynamic range. We hope that this special issue helps stimulating further collaborations and fruitful scientific exchange between and beyond the presented fields. We would like to thank the authors for their contributions and the referees for their time and their thoroughness. Our sincerest thanks go to Solange Guéhot in the EPJ D editorial office for very efficiently taking care of all administrative matters. Jürgen Eschner, Institut für Experimentalphysik, Universität Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria Alessandra Gatti, Istituto Nazionale per la Fisica della Materia, Unitá di Como, Via Valleggio 11, 22100 Como, Italy Agnàs Maītre, Laboratoire Kastler-Brossel, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France Giovanna Morigi, Abteilung Quantenphysik, Universitát Ulm, Albert-Einstein Allee 11, 89069 Ulm, Germany

  18. Using graphs to interrogate the atomic structure of polymer blends

    NASA Astrophysics Data System (ADS)

    Wodo, Olga; Ganapathysubramanian, Baskar

    2015-03-01

    The nanomorphology of polymer blend thin films critically affects performance especially in electronic devices. However, many aspects of the underlying physics linking morphology to performance are still poorly understood. Furthermore, there is increasing evidence that atomic organization can hold the key to efficient charge transport within organic electronic devices. In this work, we take advantage of recent advances in molecular dynamic simulations and quantify atomic-scale morphological aspects of the thin films. Specifically, we present a graph-based technique that allows quantifying the point-cloud data. In our approach, we first convert the point cloud data from atomistic simulation into a labelled, weighted, undirected graph and then use standard graph-based algorithms to calculate and quantify morphology features. The conversion of the CGMD-data into a graph preserves all the topological and geometric information about the internal structure, and local connectivity between individual atoms/beads (along and across the polymer chains). Our method provides hierarchical information about the charge paths that a hole/electron needs to take to reach the electrode (path length, fraction of intra-molecular hops, path balance). We showcase capabilities of our approach by analyzing coarse grained molecular simulations, and quantifying effect of various thermal treatment as well as electrode materials on the P3HT:PCBM blend.

  19. 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.

  20. Formal Nuclear and Atomic Structure of the Elements

    NASA Astrophysics Data System (ADS)

    Nduka, Amagh

    2004-05-01

    In the paper "The Space of 4-Operators and the Unification of the Fundamental Interactions" (see APS paper with log number 10016) we discussed the Fundamental Particle Scheme (not the Standard Model). As an application of the theory, we discuss in this paper formal atomic and nuclear structures and (1) deduce the correct periodic table of the elements that accounts for the missing elements of the empirically derived Chancourtois-Newlands-Lothar Meyer-Mendeleev table; and a table of the nuclides, (2) calculate the mass of the electron neutrino, and deduce the missing mass and dark matter of the universe.

  1. 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 segregation into distinct chemically-ordered (B2-type) and disordered (fcc-type) domains. This finding is significant since it provides a rational basis for streamlining the design and preparation of Pd-based nanoalloy catalysts in terms of atomic structure and phase state.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 co

  2. Determination of lead in preserved egg by flame atomic absorption spectrometry after chemically modified preconcentration.

    PubMed

    Lu, G; Wang, X; Wan, J; Fon, S; Xu, H Y

    1995-04-01

    A sensitive method for the determination of lead in preserved egg by flame absorption spectrometry using ammonium pyrrolidine dithiocarbamate-polystyrene chemically modified platinum wire matrix is presented. The modified platinum wire matrix, after preconcentrating the lead, is placed in a flame burner for direct atomization and measurement. The concentration range is linear between 5 and 500 ng/ml lead in solution and the detection limit is 0.65 ng/ml. This new technique is sensitive and convenient. PMID:18966264

  3. 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

    2013-04-19

    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

  4. 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

  5. Atomic structure of antiphase domain boundaries of a thin Al2O3 film on NiAl(110).

    PubMed

    Kulawik, M; Nilius, N; Rust, H-P; Freund, H-J

    2003-12-19

    Line defects of a thin alumina film on NiAl(110) have been studied on the atomic level with scanning tunneling microscopy at 4 K. While boundaries between two reflection domains do not expose a characteristic structure, antiphase domain boundaries are well ordered. The latter boundaries result from the insertion of a row of O atoms, as atomically resolved images of the topmost oxygen layer show. The insertion occurs only in two of the three characteristic directions of the quasihexagonal O lattice. Depending on the direction, either straight or zigzagged boundaries form. An atomic characterization of line defects on the oxide surface is a first step to correlate their topographic structure and chemical activity. PMID:14754127

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

    PubMed

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

    2015-04-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. Atomic-scale structure: From surfaces to nanomaterials

    NASA Astrophysics Data System (ADS)

    Hove, M. A. Van

    2009-06-01

    This brief overview is dedicated to Professor G. Ertl's profound influence on shaping the field of surface science. I sketch recent accomplishments toward the determination and understanding of the atomic-scale structure of nanostructures. I argue that, to properly understand nanoscience and develop nanotechnology, there is a dire need to determine many more than the ˜1,000 detailed surface structures known today. Techniques need to be adapted or invented to make this possible. As will be exhibited here, only two techniques are now essentially ready for this task: scanning tunneling microscopy, if interpreted by theory, and, to a lesser extent, x-ray diffraction. I also describe how low-energy electron diffraction is currently being developed for the same purpose.

  9. The behavior of various chemical forms of nickel in graphite furnace atomic absorption spectrometry under different chemical modification approaches

    NASA Astrophysics Data System (ADS)

    Kowalewska, Zofia

    2012-05-01

    Various organic and inorganic Ni forms were investigated using graphite furnace atomic absorption spectrometry. Experiments without chemical modification showed a wide range of characteristic mass values for Ni (from 6.7 to 29 pg) and the importance of interaction with graphite. With the aim of achieving signal unification of organic Ni forms, different ways of chemical modification were tested. Some rules that govern the behavior of Ni were found and confirmed a significant role of the organic component of the analyte molecule in the analytical process. The application of air as an internal furnace gas in the pyrolysis phase and the Pd modifier injected with the sample solution improved the signal of porphyrins, while the application of iodine and methyltrioctylammonium chloride was required for organic compounds containing oxygen-bound Ni atoms. The Ni signal was strongly diminished when an aqueous solution containing hydrochloric acid was measured with the Pd modifier injected over the sample. Using the developed analytical methods, the range of characteristic mass values for various Ni forms totally dissolved in organic or aqueous solution was 6.5-7.9 pg.

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  11. EELS measurement of the local electronic structure of copper atoms segregated to aluminum grain boundaries

    SciTech Connect

    Splinter, S.J.; Bruley, J.; Smith, D.

    1996-12-31

    It has long been known that the addition of Cu to Al interconnects improves the resistance to electromigration failure. It is generally accepted that this improvement is the result of Cu segregation to Al grain boundaries. The exact mechanism by which segregated Cu increases service lifetime is not understood, although it has been suggested that the formation of thin layers of {Theta}-CuAl{sub 2} or some metastable substoichiometric precursor, {Theta}` or {Theta}`` at the boundaries may be necessary. This paper reports measurements of the local electronic structure of Cu atoms segregated to Al grain boundaries using spatially resolved EELS in a UHV STEM. It is shown that segregated Cu exists in a chemical environment similar to that of Cu atoms in bulk {Theta}-phase precipitates.

  12. Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

    PubMed Central

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

    2014-01-01

    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. PMID:24586129

  13. Atomic structure of DUSP26, a novel p53 phosphatase

    PubMed Central

    Lokareddy, Ravi Kumar; Bhardwaj, Anshul; Cingolani, Gino

    2013-01-01

    Regulation of p53 phosphorylation is critical to control its stability and biological activity. Dual Specificity Phosphatase 26 (DUSP26) is a brain phosphatase highly overexpressed in neuroblastoma, which has been implicated in dephosphorylating phospho-Ser20 and phospho-Ser37 in the p53 transactivation domain (TAD). In this paper, we report the 1.68 crystal structure of a catalytically inactive mutant (Cys152Ser) of DUSP26 lacking the first N-terminal 60 residues (?N60-C/S-DUSP26). This structure reveals the architecture of a dual-specificity phosphatase domain related in structure to Vaccinia virus VH1. DUSP26 adopts a closed conformation of the protein tyrosine phosphatase (PTP)-binding loop, which results in an unusually shallow active site pocket and buried catalytic cysteine. A water molecule trapped inside the PTP-binding loop makes close contacts both with main chain and side chain atoms. The hydrodynamic radius (RH) of ?N60-C/S-DUSP26 measured from velocity sedimentation analysis (RH ~22.7 ) and gel filtration chromatography (RH ~21.0 ) is consistent with a globular monomeric protein of ~18 kDa. Instead in crystal, ?N60-C/S-DUSP26 is more elongated (RH ~37.9 ), likely due to the extended conformation of C-terminal helix ?9, which swings away from the phosphatase core to generate a highly basic surface. As in the case of the phosphatase MKP-4, we propose that a substrate-induced conformational change, possibly involving rearrangement of helix ?9 with respect to the phosphatase core, allows DUSP26 to adopt a catalytically active conformation. The structural characterization of DUSP26 presented in this paper provides the first atomic insight into this disease-associated phosphatase. PMID:23298255

  14. 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. PMID:26914604

  15. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Thillai Govindaraja, S.; Jose, Sujin P.; Mohan, S.

    2014-07-01

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G**, high level 6-311++G** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.

  16. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

    PubMed

    Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

    2014-07-15

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. PMID:24662754

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

    PubMed

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

    2013-07-24

    We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellmann-Feynman force and the Pulay force) without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEXSI is that it has a computational complexity much lower than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEXSI are modest. This even makes it possible to perform Kohn-Sham DFT calculations for 10?000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8, 0) boron nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of the accuracy required in a practical DFT calculation. PMID:23803312

  18. 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.

  19. Magnetic and Atomic Structure Parameters of Sc-doped Barium Hexagonal Ferrites

    SciTech Connect

    Yang,A.; Chen, Y.; Chen, Z.; Vittoria, C.; Harris, V.

    2008-01-01

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

    PubMed

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

    2011-12-01

    Oxide-dispersion-strengthened steels are the most promising structural materials for next-generation nuclear energy systems because of their excellent resistance to both irradiation damage and high-temperature creep. Although it has been known for a decade that the extraordinary mechanical properties of oxide-dispersion-strengthened steels originate from highly stabilized oxide nanoclusters with a size smaller than 5 nm, the structure of these nanoclusters has not been clarified and remains as one of the most important scientific issues in nuclear materials research. Here we report the atomic-scale characterization of the oxide nanoclusters using state-of-the-art Cs-corrected transmission electron microscopy. This study provides compelling evidence that the nanoclusters have a defective NaCl structure with a high lattice coherency with the bcc steel matrix. Plenty of point defects as well as strong structural affinity of nanoclusters with the steel matrix seem to be the most important reasons for the unusual stability of the clusters at high temperatures and in intensive neutron irradiation fields. PMID:22019943

  1. 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

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

    PubMed

    Dostl, Ji?; Pecina, Adam; Hrukov-Heidingsfeldov, Olga; Mare?kov, Lucie; Pichov, Iva; ?ez?ov, Pavlina; Lepk, Martin; Brynda, Ji?

    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? 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. PMID:26627656

  3. 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

  4. A Chemical Approach to Understanding Oxide Surface Structure and Reactivity

    NASA Astrophysics Data System (ADS)

    Enterkin, James Andrew

    Transmission electron microscopy and diffraction are powerful tools for solving complex structural problems. They complement other analytical techniques, such as x-ray diffraction, elucidating problems which cannot be solved by other techniques. One area where they are of particularly great value is in the determination of surface structures. The research presented herein uses electron microscopy and diffraction as the primary experimental techniques in the development of a chemistry of surface structures. High-resolution electron microscopy revealed that the La4Cu 3MoO12 structure has turbostratic disorder and a lower symmetry space group (Pm) than was previously found. The refinement of the x-ray data was significantly improved by using a disordered model and the Pm space group. A bond valence analysis confirmed that the disordered structure is the superior model. Strontium titanate, SrTiO3, single crystal surfaces were examined principally via transmission electron diffraction. A homologous series with intergrowths was discovered on the (110) surface of strontium titanate, marking the first time that these important concepts of solid state chemistry have been found at the surface. Atmospheric adsorbates, such as H2O and CO2, were found to help to stabilize undercoordinated surface structures on the (100) surface. It was shown that chemical bonding, bond valence, atomic coordination, and stoichiometry greatly influence the development of surface structures. Additionally, such chemistry based analysis was demonstrated to be able to predict surface structure stability and reactivity. Application of a modified Wulff construction to the observed shape of strontium titanate nanocuboids revealed that the surface structure and particle stoichiometry are interlinked, with control over one allowing equally precise control over the other. Platinum nanoparticles on the strontium titanate nanocuboids were shown via high resolution electron microscopy to have cube-on-cube epitaxy, with the shape of the platinum nanoparticles governed by the Winterbottom construction. Precise modification of the support surface will therefore allow engineering of supported metal particles with precise control over which facets are exposed. These results suggest that control over the support surface chemistry can be used to engineer thermodynamically stable, face selective catalysts.

  5. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

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

    PubMed Central

    2014-01-01

    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 0.136nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78. 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. PMID:25426003

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

    PubMed

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

    2014-01-01

    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 0.136nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78. 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. PMID:25426003

  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. Atomic structure of the actin: DNase I complex

    NASA Astrophysics Data System (ADS)

    Kabsch, Wolfgang; Mannherz, Hans Georg; Suck, Dietrich; Pai, Emil F.; Holmes, Kenneth C.

    1990-09-01

    The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined byo X-ray analysis at an effective resolution of 2.8 and 3 , respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the ?- or ?- and ?-phosphates, respectively. The motif of a five-stranded (3 sheet consisting of a (3 meander and a right handed ??? unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

  11. Formation of atomically smooth epitaxial metal films on a chemically reactive interface: Mg on Si(111)

    NASA Astrophysics Data System (ADS)

    zer, Mustafa M.; Weitering, Hanno H.

    2013-07-01

    Deposition of Mg on Si(111)7 7 produces an epitaxial magnesium silicide layer. Under identical annealing conditions, the thickness of this Mg2Si(111) layer increases with deposition amount, reaching a maximum of 4 monolayer (ML) and decreasing to 3 ML at higher Mg coverage. Excess Mg coalesces into atomically flat, crystalline Mg(0001) films. This surprising growth mode can be attributed to the accidental commensurability of the Mg(0001), Si(111), and Mg2Si(111) interlayer spacing and the concurrent minimization of in-plane Si mass transfer and domain-wall energies. The commensurability of the interlayer spacing defines a highly unique solid-phase epitaxial growth process capable of producing trilayer structures with atomically abrupt interfaces and atomically smooth surface morphologies.

  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

    2015-12-23

    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 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. PMID:26660073

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

    PubMed

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

    2015-12-18

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001). PMID:26722930

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. Chemical etching study of probe-grown ultrathin nano-oxides by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Chung, H. J.; Xie, X. N.; Sow, C. H.; Wee, A. T. S.

    2006-02-01

    We report the study of the etching characteristics of atomic force microscopy (AFM) probe-grown ultrathin oxides (AFM oxides, up to 5 nm thick). In our method, an AFM localized depth analysis technique was employed to monitor the atomic layer-by-layer etching of AFM oxides. Insights into the growth mode and etching mechanism of AFM oxides were acquired on the basis of the etching results: it was found that AFM oxide growth is related to Si out-diffusion. For the formation of ultrathin oxides in ambient conditions, it is evident that oxidation-enhanced Si diffusion facilitates the layer-by-layer oxide growth in AFM anodic oxidation. The etching rate of ultrathin AFM oxides is dependent on the SiOH silanol reactive sites. Thermal annealing could reduce the content of silanol groups and enhance the chemical stability of AFM oxides against etching.

  16. 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.

  17. 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. PMID:26849531

  18. The grasp2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

    This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectraatomic energy levels, oscillator strengths, and radiative decay ratesusing a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator ?=??. Configuration state functions (CSFs) are linear combinations of Slater determinants of atomic orbitals, and are simultaneous eigenfunctions of the atomic electronic angular momentum operator, J, and the atomic parity operator, P. Approximate atomic state functions (ASFs) are linear combinations of CSFs. A variational functional may be constructed by combining expressions for the energies of one or more ASFs. Average energy level (EAL) functionals are weighted sums of energies of all possible ASFs that may be constructed from a set of CSFs; the number of ASFs is then the same as the number of CSFs. Extended optimal level (EOL) functionals are weighted sums of energies of some subset of ASFs. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Hartree-Fock (MCDHF) equations that define an extremum of the variational functional by the self-consistent-field (SCF) method. Lists of CSFs are generated from a set of reference CSFs and rules for deriving other CSFs from these. Expansion coefficients are obtained using sparse-matrix methods for solving the relativistic configuration interaction (CI) problem. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. Biorthogonal transformation methods are employed so that all matrix elements between CSFs can be evaluated using Racah algebra. Restrictions: The maximum number of radial orbitals is limited to 120 by the packing algorithm used for 32-bit integers. The maximum size of a multiconfiguration (MC) calculation, as measured by the length of the configuration state function (CSF) list, is limited by numerical stability, processing time, or storage which may be either in memory or on disk. Numerical stability is the same as GRASP92 [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249] with a slight improvement in memory management for Version 2 codes. Sufficient disk space is needed to store angular data. In configuration interaction calculations the matrix may be either in memory or on disk. The tables of coefficients of fractional parentage, as in GRASP92, are limited to subshells with j?7/2; occupied subshells with j=9/2 are, therefore, restricted to a maximum of two electrons. Unusual features: The installation process has been simplified so that pre-processing of the raw code needed with GRASP92 can be eliminated. Dynamic memory allocation reduces the number of parameters needed to define fixed array dimensions to nine. The corrections discussed in [C. Froese Fischer, G. Gaigalas, Y. Ralchenko, Comput. Phys. Comm. 175 (2006) 739] have also been implemented. Environment variables are used to facilitate the compilation of the libraries, applications, and tools with different compilers on different platforms. Computationally intensive applications have been parallelized using the message passing interface (MPI). When standard output is redirected, prompts and critical information about the progress of a calculation or convergence are still directed to the screen through the standard error output unit. Running time: CPU time required to execute test cases: 5 min ( n=4 calculation with 2190 CSFs) and 52.7 minutes ( n=5 calculation with 6752 CSFs)

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

    PubMed

    Faulon, Jean-Loup; Brown, W Michael; Martin, Shawn

    2005-01-01

    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. PMID:16267694

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 CH3 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.

  1. Atomic Structure and Electronic Properties of c-Si/a-Si:H Interfaces in Si Heterojunction Solar Cells

    SciTech Connect

    Yan, Y.; Page, M.; Wang, Q.; Branz, H. M.; Wang, T. H.; Al-Jassim, M. M.

    2005-11-01

    The atomic structure and electronic properties of crystalline silicon/hydrogenated amorphous silicon (c-Si/a-Si:H) interfaces in silicon heterojunction (SHJ) solar cells are investigated by high-resolution transmission electron microscopy, atomic-resolution Z-contrast imaging, and electron energy loss spectroscopy. We find that all high-performance SHJ solar cells exhibit atomically abrupt and flat c-Si/a-Si:H interfaces and high disorder of the a-Si:H layers. These atomically abrupt and flat c-Si/a-Si:H interfaces can be realized by direct deposition of a-Si:H on c-Si substrates at a substrate temperature below 150 deg C by hot-wire chemical vapor deposition from pure silane.

  2. Correlation Between the Atomic and Bulk Chemical Potentials of Low work Function Metals

    SciTech Connect

    Drummond, T.J.

    1998-12-22

    An attempt is made to identify preferred values for the work functions of the rare earth elements by correlating the atomic chemical potential with the work function of the bulk elements. Trends in the alkali and alkali earth metal are evaluated in the same context. Strong linear correlation between the two quantities is observed within the IA, 11A, and IIIB (Se, Y, La) groups. Within the lanthanide series the nature of the correlation between the metallic radius and the work function suggests a dependence on the total angular momentum.

  3. 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.

  4. 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

  5. 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.

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

    PubMed

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

    2009-05-01

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

  7. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

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

  8. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

    Jnsson, P.; Gaigalas, G.; Biero?, J.; Fischer, C. Froese; Grant, I. P.

    2013-09-01

    A revised version of GRASP2K [P. Jnsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular package. The three versions are denoted v1, v2, and v3, respectively. In addition, in v3, the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3, a new program, jj2lsj, reports the percentage composition of the wave function in LSJ and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an LSJ expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in ATSP2K [C. Froese Fischer, G. Tachiev, G. Gaigalas, 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. All versions of the codes have been adapted for 64-bit computer architecture. Program SummaryProgram title: GRASP2K, version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.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.: 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, Land 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 comprehensive user manual in pdf format for the program package has been added. Restrictions: The packing algorithm restricts the maximum number of orbitals to be ?214. The tables of reduced coefficients of fractional parentage used in this version are limited to subshells with j?9/2 [5]; occupied subshells with j>9/2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of subshells of a CSF outside a common set of closed shells are determined by a parameter.def file that can be modified prior to compile time. Unusual features: The bioscl3 program reports transition data in the same format as in Atsp2K [6], and the data processing program tables of the latter package can be used. The tables program takes a name.lsj file, usually a concatenated file of all the .lsj transition files for a given atom or ion, and finds the energy structure of the levels and the multiplet transition arrays. The tables posted at the website http://atoms.vuse.vanderbilt.edu are examples of tables produced by the tables program. With the extension of coefficients of fractional parentage to j=9/2, calculations for the lanthanides and actinides become possible. Running time: CPU time required to execute test cases: 70.5 s.

  9. Single-collision studies of hot atom energy transfer and chemical reaction

    SciTech Connect

    Valentini, J.J. )

    1991-01-01

    This report discusses research in the collision dynamics of translationally hot atoms, with funding with DOE for the project Single-Collision Studies of Hot Atom Energy Transfer and Chemical Reaction,'' Grant Number DE-FG03-85ER13453. The work reported here was done during the period September 9, 1988 through October 31, 1991. During this period this DOE-funded work has been focused on several different efforts: (1) experimental studies of the state-to-state dynamics of the H + RH {yields} H{sub 2} R reactions where RH is CH{sub 4}, C{sub 2}H{sub 6}, or C{sub 3}H{sub 8}, (2) theoretical (quasiclassical trajectory) studies of hot hydrogen atom collision dynamics, (3) the development of photochemical sources of translationally hot molecular free radicals and characterization of the high resolution CARS spectroscopy of molecular free radicals, (4) the implementation of stimulated Raman excitation (SRE) techniques for the preparation of vibrationally state-selected molecular reactants.

  10. Single-collision studies of hot atom energy transfer and chemical reaction. Final report

    SciTech Connect

    Valentini, J.J.

    1991-12-31

    This report discusses research in the collision dynamics of translationally hot atoms, with funding with DOE for the project ``Single-Collision Studies of Hot Atom Energy Transfer and Chemical Reaction,`` Grant Number DE-FG03-85ER13453. The work reported here was done during the period September 9, 1988 through October 31, 1991. During this period this DOE-funded work has been focused on several different efforts: (1) experimental studies of the state-to-state dynamics of the H + RH {yields} H{sub 2} R reactions where RH is CH{sub 4}, C{sub 2}H{sub 6}, or C{sub 3}H{sub 8}, (2) theoretical (quasiclassical trajectory) studies of hot hydrogen atom collision dynamics, (3) the development of photochemical sources of translationally hot molecular free radicals and characterization of the high resolution CARS spectroscopy of molecular free radicals, (4) the implementation of stimulated Raman excitation (SRE) techniques for the preparation of vibrationally state-selected molecular reactants.

  11. Impacts of the 2010 Amazon drought on forest structure and function using CAO AToMS

    NASA Astrophysics Data System (ADS)

    Asner, G. P.; Martin, R. E.; Knapp, D. E.; Kennedy-Bowdoin, T.; Kellner, J.

    2012-12-01

    The 2010 Amazon mega-drought is thought to have had a widespread impact on forest condition, including tree mortality. However, no large-scale, high-resolution information exists on changes in forest structure, function, turnover or other processes in response to the drought. With the possibility of increasing drought frequency in the Amazon basin, it is now critical that we develop repeat, large-area studies to assess impacts and recovery. Using the Carnegie Airborne Observatory Airborne Taxonomic Mapping System (AToMS), we assessed the impacts of the 2010 drought by repeat flying of approximately 500,000 hectares of lowland humid tropical forest in the Peru Amazon. The CAO AToMS Visible-to-Near-Infrared (VNIR) and Visible-to-Shortwave-Infrared (VSWIR) imaging spectrometers recorded changes in forest canopy spectral, chemical and physiological state from 2009 to 2011. Areas of greatest functional change were observed near the Peru-Brazil border in areas under heavy forest use for selective logging. The CAO AToMS waveform Light Detection and Ranging (LiDAR) instruments measured highest rates of treefall and canopy gap formation in areas subjected to combined drought and logging, and on low fertility soils. The results provide the first spatially-explicit, large-scale and ecologically detailed information on the response of Amazonian forests to drought.

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

    PubMed

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

    2015-07-15

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

  13. 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 while opening the band gap. So far, chemists have not successfully synthesized and characterized a free-standing silicene. But recently chemists have successfully produced silicene sheets and nanoribbons over various substrates such as silver, diboride thin films, and iridium. The supporting substrate critically controls the electronic properties of silicene, and the match of the appropriate support and its use is critical in applications of silicene. PMID:24215179

  14. 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.…

  15. 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.

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

    PubMed

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

    2014-08-13

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

  17. Correlating Atomic Structure and Transport in Suspended Graphene Nanoribbons

    PubMed Central

    2015-01-01

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

  18. A new program for calculating matrix elements in atomic structure

    NASA Astrophysics Data System (ADS)

    Lima, P. M.

    1991-07-01

    The solution of many problems concerning the electronic structure of atoms requires the evaluation of the matrix elements of the Hamiltonian operator, including the electrostatic interaction. These matrix elements may be expressed as weighted sums of radial integrals. The program we describe in this paper evaluates the coefficients of the Slater integrals and, if these are given, computes all the matrix elements for a given set of configurations. This program has nearly the same purposes as Hibbert's program (Comput. Phys. Commun. 1 (1969) 359) and is also based on the Racach techniques. The main difference between this algorithm and the cited one is the method used to calculate the recoupling coefficients. While Hibbert's programs use Burke's algorithm (Comput. Phys. Commun. 1 (1970) 241) to calculate these coefficients, in our program they are computed using the graphical techniques developed by Jucys et al. (Mathematical Apparatus of the Theory of Angular Momenta, Israel Program for Scientific Translation, Jerusalem, 1962). According to this method, that we describe in another paper (Comput. Phys. Commun. 66 (1991) 89, this issue) the formulae needed to calculate the recoupling coefficients are previously derived and simplified (as a first step of the program). The use of this method may considerably reduce the running time, specially in the case of large configuration interaction matrices.

  19. 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

  20. 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

  1. A Method for the Automatic Classification of Chemical Structures

    ERIC Educational Resources Information Center

    Adamson, George W.; Bush, Judith A.

    1973-01-01

    A method has been developed for the automatic classification of chemical structures and it has been tested by applying it to the common naturally occurring amino acids. The resulting classification is reasonable from a qualitative viewpoint. (9 references) (Authors)

  2. Atomistic analysis of short range interaction and local chemical order in LPSO structures of Magnesium alloys

    NASA Astrophysics Data System (ADS)

    Fronzi, Marco; Kimizuka, Hajime; Matsubara, Kazuki; Ogata, Shigenobu

    2013-03-01

    Magnesium alloys have been object of interest as lightweight material with high strength weight ratio. In particular Long Period Stacking Ordered (LPSO) structure phases show to have a strong influence in enhancing mechanical properties of such kind alloys. However the chemical order of the interacting atomic species in the Mg lattice has not been fully understood. We perform first principles Density Functional Theory (DFT) calculation to compute formation energies as well as interaction energies of the doping atoms in both Faced Centered Cubic (FCC) and Hexagonal Close Packed (HCP) Mg lattices. In particular we consider the Mg-Al-Gd and Mg-Zn-Y ternary systems. We also calculate activation energies for vacancy assisted doping atoms diffusion in order to perform a further analysis of the kinetics of the process. In order to describe short range interaction and cluster formation in the Mg matrix, we build an on lattice potential based on first principles DFT interaction energies. By means of these inter-atomic potentials, we perform Monte Carlo simulations to analyze the chemical order occurring in LPSO Mg-Al-Gd structures.

  3. 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 information (ESI) available: Low-magnification optical images; Raman spectra of 0% and 5% H2 samples; AFM characterization; Schematic of the film before and after sulfurization annealing; Schematic illustrations of two typical Raman-active phonon modes (E12g, A1g); Raman (mapping) spectra for 40% and 80% H2 samples before and after sulfurization annealing; PL spectra. See DOI: 10.1039/c5nr00904a

  4. 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.

  5. Chemically assisted release of transition metals in graphite vaporizers for atomic spectrometry

    NASA Astrophysics Data System (ADS)

    Katskov, Dmitri; Darangwa, Nicholas; Grotti, Marco

    2006-05-01

    The processes associated with the vaporization of microgram samples and modifiers in a graphite tube ET AAS were investigated by the example of transition metals. The vapor absorption spectra and vaporization behavior of μg-amounts Cd, Zn, Cu, Ag, Au, Ni, Co, Fe, Mn and Cr were studied using the UV spectrometer with CCD detector, coupled with a continuum radiation source. The pyrocoated, Ta or W lined tubes, with Ar or He as internal gases, and filter furnace were employed in the comparative experiments. It was found that the kinetics of atomic vapor release changed depending on the specific metal-substrate-gas combination; fast vaporization at the beginning was followed by slower 'tailing.' The absorption continuum, overlapped by black body radiation at longer wavelengths, accompanied the fast vaporization mode for all metals, except Cd and Zn. The highest intensity of the continuum was observed in the pyrocoated tube with Ar. For Cu and Ag the molecular bands overlapped the absorption continuum; the continuum and bands were suppressed in the filter furnace. It is concluded that the exothermal interaction of sample vapor with the material of the tube causes the energy evolution in the gas phase. The emitted heat is dispersed near the tube wall in the protective gas and partially transferred back to the surface of the sample, thus facilitating the vaporization. The increased vapor flow causes over-saturation and gas-phase condensation in the absorption volume at some distance from the wall, where the gas temperature is not affected by the reaction. The condensation is accompanied by the release of phase transition energy via black body radiation and atomic emission. The particles of condensate and molecular clusters cause the scattering of light and molecular absorption; slow decomposition of the products of the sample vapor-substrate reaction produces the 'tailing' of atomic absorption signal. The interaction of graphite with metal vapor or oxygen, formed in the decomposition of metal oxide, is the most probable source of chemical energy, which facilitates the vaporization. Intensity of the process depends on chemical properties of the sample and substrate and efficiency of mass and heat transfer by the protective gas. The discussed mechanism of chemically assisted vapor release signifies the energy exchange between all participants of the vaporization process in ET AAS including the matrix, modifier, purge gas and analyte. The finding contributes in the ET AAS theory regarding the mechanisms of vaporization and mass transfer in the presence of matrix and modifiers.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-05-30

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

  8. Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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. In this article, 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.

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

    DOE PAGESBeta

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

    2015-08-29

    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.

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

    SciTech Connect

    Paesler, M.; Sayers, D.

    1988-12-01

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

  11. 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 gradient, making these oriented cracks equivalent to vertical hot plates, thereby imparting a large lateral component and preferred direction to upper mantle circulation. The latent heat release limits lower mantle flux to 1 TW and its temperature change to 500 K High lower mantle temperatures require a bulk composition more like the Moon than chondrites, which is consistent with proposals that calcuim-aluminum inclusions constitute a presolar reservoir near the nebula center. From oxygen isotopes and chemical composition of meteorites, we provide a new class of meteoritic model, based on mixing and not volatile element depletion, for the types and amounts of Earth's heat producing elements. Our model permits crust preservation at ~ 4 Ga, whereas hypothetical primordial heat would delay this significantly. The lower mantle is chemically distinct from the peridotite (chondritic) upper mantle, being comprised of refractory phases with much higher Ca, Al and Ti contents than previously considered. Huge changes in chemistry and temperature are required across the transition zone and profoundly affect the workings of the Earth. The lower mantle formed during gravitational sorting very early on, as did the core, in the drive towards energy minimization.

  12. SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

    PubMed Central

    Hattori, Masahiro; Tanaka, Nobuya; Kanehisa, Minoru; Goto, Susumu

    2010-01-01

    One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways. Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www.genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome.jp/tools/subcomp/) for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases. The SIMCOMP is a graph-based method for searching the maximal common subgraph isomorphism by finding the maximal cliques in the association graph. In contrast, the SUBCOMP is an extended method for solving the subgraph isomorphism problem. The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks. PMID:20460463

  13. Chemical name to structure: OPSIN, an open source solution.

    PubMed

    Lowe, Daniel M; Corbett, Peter T; Murray-Rust, Peter; Glen, Robert C

    2011-03-28

    We have produced an open source, freely available, algorithm (Open Parser for Systematic IUPAC Nomenclature, OPSIN) that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using an approach based on a regular grammar. This grammar is used to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an XML parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. Results from OPSIN on various computer generated name/structure pair sets are presented. These show exceptionally high precision (99.8%+) and, when using general organic chemical nomenclature, high recall (98.7-99.2%). This software can serve as the basis for future open source developments of chemical name interpretation. PMID:21384929

  14. Semi-empirical predictions of even atomic energy levels and their hyperfine structure for the scandium atom

    SciTech Connect

    Dembczynski, J. . E-mail: Jerzy.Dembczynski@put.poznan.pl; Elantkowska, M.; Ruczkowski, J.; Stefanska, D.

    2007-01-15

    We report fine and hyperfine structure analysis of the system of even configurations of the Sc atom in a large multi-configuration basis. The complete energy scheme in the energy region up to about 50,000 cm{sup -1} has been established with the predicted values of the hyperfine cture constants A. The effects of the configuration interaction in the fine and hyperfine structure are discussed.

  15. Ring-system-based Chemical Structure Enumeration for de Novo Design.

    PubMed

    Miyao, Tomoyuki; Kaneko, Hiromasa; Funatsu, Kimito

    2016-01-01

    De novo molecular design aims to propose molecules exhibiting desired properties and/or activities, as constructed from scratch. Although this approach opposes the widely used virtual screening (VS), the same criteria should be applied, such as ones based on substructure filters, and quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) regression models. QSPR/QSAR, which enables us to predict properties/activities by making use of experimental data, are widely used in academia as well as in industry. Herewith, we present a novel chemical structure generation system by combining fragments whose final chemical structures satisfy the aforementioned criteria. Using inverse analysis, QSPR/QSAR models determine a specific region in chemical space corresponding to a set of desired values by a designer. Chemical structures are generated by combining ring systems, as well as atom fragments, in every possible way until violating the upper bounds of that region. We also show the results of inverse-QSAR analysis for the human Alpha-2A adrenergic receptor. This suggests that our system has features preferable to VS-like methods in terms of the number of generated structures. PMID:26725676

  16. 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.

  17. Room-temperature chemical vapor deposition and mass detection on a heated atomic force microscope cantilever

    NASA Astrophysics Data System (ADS)

    Sunden, Erik O.; Wright, Tanya L.; Lee, Jungchul; King, William P.; Graham, Samuel

    2006-01-01

    This letter reports the localized room-temperature chemical vapor deposition of carbon nanotubes (CNTs) onto an atomic force microscope cantilever having an integrated heater, using the cantilever self-heating to provide temperatures required for CNT growth. Precise temperature calibration of the cantilever was possible and the CNTs were synthesized at a cantilever heater temperature of 800°C in reactive gases at room temperature. Scanning electron microscopy confirmed the CNTs were vertically aligned and highly localized to only the heater area of the cantilever. The cantilever mechanical resonance decreased from 119.10kHzto118.23kHz upon CNT growth, and then returned to 119.09kHz following cantilever cleaning, indicating a CNT mass of 1.4×10-14kg. This technique for highly local growth and measurement of deposited CNTs creates new opportunities for interfacing nanomaterials with microstructures.

  18. Chemical reactions of tellurium in graphite tubes of atomic absorption spectrometry

    NASA Astrophysics Data System (ADS)

    Müller-Vogt, German; Kübler, Markus; Lussac, Cédrine; Wendl, Wolfgang; Würfel, Peter

    2000-05-01

    The chemical reactions of tellurium were investigated in uncoated, pyrolytic graphite-coated, and zirconium-treated polycrystalline electrographite tubes. After drying, tellurium is present as TeO 2, which is reduced by the graphite to the volatile suboxide TeO. This molecule was detected in the gas phase by molecular absorption spectroscopy. In coated tubes, this reduction process occurs at lower temperatures compared to uncoated and Zr-treated tubes, and shows a faster reaction rate. The suboxide is reduced to elemental Te on collision with the graphite tube wall. This transport process via the gas phase was observed by vaporization from L'vov platforms and subsequent separate atomization from wall and platform. In uncoated tubes, tellurium could be stabilized to temperatures above 1200°C due to intercalation, which was proven by re-oxidation experiments.

  19. 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.

  20. Chemical Vapor Deposition of High-Quality and Atomically Layered ReS₂.

    PubMed

    He, Xuexia; Liu, Fucai; Hu, Peng; Fu, Wei; Wang, Xingli; Zeng, Qingsheng; Zhao, Wu; Liu, Zheng

    2015-10-28

    Recently, anisotropic 2D materials, such as black phosphorus and rhenium disulfides (ReS2 ), have attracted a lot attention because of their unique applications on electronics and optoelectronics. In this work, the direct growth of high-quality ReS2 atomic layers and nanoribbons has been demonstrated by using chemical vapor deposition (CVD) method. A possible growth mechanism is proposed according to the controlled experiments. The CVD ReS2-based filed-effect transistors (FETs) show n-type semiconducting behavior with a current on/off ratio of ≈10(6) and a charge carrier mobility of ≈9.3 cm(2) Vs(-1). These results suggested that the quality of CVD grown ReS2 is comparable to mechanically exfoliated ReS2, which is also further supported by atomic force microscopy imaging, high-resolution transmission electron microscopy imaging and thickness-dependent Raman spectra. The study here indicates that CVD grown ReS2 may pave the way for the large-scale fabrication of ReS2-based high-performance optoelectronic devices, such as anisotropic FETs and polarization detection. PMID:26305164

  1. 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.

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

    PubMed

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

    2015-05-14

    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. PMID:25876755

  3. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige

    2000-01-01

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

  4. Graphene-Covered Photonic Structures for Optical Chemical Sensing

    NASA Astrophysics Data System (ADS)

    Vasi?, Borislav; Gaji?, Rado

    2015-08-01

    Graphene applications in chemical sensing are based on the chemical doping of graphene. In this process, molecules adsorbed on graphene serve as charge-carrier donors or acceptors, thus changing the graphene conductivity. While the previous studies have been focused on chemical sensors with electrical detection, we theoretically investigate chemical sensing based on photonic structures covered with graphene. By considering chemical doping of graphene as a small perturbation, we show that optimal photonic structures operate at low-terahertz frequencies, with the reflectance intensity as the output signal. In order to achieve an efficient chemical sensing, photonic structures should provide the electric-field enhancement within the graphene plane. As a result, the proposed structure consists of the metallic mirror and quarter-wavelength-thick dielectric spacer with graphene on the top of it. The sensitivity is maximized when the Fermi energy in the graphene not exposed to the environment is around 30 meV. By taking the resolution for the reflectance measurement of 1%, we show that the proposed sensing structure can detect graphene doping by 150 electrons or holes per square micrometer in the dynamic range of around 3000 charge carriers.

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

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    Graphene - a single atom thick two dimensional sheet of sp 2 bonded carbon atoms arranged in a honeycomb lattice - has shown great promise for both fundamental research & applications because of its unique electrical, optical, thermal, mechanical and chemical properties. Derivatization of graphene unlocks a plethora of novel properties unavailable to their pristine parent "graphene". In this dissertation we have synthesized various structural and chemical derivatives of graphene; characterized them in detail; and leveraged their exotic properties for diverse applications. We have synthesized protein/DNA/ethylenediamine functionalized derivatives of graphene via a HATU catalyzed amide reaction of primary-amine-containing moieties with graphene oxide (GO) -- an oxyfunctional graphene derivative. In contrast to non-specificity of graphene, this functionalization of GO has enabled highly specific interactions with analytes. Devices fabricated from the protein (concanavalin -- A) and DNA functionalized graphene derivatives were demonstrated to enable label-free, specific detection of bacteria and DNA molecules, respectively, with single quanta sensitivity. Room temperature electrical characterization of the sensors showed a generation of ˜ 1400 charge carriers for single bacterium attachment and an increase of 5.6 X 1012 charge carriers / cm2 for attachment of a single complementary strand of DNA. This work has shown for the first time the viability of graphene for bio-electronics and sensing at single quanta level. Taking the bio-interfacing of graphene to the next level, we demonstrate the instantaneous swaddling of a single live bacterium (Bacillus subtilis ) with several hundred sq. micron (˜ 600 mum2) areal protein-functionalized graphene sheets. The atomic impermeability and high yield strength of graphene resulted in hermetic compartmentalization of bacteria. This enabled preservation of the dimensional and topological characteristics of the bacterium against the degrading effects of harsh environments such as the ultrahigh vacuum (˜ 10-5 Torr) and high intensity electron beam (˜ 150 A/cm2) in a transmission electron microscope (TEM) column. While an unwrapped bacterium shrank by ˜ 76% and displayed significant charge buildup in the TEM column; a wrapped bacterium remained uncontracted and undamaged owing to the graphenic wraps. This work has shown for the first time an impermeable graphenic encasement of bacteria and its application in high vacuum TEM imaging without using any lengthy traditional biological TEM sample preparation techniques. In an inch-scale, we fabricated robust free-standing paper composed of TWEEN/Graphene composite which exhibited excellent chemical stability and mechanical strength. This paper displayed excellent biocompatibility towards three mammalian cell lines while inhibiting the non-specific binding of bacteria (Bacillus cereus). We predict this composite and its derivatives to have excellent applications in biomedical engineering for transplant devices, invasive instrument coatings and implants. We also demonstrate a novel, ultra-fast and high yield process for reducing GO to reduced graphene oxide (RGO) using a facile hydride-based chemistry. The RGO sheets thus-produced exhibited high carrier mobilities (˜ 100-600 cm2/V·s) and reinstatement of the ambipolar characteristic of graphene. Raman spectra and UV-Vis spectroscopy on the RGO sheets displayed a high degree of restoration of the crystalline sp2 lattice with relatively low defects. We fabricated graphene nanoribbons (GNRs) -- 1D structural derivatives of graphene -- using a nano-scale cutting process from highly oriented pyrolytic graphite (HOPG) blocks, with widths pre-determinable between 5 nm to 600 nm. The as-produced GNRs had very high aspect ratio in the longitudinal direction (˜ 0.01); exhibited predominantly mono-layered structure (< 10% bilayer); and smooth edges (Raman ID/G ˜ 0.25 -0.28). Low temperature electrical transport measurements on back-gated thin film GNR devices were performed and a carrier mobility of ˜ 20 +/- 4 cm2/V·s with sheet resistances of 2.2-5.1 MO / □ was extracted. Despite the ˜ 50 nm thicknesses of the films, a clear bandgap scaling was observed with transport via variable range hopping (VRH) in 2 and 3 dimensions. This work demonstrates the first fully functional narrow pristine GNR thin-film field effect transistors (FETs). In addition we fabricated graphene quantum dots (GQDs) -- 0D derivatives of graphene with dimensions < 100 nm -- using a slight variation of our nano-scale cutting strategy, where the cleavage process is carried out in two dimensions. A high degree of control on the dimensions (Std. Dev. of ˜ 5 nm for 50 X 50 nm square GQDs) and shape (pre-determinable between square, rectangle, triangle and trapezoid) of the as-synthesized GQDs is demonstrated. The optical properties of the GQDs such as the UV-Vis absorbance and photoluminescence were studied and their facile tunability was demonstrated depending on their dimensions. This work demonstrates for the first time the high throughput fabrication of GQDs with tunable dimensions and shape.

  6. SYBYL line notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries.

    PubMed

    Homer, R Webster; Swanson, Jon; Jilek, Robert J; Hurst, Tad; Clark, Robert D

    2008-12-01

    SYBYL line notation (SLN) is a powerful way to represent molecular structures, reactions, libraries of structures, molecular fragments, formulations, molecular queries, and reaction queries. Nearly any chemical structure imaginable, including macromolecules, pharmaceuticals, catalysts, and even combinatorial libraries can be represented as an SLN string. The language provides a rich syntax for database queries comparable to SMARTS. It provides full Markush, R-Group, reaction, and macro atom capabilities in a single unified notation. It includes the ability to specify 3D conformations and 2D depictions. All the information necessary to recreate the structure in a modeling or drawing package is present in a single, concise string of ASCII characters. This makes SLN ideal for structure communication over global computer networks between applications sitting at remote sites. Unlike SMILES and its derivatives, SLN accomplishes this within a single unified syntax. Structures, queries, compounds, reactions, and virtual libraries can all be represented in a single notation. PMID:18998666

  7. Local atomic and electronic structures around Mg and Al dopants in LiNiO2 electrodes studied by XANES and ELNES and first-principles calculations

    NASA Astrophysics Data System (ADS)

    Tatsumi, Kazuyoshi; Sasano, Yusuke; Muto, Shunsuke; Yoshida, Tomoko; Sasaki, Tsuyoshi; Horibuchi, Kayo; Takeuchi, Yoji; Ukyo, Yoshio

    2008-07-01

    We investigated the local atomic and electronic structures around the dopants Mg and Al in a LiNiO2 -based cathode material by the combination analysis of their K shell electron energy-loss near-edge structures, x-ray absorption near-edge structures, and first-principles calculations. The occupation sites of the dopants in initial and cycled samples were examined. On the basis of the atomic structures and chemical bonding states of the models whose theoretical spectra were most consistent with the experimental spectra, we discussed the effects of Al and Mg on Li diffusion and their roles in suppressing the degradation of battery properties.

  8. 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 and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.

  9. 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 S668 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics. PMID:26254642

  10. 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. PMID:23025278

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

    PubMed Central

    Andujar-De Sanctis, Ivonne L.

    2012-01-01

    Intramolecular 13C kinetic isotope effects were determined for the dimerization of methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newtons second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity. PMID:23025278

  12. Novel chemical route for atomic layer deposition of MoS? thin film on SiO?/Si substrate.

    PubMed

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

    2014-11-01

    Recently MoS? 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 MoS? due to a lack of suitable chemistry. Here we report MoS? growth by ALD using molybdenum hexacarbonyl and dimethyldisulfide as Mo and S precursors, respectively. MoS? can be directly grown on a SiO?/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)?g and A?g) of 2H-MoS? 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 MoS? layers to be aligned with its basal plane parallel to the substrate. PMID:25340905

  13. 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.

  14. The chemical shifts of Xe in the cages of clathrate hydrate Structures I and II

    NASA Astrophysics Data System (ADS)

    Stueber, Dirk; Jameson, Cynthia J.

    2004-01-01

    We report, for the first time, a calculation of the isotropic NMR chemical shift of 129Xe in the cages of clathrate hydrates Structures I and II. We generate a shielding surface for Xe in the clathrate cages by quantum mechanical calculations. Subsequently this shielding surface is employed in canonical Monte Carlo simulations to find the average isotropic Xe shielding values in the various cages. For the two types of cages in clathrate hydrate Structure I, we find the intermolecular shielding values [σ(Xe@512 cage)-σ(Xe atom)]=-214.0 ppm, and [σ(Xe@51262 cage)-σ(Xe atom)]=-146.9 ppm, in reasonable agreement with the values -242 and -152 ppm, respectively, observed experimentally by Ripmeester and co-workers between 263 and 293 K. For the 512 and 51264 cages of Structure II we find [σ(Xe@512 cage)-σ(Xe atom)]=-206.7 ppm, and [σ(Xe@51264 cage)-σ(Xe atom)]=-104.7 ppm, also in reasonable agreement with the values -225 and -80 ppm, respectively, measured in a Xe-propane type II mixed clathrate hydrate at 77 and 220-240 K by Ripmeester et al.

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

    NASA Astrophysics Data System (ADS)

    Wells, Jack

    2013-05-01

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

  16. Modeling the Atomic-to-molecular Transition and Chemical Distributions of Turbulent Star-forming Clouds

    NASA Astrophysics Data System (ADS)

    Offner, Stella S. R.; Bisbas, Thomas G.; Viti, Serena; Bell, Tom A.

    2013-06-01

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C+, C, H2, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H2 abundances are discrepant in the boundary regions (A v <= 5), which is due to the different number of rays used by the two approaches.

  17. MODELING THE ATOMIC-TO-MOLECULAR TRANSITION AND CHEMICAL DISTRIBUTIONS OF TURBULENT STAR-FORMING CLOUDS

    SciTech Connect

    Offner, Stella S. R.; Bisbas, Thomas G.; Viti, Serena; Bell, Tom A.

    2013-06-10

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

  18. 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.

  19. 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 are pulled apart has given complementary information such as the stiffness and rupture force of the molecule-metal link bond. Overall, while the BJ technique does not produce a single molecule circuit for practical applications, it has proved remarkably versatile for fundamental studies. Measured data and analysis have been combined with atomic-scale theory and calculations, typically performed for representative junction structures, to provide fundamental physical understanding of structure-function relationships. This Account integrates across an extensive series of our specific nanoscale junction studies which were carried out with the STM- and AFM-BJ techniques and supported by theoretical analysis and density functional theory based calculations, with emphasis on the physical characteristics of the measurement process and the rich data sets that emerge. Several examples illustrate the impact of measured trends based on the most probable values for key characteristics (obtained from ensembles of order 1000-10 000 individual junctions) to build a solid picture of conductance phenomena as well as attributes of the link bond chemistry. The key forward-looking question posed here is the extent to which the full data sets represented by the individual trajectories can be analyzed to address structure-function questions at the level of individual junctions. Initial progress toward physical modeling of conductance of individual junctions indicates trends consistent with physical junction structures. Analysis of junction mechanics reveals a scaling procedure that collapses existing data onto a universal force-extension curve. This research directed to understanding the distribution of structures and physical characteristics addresses fundamental questions concerning the interplay between chemical control and stochastically driven diversity. PMID:26938931

  20. 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.

  1. 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.

  2. Atomic-Resolution X-ray Energy-Dispersive Spectroscopy Chemical Mapping of Substitutional Dy Atoms in a High-Coercivity Neodymium Magnet

    NASA Astrophysics Data System (ADS)

    Itakura, Masaru; Watanabe, Natsuki; Nishida, Minoru; Daio, Takeshi; Matsumura, Syo

    2013-05-01

    We have investigated local element distributions in a Dy-doped Nd2Fe14B hot-deformed magnet by atomic-column resolution chemical mapping using an X-ray energy-dispersive spectrometer (XEDS) attached to an aberration-corrected scanning transmission electron microscope (Cs-corrected STEM). The positions of the Nd and Dy atomic columns were visualized in the XEDS maps. The substitution of Dy was limited to a surface layer 2-3 unit cells thick in the Nd2Fe14B grains, and the Dy atoms preferentially occupied the 4f-Nd sites of Nd2Fe14B. These results provide further insights into the principal mechanism governing the coercivity enhancement due to Dy doping.

  3. An ab initio study of structure, stability, and spectroscopic parameters of 5-atomic [C, C, H, N, S] isomers

    NASA Astrophysics Data System (ADS)

    Gronowski, Marcin; Kołos, Robert

    2015-06-01

    This theoretical study is focused on predicting structures, energetics, and selected spectroscopic constants for a range of 5-atomic chemical species sharing the [C, C, H, N, S] stoichiometry, including thioformyl cyanide and iminoethenethione. An in-depth study carried out on the four most stable isomers have yielded (i) structures and energy for the lowest singlet and triplet excited electronic states; (ii) anharmonic vibrational frequencies and IR absorption intensities for the fundamental, overtone and combination modes; (iii) molecular parameters of interest to microwave spectroscopy: rotational constants, electric dipole moments, and quadrupole coupling constants.

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

    PubMed Central

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

    2014-01-01

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

  5. 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. PMID:26905782

  6. Quasilattice-Conserved Optimization of the Atomic Structure of Decagonal Ael-Co-Ni Quasicrystals

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

    2015-03-01

    The detailed atomic structure of quasicrystals has been an open question for decades. Here, we present a quasilattice-conserved optimization method (quasiOPT), with particular quasiperiodic boundary conditions. As the atomic coordinates described by basic cells and quasilattices, we are able to maintain the self-similarity characteristics of qusicrystals with the atomic structure of the boundary region updated timely following the relaxing region. Exemplified with the study of decagonal Al-Co-Ni (d-Al-Co-Ni), we propose a more stable atomic structure model based on Penrose quasilattice and our quasiOPT simulations. In particular, "rectangle-triangle" rules are suggested for the local atomic structures of d-Al-Co-Ni quasicrystals.

  7. 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. PMID:25958863

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

    NASA Astrophysics Data System (ADS)

    Heyrovska, Raji; Narayan, Sara

    2009-04-01

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

  9. 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.; Ravikumar, V.; Dravid, V.P.

    1993-12-01

    The macroscopic properties of many materials are controlled by the structure and chemistry at 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 (EELS) at a spatial resolution approaching 0.22nm. In this paper we have combined the structural information available in the Z-contrast images with the bonding information obtained from the fine structure within the EELS edges to determine the grain boundary structure in a SrTiO{sub 3} bicrystal.

  10. Atomic and electronic structures of Si(1 1 1)-[Formula: see text]-Au and (6 6)-Au surfaces.

    PubMed

    Patterson, C H

    2015-12-01

    Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the [Formula: see text]-Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the [Formula: see text]-Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the [Formula: see text]-Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the [Formula: see text]-Au phase. Extra Au atoms bound in interstitial sites of the [Formula: see text]-Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a [Formula: see text]-Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the [Formula: see text]-Au structure. The [Formula: see text]-Au phase is 2D chiral and this is evident in computed and actual STM images. [Formula: see text]-Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the [Formula: see text]-Au and [Formula: see text]-Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given. PMID:26459741

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  12. 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.

  13. 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 ?Ga with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time ?? can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations. PMID:25933773

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  15. 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.

  16. 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).

  17. 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.

  18. Atomic and electronic structure of interfaces in materials systems for future semiconductor devices

    NASA Astrophysics Data System (ADS)

    Lopatin, Sergei

    Because of the intrinsic limits of the Si/SiO2 based industry, there is a great trend towards the monolithic integration of new materials into already well developed silicon technology. Having lasted for several decades now, downscaling reaches the limit, in which a critical device dimension approaches the size of one atom. At this level of the miniaturization, it is not the bulk material, but the interface between the two materials that what controls the properties of the resulting optoelectronic device. Thus, the characterization of precise atomic arrangements at different interfaces and the influence of these arrangements on the optoelectronic properties of interfaces is required. Therefore, in this study, a combination of scanning transmission electron microscopy (STEM) techniques and density functional theory calculations was used as a research tool for the characterization of interfaces. The STEM instruments used for the study were equipped with prototypes of spherical aberration correctors, enabling to achieve the highest resolution currently available both in space and energy. The combination of experimental and theoretical methods was applied to study interfaces between Si/GaAs, Si/Ge, Ge/SiO2, Si/HfO2 and Si/Al2O3. As the result of the present research, a new dislocation configuration at the Si/GaAs interface was reported for the first time. The influence of this dislocation structure on the electrical properties of the Si/GaAs interface was analyzed. Also, the transition from Si to GaAs and from Si to Ge at corresponding interfaces was described with atomic precision. For the first time, the interface between Ge and SiO2 was shown to have "ideal" characteristics (chemical abruptness and sharpness). This indicates the potential, both for a more successful use of Ge in high-speed devices and for advances in interface engineering to enhance performance in electronic devices. The features of Si/HfO2 and Si/Al2O3 interfaces, namely the distribution and bonding of Si and Hf across the interface, and the formation of charged SiO2 islands at the Si/Al2O3 interface were also studied. These results for materials systems show the significance of a basic understanding of the atomic structures of interfaces for a rapid development of new electronic devices.

  19. Supramolecular structure of human aortic valve and pericardial xenograft material: atomic force microscopy study.

    PubMed

    Jastrzebska, Maria; Mróz, Iwona; Barwiński, Bogdan; Zalewska-Rejdak, Justyna; Turek, Artur; Cwalina, Beata

    2008-01-01

    Pericardial tissue (bovine or porcine), chemically stabilized with glutaraldehyde (GA), is widely used in cardiovascular surgery in the form of bioprosthetic valves. GA reacts with tissue proteins and creates inter- and intra-molecular cross-links, resulting in improved durability. However, tissue calcification and mechanical damage are still unresolved problems. The purpose of this study was to examine the surface topography of normal human aortic valve and GA-stabilized porcine pericardium tissue in order to gain comparative insight into supramolecular structure of both tissues. The analysis was focused on morphologic evaluation of collagen constituents of the tissues. Atomic force microscopy working in the contact mode in air was employed in the study. Considerable diversity in the spatial orientation of collagen fibrils for the human aortic valve and pericardial tissue were observed. It was found that different forms of collagen fibril packing, i.e. dense and "in phase" or loose, could have an impact on the collagen D-banding pattern. Stabilization with GA introduced significant changes in the surface topography of collagen fibrils and in their spatial organization on the tissue surface. Strong disturbance in the fibril's D-spacing was observed. It was also suggested, that the observed structural changes at the supramolecular level might make an important contribution to the progressive damage and calcification of the tissue. The presented results demonstrate that the AFM method can be useful for non-destructive structural characterization of heart valves and bioprosthetic heart valve material. PMID:17597365

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

    PubMed Central

    2013-01-01

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

  1. Atomic structure of cascades of atomic displacements in metals and alloys after different types of radiation

    NASA Astrophysics Data System (ADS)

    Ivchenko, V. A.

    2016-02-01

    Using the methods of field ion microscopy, we studied radiation induced defects on an atomically clean surface and within a subsurface volume of platinum initiated by the interaction of neutron (E > 0.1MeV) and Ar+ beams (E = 30 keV). It is shown that the interaction of fast neutrons (E > 0.1 MeV) F = 6.7-1021 m-2, F = 3.5-1022 m-2 with matter leads to the formation in the amount of platinum such as radiation damage which occur after ion irradiation by beams of charged Ar+ ions with E = 30 keV, F = 1020 ion/m2. They are observed at a depth of about 1.5-2 nm irradiated under the surface of Pt by ions Ar+. Thus, we have carried out modeling of neutron impact with matter when replacing the neutron beam by an ion beam that causes the same radiation damage in the bulk of the material. Experimental results on atomic-spatial investigation of radiative defect formation in surface layers of materials, initiated by neutron bombardment (of Pt, E > 0.1 MeV) and ion implantation (in Cu3Au: E = 40 keV, F = 1020 ion/m2, j = 10-3 A/cm2), are considered. Quantitative estimates obtained for the size, shape, and volume fraction of cascades of atomic displacements formed under various types of irradiation in the surface layers of the materials. It is showing that the average size of radiation clusters after irradiation of platinum to a fast neutron fluence of 6.7-1022 m-2 (E > 0.1 MeV) is about 3.2 nm. The experimentally established average size of a radiation cluster (disordered zone) in the alloy after ion bombardment is 4×4×1.5 nm.

  2. Direct Determination of Grain Boundary Atomic Structure in SrTiO3.

    PubMed

    McGibbon, M M; Browning, N D; Chisholm, M F; McGibbon, A J; Pennycook, S J; Ravikumar, V; Dravid, V P

    1994-10-01

    An atomic structure model for a 25 degrees [001] symmetric tilt grain boundary in SrTiO(3) has been determined directly from experimental data with the use of high-resolution Z-contrast imaging coupled with electron energy loss spectroscopy. The derived model of the grain boundary was refined by bond-valence sum calculations and reveals candidate sites for dopant atoms in the boundary plane. These results show how the combined techniques can be used to deduce the atomic structure of defects and interfaces without recourse to preconceived structural models or image simulations. PMID:17814005

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

    SciTech Connect

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

    2012-03-09

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

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

    PubMed Central

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

    2014-01-01

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

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

    PubMed

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

    2014-01-01

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  7. Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules

    NASA Astrophysics Data System (ADS)

    Suewattana, Malliga

    In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules. In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. At higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms. In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.

  8. 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. PMID:26417893

  9. 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.

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

    PubMed Central

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

    2013-01-01

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

  11. PACSY, a relational database management system for protein structure and chemical shift analysis

    PubMed Central

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

    2012-01-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

  12. [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

  13. 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)

  14. 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…

  15. Formation of Graphene-on-Diamond Structure by Graphitization of Atomically Flat Diamond (111) Surface

    NASA Astrophysics Data System (ADS)

    Tokuda, Norio; Fukui, Makoto; Makino, Toshiharu; Takeuchi, Daisuke; Yamsaki, Satoshi; Inokuma, Takao

    2013-11-01

    We succeeded in the formation of a graphene-on-diamond (GOD) structure by the graphitization of a diamond (111) surface. Before the graphitization, atomically flat diamond (111) surfaces were formed by homoepitaxial lateral growth. The graphene layers, which were formed on the atomically flat diamond (111) surfaces horizontally, were observed by cross-sectional high-resolution transmission electron microscopy.

  16. 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'

  17. 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'…

  18. 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

  19. 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.

  20. Quantum Chemical 13Ca Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation

    SciTech Connect

    Vila, J.; Aramini, J; Rossi, P; Kuzin, A; Su, M; Seetharaman, J; Xiao, R; Tong, L; Montelione, G; Scheraga, H

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-?-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13C? chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13C? chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13C? chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13C? chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-A resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13C? chemical shifts in solution than the 3BHP crystal structure. In addition, the 13C?-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.

  1. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

    PubMed

    Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

    2014-01-14

    The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates. PMID:26579896

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

    PubMed

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

    2014-02-17

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

  3. 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

  4. Emergence of heterogeneous structures in chemical reaction-diffusion networks.

    PubMed

    Xuan, Qi; Du, Fang; Wu, Tie-Jun; Chen, Guanrong

    2010-10-01

    This paper suggests that reaction-diffusion processes, rather than pure topological rules, are responsible for the emergence of heterogeneous structures of complex chemical reaction networks. In such a network, chemical substances react in each node and diffuse between connected nodes. At the same time, each node is able to sense the difference between its own state and the environmental conditions and can rearrange its neighbors via a local rewiring process so as to eliminate the sensed difference. Then, the network, even originally homogeneous, will develop a heterogeneous structure under certain environmental conditions. Such a resultant heterogeneous network may be disassortative, highly clustering, and small world as well. This implies that the reaction-diffusion equilibrium can be statistically controlled by slightly changing the structure of the underlying network. This structure-control mechanism may be especially useful in the situations where some other macroscopic measurements, such as temperature and pressure, are not allowed to be changed through the process. PMID:21230354

  5. Emergence of heterogeneous structures in chemical reaction-diffusion networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Du, Fang; Wu, Tie-Jun; Chen, Guanrong

    2010-10-01

    This paper suggests that reaction-diffusion processes, rather than pure topological rules, are responsible for the emergence of heterogeneous structures of complex chemical reaction networks. In such a network, chemical substances react in each node and diffuse between connected nodes. At the same time, each node is able to sense the difference between its own state and the environmental conditions and can rearrange its neighbors via a local rewiring process so as to eliminate the sensed difference. Then, the network, even originally homogeneous, will develop a heterogeneous structure under certain environmental conditions. Such a resultant heterogeneous network may be disassortative, highly clustering, and small world as well. This implies that the reaction-diffusion equilibrium can be statistically controlled by slightly changing the structure of the underlying network. This structure-control mechanism may be especially useful in the situations where some other macroscopic measurements, such as temperature and pressure, are not allowed to be changed through the process.

  6. 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

    2016-01-01

    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-like properties. PMID:26771590

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

    PubMed

    Stashans, Arvids; Chamba, Gaston; Pinto, Henry

    2008-02-01

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

  8. Desorption chemical ionization and fast atom bombardment mass spectrometric studies of the glucuronide metabolites of doxylamine.

    PubMed

    Lay, J O; Korfmacher, W A; Miller, D W; Siitonen, P; Holder, C L; Gosnell, A B

    1986-11-01

    Three glucuronide metabolites of doxylamine succinate were collected in a single fraction using high-performance liquid chromatography (HPLC) from the urine of dosed male Fischer 344 rats. The metabolites were then separated using an additional HPLC step into fractions containing predominantly a single glucuronide metabolite. Analysis of the metabolites by methane and ammonia desorption chemical ionization, with and without derivatization, revealed fragment ions suggestive of a hydroxylated doxylamine moiety. Identification of the metabolites as glucuronides of doxylamine, desmethyldoxylamine and didesmethyldoxylamine was accomplished, based on determination of the molecular weight and exact mass of each metabolite using fast atom bombardment (FAB) ionization. This assignment was confirmed by the fragmentation observed in FAB mass spectrometric and tandem mass spectrometric experiments. Para-substitution of the glucuronide on the phenyl moiety was observed by 500-MHz nuclear magnetic resonance (NMR) spectrometry. A fraction containing all three glucuronide metabolites, after a single stage of HPLC separation, was also analysed by FAB mass spectrometry, and the proton- and potassium-containing quasimolecular ions for all three metabolites were observed. PMID:2948588

  9. 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)

  10. Atomic detail of chemical transformation at the transition state of an enzymatic reaction

    PubMed Central

    Saen-oon, Suwipa; Quaytman-Machleder, Sara; Schramm, Vern L.; Schwartz, Steven D.

    2008-01-01

    Transition path sampling (TPS) has been applied to the chemical step of human purine nucleoside phosphorylase (PNP). The transition path ensemble provides insight into the detailed mechanistic dynamics and atomic motion involved in transition state passage. The reaction mechanism involves early loss of the ribosidic bond to form a transition state with substantial ribooxacarbenium ion character, followed by dynamic motion from the enzyme and a conformational change in the ribosyl group leading to migration of the anomeric carbon toward phosphate, to form the product ribose 1-phosphate. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. TPS identified (i) compression of the O4′···O5′ vibrational motion, (ii) optimized leaving group interactions, and (iii) activation of the phosphate nucleophile as the reaction proceeds through the transition state region. Dynamic motions on the femtosecond timescale provide the simultaneous optimization of these effects and coincide with transition state formation. PMID:18946041

  11. 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 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 of certain fragments.

  12. Computer generation of chemical structures using the gem program

    NASA Astrophysics Data System (ADS)

    Shcherbukhin, Vladimir V.; Molchanova, Marina S.; Zefirov, Nikolai S.

    1995-04-01

    A new program for generating chemical structures starting from the given molecular formula is described. The generation includes two stages. The first step is exhaustive combinatorial enumeration of molecular graphs with the given gross formula by the GEM structural generator. At the second step, these molecular graphs in the form of connectivity matrices are converted to 3D models by the MOLGEO program. The possible applications of this software are discussed.

  13. Voronoia4RNA—a database of atomic packing densities of RNA structures and their complexes

    PubMed Central

    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. PMID:23161674

  14. Plumes clustering around thermo-chemical structures with steep edges

    NASA Astrophysics Data System (ADS)

    Tan, E.

    2011-12-01

    The two Large Low Shear Velocity Provinces (LLSVPs) at the base of lower mantle are prominent features in all shear wave tomography models. LLSVPs cover about 20% of the core-mantle boundary (CMB) by area and have high elevation, extending at least 500 km above the CMB. Various lines of evidence suggest that the LLSVPs are thermo-chemical and are stable on the order of hundreds of million years. Reconciling the observed high elevation of LLSVPs and the conceived longevity is difficult in dynamic models unless the LLSVPs are made of high bulk modulus material. Hotspots and Large Igneous Province (LIP) eruption sites tend to cluster around the edges of LLSVPs. In iso-chemical models, plume roots commonly locate near the edges of slabs, which have strong lateral temperature gradients at the CMB. However, in thermo-chemical models, plumes are more likely to root on crests of the chemical anomalies. With 3-D global spherical dynamic models, we investigate the relation between the location of plumes and of chemical structures, which are composed of dense, high bulk modulus material. With reasonable values of bulk modulus and density anomalies, we find that the anomalous material forms dome-like structures with steep edges, which can survive for billions of years before being entrained. We find that more plumes occur near the edges, rather than on top, of the chemical domes. Moreover, plumes near the edges of domes have higher temperature than those atop the domes. We adjust the surface temperature to control the strength of the downwellings. When surface temperature is high and downwellings are weak or absent, plumes can originate from everywhere on the CMB. Only when the surface temperature are cold and downwellings are strong enough, the downwellings start pushing plumes toward the edges of the thermo-chemical structures. We conclude that the observed clustering of plumes around LLSVPs indicates that (1) LLSVPs have steep edges and (2) subducted slabs can reach to the CMB.

  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. Nuclear Pore Complex: From Structural View to Chemical Tools.

    PubMed

    Wong, Richard W

    2015-10-22

    Nuclear pore complexes (NPCs) are the macromolecular turnstiles between the cytoplasm and the nucleus that control the trafficking of proteins, RNAs and viruses. The giant NPC structures are extremely complex. Here, I highlight several recent findings on NPC architectures, and briefly discuss how chemical biologists might use this information to design synthetic devices and improve strategies for nuclear drug delivery. PMID:26496682

  17. STRUCTURAL FEATURES ASSOCIATED WITH DEGRADABLE AND PERSISTENT CHEMICALS

    EPA Science Inventory

    A multivariate statistical method and a heuristic method were employed to examine the structural features associated with the persistence of degradation of 287 chemicals tested with the standard biochemical oxygen demand(BOD) procedure. The data base consisted of 196 'degradable'...

  18. Chemical Patents and Structural Information: The Sheffield Research in Context.

    ERIC Educational Resources Information Center

    Downs, Geoff M.; Barnard, John M.

    1998-01-01

    Outlines the importance of chemical patents as an information source, highlighting the area of structural information and some of the special characteristics of the generic (Markush) type of description. Summarizes important research at Sheffield University (United Kingdom) performed from 1979 to 1995 by a team led by Mike Lynch. (PEN)

  19. Effect of Chemical Structure on Elastohydrodynamic Traction Coefficient

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. Atomic structure of silicene nanoribbons on Ag(110)

    NASA Astrophysics Data System (ADS)

    Tchalala, Mohammed Rachid; Enriquez, Hanna; Mayne, Andrew J.; Kara, Abdelkader; Dujardin, Grald; Ait Ali, Mustapha; Oughaddou, Hamid

    2014-03-01

    The growth of silicene nano-ribbons (NRs) on Ag(110) substrate is re-investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Deposition of one silicon monolayer at 230C induces the formation of one-dimensional 1.6 nm wide silicene nanoribbons into a well-ordered compact array with a nanometer-scale pitch of just 2 nm. Based on the STM analysis we derived an atomic model of the silicene nanoribbons (NRs) where they are substantially buckled, and quantum confinement of the electrons in the NRs contribute to electronic density of states.

  1. 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).

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

    SciTech Connect

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

    1997-04-01

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

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

    SciTech Connect

    Kim, Min-Geun; Jang, Hong-Lae; Cho, Seonho

    2013-05-01

    An efficient adjoint design sensitivity analysis method is developed for reduced atomic systems. A reduced atomic system and the adjoint system are constructed in a locally confined region, utilizing generalized Langevin equation (GLE) for periodic lattice structures. Due to the translational symmetry of lattice structures, the size of time history kernel function that accounts for the boundary effects of the reduced atomic systems could be reduced to a single atoms degrees of freedom. For the problems of highly nonlinear design variables, the finite difference method is impractical for its inefficiency and inaccuracy. However, the adjoint method is very efficient regardless of the number of design variables since one additional time integration is required for the adjoint GLE. Through numerical examples, the derived adjoint sensitivity turns out to be accurate and efficient through the comparison with finite difference sensitivity.

  4. The FAMU experiment: muonic atoms to probe the proton structure

    NASA Astrophysics Data System (ADS)

    Guffanti, D.; FAMU collaboration

    2016-02-01

    The goal of the FAMU experiment is the measurement of the proton Zemach radius using muonic hydrogen, a subject that has raised much interest in recent years due to its implications in the so-called proton radius puzzle. In order to extract the Zemach radius, the FAMU collaboration aims at measuring the hyperfine splitting of the µp ground state, since the effect of the proton finite size affects the HF transition energy. The proposed experimental method requires a detection system which is suited for time resolved X-ray spectroscopy: in this contribution the results of the first measurements performed at the RIKEN-RAL muon facility in order to verify the fitness of the detection system in the pulsed intense muon beam are presented. The characteristic X-rays from atomic transitions in muonic atoms formed in different targets have been detected using a HPGe detector and five scintillating counters based on LaBr3(Ce) crystals, whose output has been recorded for 5 ps using a 500 MHz digitizer to measure both the energy and the time spectrum of the detected events. With a detailed pulse analysis considering pile-up events, both the expected characteristic X-rays and lifetimes of various elements were measured, paving the way for future measurements to be carried out in early 2016.

  5. 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

  6. 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.

  7. STM study of the atomic structure of the icosahedral Al-Cu-Fe fivefold surface

    NASA Astrophysics Data System (ADS)

    Cai, T.; Fourne, 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.

  8. Atomic accuracy in predicting and designing non-canonical RNA structure

    PubMed Central

    Das, Rhiju; Karanicolas, John; Baker, David

    2010-01-01

    We present a Rosetta full-atom framework for predicting and designing the non-canonical motifs that define RNA tertiary structure, called FARFAR (Fragment Assembly of RNA with Full Atom Refinement). For a test set of thirty-two 6-to-20-nucleotide motifs, the method recapitulated 50% of the experimental structures at near-atomic accuracy. Additionally, design calculations recovered the native sequence at the majority of RNA residues engaged in non-canonical interactions, and mutations predicted to stabilize a signal recognition particle domain were experimentally validated. PMID:20190761

  9. Electronic and atomic structure of Co/Ge nanoislands on the Ge(111) surface

    NASA Astrophysics Data System (ADS)

    Muzychenko, D. A.; Schouteden, K.; Van Haesendonck, C.

    2013-11-01

    We report on a detailed investigation of the electronic and atomic structure of nanometer-size Co/Ge islands obtained by solid-state reactive deposition of Co atoms on a Ge(111)c(28) surface. Relying on scanning tunneling microscopy (STM) and spectroscopy (STS) measurements combined with density functional theory based calculations, the atomic structure of the Co/Ge(111)1313R13.9? surface reconstruction is determined. Real-space STM imaging combined with Fourier-transform analysis reveals the coexistence of two inequivalent phases of 1313R13.9? reconstructed Co/Ge nanoislands that are rotated by +13.9? and -13.9? with respect to the [211] direction. STS spectra probe a small band gap that varies within the 1313R13.9? surface unit cell between 10 and 250meV, suggesting local metallic behavior. According to the proposed atomic-structure model, each Co/Ge(111)1313R13.9? surface unit cell contains one Ge adatom and six Co atoms that are located at hollow sites below the top surface Ge layer and that are stacked in the form of an equilateral triangle. The Ge adatom is located asymmetrically with respect to the Co triangle and occupies two different, yet physically equivalent, positions, giving rise to two chiral phases of Co/Ge nanoislands. The Co/Ge valence band is dominated by Co atom derived 3d states, while states in the conduction band stem from Ge adatom and Ge rest-atom derived states. Analysis of the bonding properties confirms the stability of the proposed Co/Ge atomic structure and reveals significant charge transfer from Co atoms to Ge rest atoms, suggesting ionic or metallic-covalent interaction.

  10. Resolving the structure of Ti3C2Tx MXenes through multilevel structural modeling of the atomic pair distribution function

    DOE PAGESBeta

    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

  11. 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. PMID:26444084

  12. 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.

  13. 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.

  14. Atomic structure of the (310) twin in niobium: Experimental determination and comparison with theoretical predictions

    NASA Astrophysics Data System (ADS)

    Campbell, Geoffrey H.; Foiles, Stephen M.; Gumbsch, Peter; Rhle, Manfred; King, Wayne E.

    1993-01-01

    The atomic structure of the (310) twin in Nb was predicted using interatomic potentials derived from the embedded atom method (EAM), Finnis-Sinclair theory (FS), and the model generalized pseudopotential theory (MGPT). The EAM and FS predicted structures with crystal translations which break mirror symmetry. The MGPT predicted one stable structure which possessed mirror symmetry. This defect was experimentally determined to have mirror symmetry. These findings emphasize that the angular dependent interactions modeled by the MGPT are important for determining defect structures in bcc transition metals.

  15. Towards Chemical Structure Resolution with Nanoscale Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kong, Xi; Stark, Alexander; Du, Jiangfeng; McGuinness, Liam P.; Jelezko, Fedor

    2015-08-01

    Nuclear magnetic resonance spectroscopy has approached the limit of single-molecule sensitivity; however, the spectral resolution is currently insufficient to obtain detailed information on chemical structure and molecular interactions. Here we demonstrate more than 2 orders of magnitude improvement in spectral resolution by performing correlation spectroscopy with shallow nitrogen-vacancy magnetic sensors in diamond. In principle, the resolution is sufficient to observe chemical shifts in approximately 1 T magnetic fields and is currently limited by molecular diffusion at the surface. We measure oil diffusion rates of D =0.15 - 0.2 nm2/? s within (5 nm )3 volumes at the diamond surface.

  16. Structure of adsorbed monolayers. The surface chemical bond

    SciTech Connect

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

    1984-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

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

  18. 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.

  19. 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.

  20. 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.

  1. Atomic structure and chemistry of human serum albumin

    NASA Technical Reports Server (NTRS)

    He, Xiao M.; Carter, Daniel C.

    1992-01-01

    The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

  2. 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

  3. Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry.

    PubMed

    Bruhn, C G; Huerta, V N; Neira, J Y

    2004-01-01

    Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was not satisfactory, whereas Ir and Rh were effective modifiers and rendered better relative sensitivity for As by a factor of 1.4 and 1.9, respectively compared to the case without modifier. Upon optimization of thermal conditions for As in pre-reduced Ir (2.0 microg) and Rh (2.0 microg) modifiers and in the digest solutions of the study matrices, Rh (2.0 microg) was more effective modifier and was selected as such. The mean within-day repeatability was 2.8% in consecutive measurements (25-100 microg L(-1)) (3 cycles, each of n=6) and confirmed good short-term stability of the absorbance measurements. The mean reproducibility was 4.4% (n=20 in a 3-day period) and the detection limit (3 sigmablank/slope) was 29 pg (n=15). The useful coil lifetime in Rh modifier was extended to 300-400 firings. Validation was by determination of As in the certified reference material (CRM) of "Oyster tissue" solution with a percentage relative error (Erel%) of 2% and percentage relative standard deviation (RSD%) of 3% (n=4), and by analytical recovery of As spiked in CRM of human hair [94 +/- 8% (n=4)]. The methodology is simple, fast (sample readout frequency 21 h(-1)), reliable, of low cost, and was applied to the determination of As in hair samples of exposed and unexposed workers. PMID:14598009

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

  5. Atomic characterization of monolayer doped graphene sheets synthesized by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Lu, R. T.; Li, Q.; Botello-Mndez, A.; Charlier, J. C.; Wang, B.; Berkdemir, A.; Gutirrez, H. R.; Zhu, J.; Terrones, H.; Pan, M. H.; Terrones, M.

    2012-02-01

    Large-area, high-quality monolayer nitrogen (or boron)-doped graphene sheets were synthesized on copper foils by a modified chemical vapor deposition (CVD) apparatus. As-grown graphene sheets could be easily transferred from copper foils onto different substrates (e.g. silicon/silicon dioxide wafers). Compared with pristine graphene, nitrogen (or boron)-doped graphene shows strong D-band caused by doping and structural defects formed within the lattice. Scanning tunneling microscopy (STM) and spectroscopy (STS) reveal that the defects in the doped graphene samples arrange in different geometrical configurations. The localized states in the valence and conduction bands are in accordance with the type of dopant and bonding type. These experimental results are in agreement with first principles calculations of LDOS of doped graphene and STM image simulations.

  6. Applications of the Cambridge Structural Database in chemical education1

    PubMed Central

    Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

    2010-01-01

    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 metalorganic 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

  7. Atomic structure and dynamic behaviour of truly one-dimensional ionic chains inside carbon nanotubes.

    PubMed

    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. PMID:25218060

  8. (Sub)structure Searches in Databases Containing Generic Chemical Structure Representations.

    ERIC Educational Resources Information Center

    Schoch-Grubler, Ursula

    1990-01-01

    Reviews three database systems available for searching generic chemical structure representations: (1) Derwent's Chemical Code System; (2) IDC's Gremas System; and (3) Derwent's Markush DARC System. Various types of searches are described, features desirable to users are discussed, and comparison searches are described that measured recall and…

  9. 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.

  10. Nano structured carbon nitrides prepared by chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Karuppannan, Ramesh; Prashantha, M.

    2010-08-01

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

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

    PubMed

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

    2015-11-01

    Four complex intermetallic compounds BaAu(6±x)Ga(6±y) (x = 1, y = 0.9) (I), BaAu(6±x)Al(6±y) (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104-112, Fm3̅c), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution ("coloring scheme"). Chemical bonding analyses for two different "EuAu6Tr6" models reveal maximization of the number of heteroatomic Au-Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the "EuAu6Tr6" models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. The effective moments of 8.3 μB/f.u., determined from Curie-Weiss fits, point to divalent oxidation states for europium in both III and IV. PMID:26479308

  12. Imaging biological structures with the cryo atomic force microscope.

    PubMed Central

    Zhang, Y; Sheng, S; Shao, Z

    1996-01-01

    It has long been recognized that one of the major limitations in biological atomic force microscopy (AFM) is the softness of most biological samples, which are easily deformed or damaged by the AFM tip, because of the high pressure in the contact area, especially from the very sharp tips required for high resolution. Another is the molecular motion present at room temperature due to thermal fluctuation. Using an AFM operated in liquid nitrogen vapor (cryo-AFM), we demonstrate that cryo-AFM can be applied to a large variety of biological samples, from immunoglobulins to DNA to cell surfaces. The resolution achieved with cryo-AFM is much improved when compared with AFM at room temperature with similar specimens, and is comparable to that of cryo-electron microscopy on randomly oriented macromolecules. We will also discuss the technical problems that remain to be solved for achieving even higher resolution with cryo-AFM and other possible applications of this novel technique. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:8889193

  13. Pre-service physics teachers' ideas on size, visibility and structure of the atom

    NASA Astrophysics Data System (ADS)

    nl, Pervin

    2010-07-01

    Understanding the atom gives the opportunity to both understand and conceptually unify the various domains of science, such as physics, chemistry, biology, astronomy and geology. Among these disciplines, physics teachers are expected to be particularly well educated in this topic. It is important that pre-service physics teachers know what sort of theories regarding the atom they will bring into their own classrooms. Six tasks were developed, comprising size, visibility and structure of the atom. These tasks carried out by pre-service physics teachers were examined by content analysis and six categories were determined. These are size, visibility, subatomic particles, atom models, electron orbit and electron features. Pre-service physics teachers' ideas about the atom were clarified under these categories.

  14. Evolution of atomic collision cascades in vanadium crystal with internal structure

    SciTech Connect

    Psakhie, S. G. Zolnikov, K. P.; Kryzhevich, D. S.; Zheleznyakov, A. V.; Chernov, V. M.

    2009-11-15

    The formation of radiation-damage regions (radiation-damage cascades) in vanadium crystallites with internal structures (intergrain boundary) has been simulated by the molecular-dynamic method. The interatomic interaction is described within the embedded-atom method. A relatively small number of clusters of intrinsic point defects (vacancies and self-interstitial atoms) are formed both in ideal vanadium crystallites and in crystallites with boundaries after the relaxation of atomic-displacement cascades. The evolutionary character of atomic-displacement cascades is determined in many respects by the presence of extended boundaries in materials. The intergrain boundaries hinder the propagation of atomic-displacement cascades and store many radiation-induced defects.

  15. 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. PMID:24356941

  16. 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; Rohrmller, 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. PMID:23581355

  17. Fast Optical Chemical and Structural Classification of RNA.

    PubMed

    Morla-Folch, Judit; Xie, Hai-Nan; Alvarez-Puebla, Ramon A; Guerrini, Luca

    2016-02-23

    As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs. PMID:26831953

  18. Flame-in-gas-shield miniature flame hydride atomizers for ultra trace element determination by chemical vapor generation atomic fluorescence spectrometry

    NASA Astrophysics Data System (ADS)

    D'Ulivo, A.; Paolicchi, I.; Onor, M.; Zamboni, R.; Lampugnani, L.

    2009-01-01

    Flame-in-gas shield miniature hydride atomizers (FIGS) have been investigated and evaluated in view of their alternative use to miniature diffusion flame hydride atomizer (MDF) to determination of hydride forming elements by atomic fluorescence spectrometry (AFS). Chemical vapour generation (CVG) by aqueous phase derivatization by NaBH 4 in a continuous flow generator (CF) was employed for the generation of volatile hydrides of As, Sb, Bi, Se, Te and Sn. A dispersive AFS apparatus using electrodeless discharge lamps (EDL) as the excitation sources has been employed for both spectra acquisition and analytical determinations. The characteristics of FIGS in terms of background emission spectra, most intense AF spectral lines and limits of detection were compared with those of most popular MDF. FIGS presents a lower background emission with respect to MDF, allowing also the control of the molecular fluorescence of OH radicals in the determination of bismuth. Limits of detection for FIGS compare very well with to those obtained by MDF giving improvement factor of 5.5, 4.4, 3.6, 3.6, 0.7 an 0.5 for Bi, As, Se, Son, Te and Sb. Accuracy of FIGS has proven by determination of arsenic and antimony in seawater (NASS-5) and river water (SRLS-4) certified reference materials and bismuth in unalloyed copper (CuV 398, CuVI 399) standard reference materials by dispersive CVG-AFS.

  19. 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.

  20. Structural and chemical aspects of the design of multiferroic materials

    NASA Astrophysics Data System (ADS)

    Akbashev, A. R.; Kaul, Andrei R.

    2011-12-01

    The existing approaches to the chemical design of multiferroic materials are described in detail. The structural and functional features of the known homogeneous multiferroics and the latest advances in the field of multiferroics are considered. The features of synthesis of composite magnetoelectrics with specified properties are considered separately. The special emphasis is made on epitaxial stabilization as a key method for the production of new magnetoelectric materials and controlled change of their physical properties. The bibliography includes 218 references.

  1. The chemical structure of the pigments in Ara macao plumage.

    PubMed

    Stradi, R; Pini, E; Celentano, G

    2001-08-01

    Parrots (Psittaciformes) harbor unusually bright, non-carotenoid, feather pigments. We successfully extracted and purified a sufficient quantity of pigment from the red plumage of the Scarlet Macaw (Ara macao) for a partial chemical analysis. The extracts were analyzed by HPLC coupled with UV-VIS and mass spectroscopy before and after total hydrogenation. We found at least four pigment components. We propose a linear polyenal structure comparable with the molecules tetradecahexenal, hexadecaheptenal, octadecaoctenal and eicosanonenal. PMID:11470444

  2. 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.

  3. Atomic structure and spectral perturbations in hot dense plasmas

    NASA Astrophysics Data System (ADS)

    Nguyen, Hoe; Grumberg, Jeanne; Leboucher-Dalimier, Elisabeth; Malnoult, Philippe; Arranz, Jean-Pierre; Brisard, Monique; Reggadi, Abdelkader; Poquerusse, Alain

    1991-05-01

    Interaction mechanisms between the quantic structures of multicharged ions and dense plasmas are studied. The theoretical research aims at better understanding the microscopic aspects of equilibrium equations in ultradense plasmas and at developing optical diagnostic methods for such plasmas. It is concluded that the facilities allow such research to be performed.

  4. Correlating the structural, chemical, and optical properties at nanometer resolution

    NASA Astrophysics Data System (ADS)

    Gu, L.; zdl, V. B.; Sigle, W.; Koch, C. T.; Srot, V.; van Aken, P. A.

    2010-01-01

    Valence electron spectroscopic imaging (VESI) techniques, taking advantages of the energy-losses suffered by inelastic scattering of the fast electrons in the transmission electron microscope, offer an inherently high spatial resolution to characterize the electronic structure of materials close to the Fermi level. Here we demonstrate that the combination of an electron monochromator and a highly dispersive imaging energy filter, which has become available only recently, allows reliable measurements of local bandgaps on the nanometer scale. In addition, the correlations of structural, chemical, and optical properties can be revealed via VESI using monochromated electrons with a high spatial resolution.

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

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the HoneycuttAnderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

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

    PubMed

    Debela, T T; Wang, X D; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-02-01

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K. PMID:24334654

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

    PubMed Central

    Cao, Jianming; Ihee, Hyotcherl; Zewail, Ahmed H.

    1999-01-01

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

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

    SciTech Connect

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

    2008-06-30

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

  9. Insensitivity of atomic point contact conductance to a moiré structure

    NASA Astrophysics Data System (ADS)

    Kim, Howon; Hasegawa, Yukio

    2016-02-01

    To elucidate the mechanism of electron transport through atomic point contacts, we investigated the contact-site dependence of electrical conductance on the periodical structure of a moiré pattern observed on a Pb overlayer by scanning tunneling microscopy (STM). In order to eliminate the influence of atomic-site dependence on the conductance, we measured the point contact conductance on sites equivalent in an atomic surface lattice but different in the moiré periodical structure, and found that the conductance does not depend on the contrast of the moiré pattern. The moiré-insensitive conductance indicates a dominant role of local atomic geometry in the point contact conductance. We also revealed that apparent barrier height in the tunneling regime is dependent on the contrast of the moiré pattern, and that the moiré contrast observed by STM on a 7-monolayer thin film originates from the barrier height difference at small bias voltages.

  10. Lamellar structures in rat ova and their chemical composition.

    PubMed

    Dvork, M; Trvnk, P; Stankov, J; Stastn, J; Cech, S

    1975-01-01

    The paper represents a study of the chemical composition of lamellar structures in rat ova during cleavage based on the morphology of their submicroscopic structure after the action of various fixatives and various methods of contrasting ultrathin sections and on the employment of cytochemical methods. Reactions to RNA, polysaccharides, acid and alkaline phosphatase, non-specific esterase, glucoso-6-phosphatase and succinate dehydrogenase were tested on a submicroscopic level; lipids were tested on a light-microscopic level. The results have shown that the lamellae are composed of proteins. No RNA, polysaccharides, lipids or any of the investigated enzymes were detected in lamellar structures. Lamellar structures, therefore, are considered to be storage material chiefly used in the second half of the cleavage for developmental processes in the rat ovum. PMID:185827

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

    SciTech Connect

    Browning, N.D.; McGibbon, M.M.; McGibbon, A.J.; Chisholm, M.F.; Pennycook, S.J.; Ravikumar, V.; Dravid, V.P.

    1994-03-01

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

  12. 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.

  13. Atomic structure of the 310 twin in niobium: Theoretical predictions and comparison with experimental observation

    NASA Astrophysics Data System (ADS)

    Campbell, G. H.; King, W. E.; Foiles, S. M.; Ruehle, M.

    1992-11-01

    High-resolution transmission electron microscopy (HREM) has been used to characterize the atomic structure of the symmetric 36.9(degrees) tilt grain boundary with zone (001) tilt axes forming a twin about (310) in Nb. The projected structure was imaged along two different directions in the plane of the boundary and was compared to model structures through high-resolution image simulation. The atomic structure of this (Sigma)-5 boundary was predicted with atomistic simulations using interatomic potentials derived from the Embedded Atom Method (EAM), Finnis-Sinclair (FS), and the Model Generalized Pseudopotential Theory (MGPT). The EAM and FS predicted structures with translations of the adjacent crystals which break mirror symmetry. The MGPT predicted one stable structure with mirror symmetry. The atomic structure of the (310) twin in Nb was found by HREM to be mirror symmetric. These findings indicate that the angular dependent interactions modeled in the MGPT are important for determining the grain boundary structures of bcc transition metals.

  14. 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.

  15. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    DOE PAGESBeta

    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. Characterization of asphaltene structure using atomic force microscopy.

    PubMed

    Sabbaghi, S; Shariaty-Niassar, M; Ayatollahi, Sh; Jahanmiri, A

    2008-09-01

    In this study, at the first stage, asphaltene was extracted. The roughness of asphaltene coating at different rpm was studied using an image analysis confocal microscopy. The basics of quantum mechanics and statistical thermodynamics are used to predict the potential energy and the intermolecular forces of asphaltene molecules. The functional forms for the potential energy and intermolecular forces are evaluated. Our final goal is to be able to observe and determine the surface structures of asphaltene micelles with scanning probe microscopes. So, the focus of the work on these unusual molecules is to characterize their structure, dynamics and thermodynamics and to establish the relationship between these properties and petroleum fluid behaviour. The existence of various nanostructures of asphaltene in petroleum has been extensively discussed. A set of fitted data is used to check the validity of the calculated results. The good agreement between the proposed models and the data is promising. PMID:18754991

  17. Structure and chemical bonding of UAuGe

    NASA Astrophysics Data System (ADS)

    Gibson, B. J.; Kremer, R. K.; Jepsen, O.; Garrett, J. D.; Hoffmann, R.-D.; Pttgen, R.

    2001-04-01

    UAuGe was prepared from the elements by reaction in an arc-melting furnace and subsequent annealing at about 1200 K in a water-cooled silica tube in a high-frequency furnace. UAuGe crystallizes from the melt and is also stable at 920 K. It has the hexagonal YPtAs-type structure: P63/mmc, with a = 435.26(4) pm, c = 1547.4(1) pm, V = 0.2539(1) nm3, wR2 = 0.0785, 144 F2-values, and 12 variables. The structure of UAuGe may be considered as a superstructure with a quadrupled c-axis of the well known AlB2 type. The gold and germanium atoms order on the boron positions and form two-dimensionally infinite puckered layers of Au3Ge3 hexagons with intralayer Au-Ge distances of 257 pm. Between adjacent layers the gold atoms have weak secondary Au-Au interactions with Au-Au distances of 327 pm. Ab initio calculations of the electronic band structure using the tight-binding linear muffin-tin orbital method are presented. The bonding is illustrated by valence charge density and crystal orbital Hamiltonian population plots which are compared with those of ScAuSi which has a similar structure with Au-Au interactions between the layers. The Au-Au bonding is however much weaker in UAuGe than in ScAuSi. Resistivity measurements exhibit a non-metallic temperature dependence. The increase in resistivity towards lower temperatures is uncharacteristic of intermetallic compounds, and may be fitted to a Curie-Weiss-type formula, suggesting a direct correlation to the magnetic ordering. A maximum in the resistivity is observed at T = 26(1) K.

  18. 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.

  19. Student perception and conceptual development as represented by student mental models of atomic structure

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

    The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

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

    SciTech Connect

    Vedrinskii, R. V.; Lemeshko, M. P.; Novakovich, A. A.; Nazarenko, E. S.; Nassif, V.; Proux, O.; Joly, Y.

    2006-04-01

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

  1. Atomic structure of solid and liquid polyethylene oxide

    SciTech Connect

    Johnson, J.A.; Saboungi, M.; Price, D.L.; Ansell, S.; Russell, T.P.; Halley, J.W.; Nielsen, B.

    1998-10-01

    The structure of polyethylene oxide (PEO) was investigated by neutron scattering in both semicrystalline and liquid states. Deuterated samples were studied in addition to the protonated ones in order to avoid the large incoherent scattering of hydrogen and identify features in the pair correlation functions attributable to C{endash}H pairs. Analysis of the deuterated sample gave additional information on the C{endash}O and C{endash}C pairs. The results are compared with molecular-dynamics simulations of liquid PEO. {copyright} {ital 1998 American Institute of Physics.}

  2. Determination of the chemical valence of atoms at a heterophase interface by x-ray diffraction measurements of crystal truncation rod intensity at an atomic absorption edge

    SciTech Connect

    Specht, E.D.; Walker, F.J.

    1992-01-01

    We report the application of a novel technique for determining the oxidation state of atoms at a buried interface. We have measured the energy dependence of the x-ray diffraction from an interface between an Al{sub 2}O{sub 3} substrate and a 100 nm Cr{sub 2}O{sub 3} film. As the energy of the x-rays is tuned through the Cr K absorption edge, diffracted intensity varies with the scattering power of Cr atoms at the interface. By comparing the near edge structure of the interface scattering with that of standard samples, we have determined that Cr{sup +3} is the predominant state at the interface.

  3. 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.

  4. 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 vapor generation atomic fluorescence spectrometry method was validated by analyzing the TORT-1 certificate reference material, which contains only monomethylmercury, and obtaining 83 ± 5% of monomethylmercury recovered, respectively. This method was also applied to the determination of monomethylmercury in saliva samples.

  5. 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.

  6. 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.

  7. Relationships between chemical structure and biological properties of progestogens.

    PubMed

    Rozenbaum, H

    1982-03-15

    Progestogens are classified according to chemical structure, biological properties, and affinity for hormonal receptors. However, it is difficult to draw firm conclusions about the chemical structure and biological properties of progestogens. The progestational activity of a progestogen is related to some functional groups on the steroid nucleus. Some modifications may result in unexpected or unwanted subsidiary activities (androgenic, estrogenic, and glucocorticoid activity). Progestogen compounds lacking a 3-keto group are relatively poorly bound and thus have a very low affinity for steroid hormone receptors. However, others such as lynestrol and allylestrenol show a potent in vivo biological activity when administered orally or subcutaneously. Conversion of C-19 steroids to estrogens has been reported in postmenopausal women in whom androstenedione is partially converted by fat tissues to estrone and in premenopausal women in whom up to 40 mcg/day of estrone may arise by conversion of C-19 steroids. In experiments with ovariectomized female rats, it has been suggested that endogenous conversion of certain progestogens to biologically significant amounts of estrogen metabolites may occur in the gastrointestinal tract or in the liver. Progestogens have been associated with the following metabolic effects: hepatid dysfunction, hypertension, reduction in high density lipoprotein cholesterol/triglyceride levels, and decreased glucose tolerance/increased serum insulin. Chemically, there are very few differences between the progestogenic compounds. However, slight modification of the steroid molecule can lead to great differences in the steroid's metabolic effects. Each progestogen should thus be considered separately. PMID:7065053

  8. Chemical and structural changes in blood undergoing laser photocoagulation.

    PubMed

    Black, John F; Barton, Jennifer Kehlet

    2004-01-01

    The treatment of cutaneous vascular lesions (port wine stains etc.) using lasers has been guided by theories based on the "cold" or room-temperature optical properties of the hemoglobin target chromophore. We have recently presented evidence showing that under the influence of laser irradiation, the optical properties of blood in vitro are time and temperature dependent. Such complications are not currently subsumed into the in vivo theory. Here, we study the time-domain optical properties of blood undergoing photocoagulation in vitro using two newly developed time-resolved techniques. We also study the asymptotic effect of laser photocoagulation on the chemical and structural properties of the components of the blood matrix. We present evidence showing that the photocoagulation process involves significant changes in the optical absorption and scattering properties of blood, coupled with photothermally induced chemical and structural changes. We demonstrate the first use of a laser to deliberately generate magnetic resonance imaging contrast in vitro. We show that this technique offers significant potential advantages to in vivo intravenous chemical contrast agent injection. PMID:15339203

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

    NASA Astrophysics Data System (ADS)

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

    1997-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    The energetic stability, atomic and electronic structures of ?-graphyne and its derivatives (?-GYs) with extended carbon chains were investigated by density functional (DF) calculations in this work. The studied ?-GYs consist of hexagon carbon rings sharing their edges with carbon atoms N=1-10. The structure and energy analyses show that ?-GYs with even-numbered carbon chains have alternating single and triple C-C bonds (polyyne), energetically more stable than those with odd-numbered carbon chains possessing continuous double C-C bonds (polycumulene). The calculated electronic structures indicate that ?-GYs can be either metallic (odd N) or semiconductive (even N) depending on the parity of number of atoms on hexagon edges despite the edge length. The semiconducting ?-graphyne derivatives are found to possess Dirac cones (DC) with small direct band gaps 2-40 meV and large electron velocities 0.554106-0.671106 m/s, 70-80% of that of graphene. Our DF studies suggest that introducing sp carbon atoms into the hexagon edges of graphene opens up an avenue to switch between metallic and DC electronic structures via tuning the parity of the number of hexagon edge atoms.

  11. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    NASA Astrophysics Data System (ADS)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

  12. Quantitative chemical and structural ordering of Heusler CoxMnyGez (111) epitaxial films

    NASA Astrophysics Data System (ADS)

    Tsui, Frank; Collins, Brian; He, Liang; Chu, Yong

    2014-03-01

    Heusler alloys are attractive spintronic materials, owing to the predicted half-metallicity and their compatibility with epitaxial semiconductor heterostructures. Chemical defects have been suggested as the cause of low spin-polarizations measured in these materials. We report a systematic investigation into the structural and chemical ordering of CoxMnyGey films grown epitaxially on Ge (111) substrates, as a function of composition near the Heulser Co2MnGe stoichiometry. X-ray diffraction experiments show that the structural ordering is extremely sensitive to the Co-Mn atomic ratio with the best ordering occurring at compositions rich in Ge, i.e. off the Heulser stoichiometry. A new multi-edge anomalous diffraction technique has been employed to measure the elemental occupancy of the lattice sites. The measurements and analysis reveal that the dominant chemical defect is Mn-Ge site swapping with no detectable Co-Mn swapping, at variance with the predictions based on density functional theory. The observed shift for the most ordered composition from that of the bulk has been attributed to epitaxial constraints. The finding provides impetus for exploring spin polarization at off-stoichiometric compositions. The work is supported in part by DOE BES DE-FG02-05ER46216.

  13. Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

    NASA Astrophysics Data System (ADS)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

    2014-05-01

    The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

  14. 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.

  15. BreitPauli 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 BreitPauli approximation by adding mass-correction, Darwin, and spinorbit 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 DiracFock 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.

  16. 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 atom, provides information about the electronic structure of graphene and is particularly sensitive to the sign and magnitude of the charge transfer between graphene and any surface adsorbed species. Results: (A) Graphene on SiO2 In an effort designed to unravel aspects of the mechanisms for chemistry on graphene surfaces, STM and STS were employed to show that graphene on SiO2 is oxidized at lower temperatures than either graphite or multi-layer graphene. Two independent factors control this charge transfer: (1) the degree of graphene coupling to the substrate, and (2) exposure to oxygen and moisture. (B) Graphene on Copper In the case of graphene grown on copper surfaces, we found that the graphene grows primarily in registry with the underlying copper lattice for both Cu(111) and Cu(100). On Cu(111) the graphene has a hexagonal superstructure with a significant electronic component, whereas it has a linear superstructure on Cu(100). (C) Nitrogen Doped Graphene on Copper Using STM we have also studied the electronic structure and morphology of graphene films grown on a copper foil substrate in which N atoms substitute for carbon in the 2-D graphene lattice. The salient features of the results of this study were: (1) Nitrogen doped graphene on Cu foil exhibits a triangular structure with an “apparent” slight elevation of ~ 0.8 Å at N atom substitution sites; (2) Nitrogen doping results in ~0.4 electrons per N atom donated to the graphene lattice; (3) Typical N doping of graphene on Cu foil shows mostly single site Carbon atom displacement (~ 3N/1000C); (4) Some multi-site C atom displacement is observed (<10% of single site events). (D) Boron Doped Graphene on Copper We also used scanning tunneling microscopy and x-ray spectroscopy to characterize the atomic and electronic structure of boron-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 free carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying substrate while nitrogen does not. The local bonding differences between boron and nitrogen dopants lead to large-scale differences in dopant distribution and in the structure of the doped graphene films. The distribution of dopants was observed to be completely random in the case of boron, while nitrogen displayed strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. It is our expectation that a better understanding of carbon chemistry, especially the reactions of graphene flakes, will provide data that can ultimately be used to reduce particulate emissions from the burning of fossil fuels.

  17. 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(?) 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. PMID:23713774

  18. Atomic structure of a ?3 [110]/(111) grain boundary in CeO2

    NASA Astrophysics Data System (ADS)

    Feng, B.; Hojo, H.; Mizoguchi, T.; Ohta, H.; Findlay, S. D.; Sato, Y.; Shibata, N.; Yamamoto, T.; Ikuhara, Y.

    2012-02-01

    The atomic structure of a ?3 [110]/(111) grain boundary in CeO2 was studied by scanning transmission electron microscopy, electron energy loss spectroscopy, and the first-principles calculations. It was revealed that this grain boundary does not promote the formation of oxygen vacancies and keeps oxygen stoichiometry, which is different from that of ?5 CeO2 grain boundary studied previously [H. Hojo, T. Mizoguchi, H. Ohta, S. D. Findlay, N. Shibata, T. Yamamoto, and Y. Ikuhara, Nano Lett. 10, 4668 (2010)]. It was found that the difference in grain boundary oxygen stoichiometry is correlated with the grain boundary atomic structure.

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

    SciTech Connect

    Zhang, Zaoli; Rashkova, B.; Dehm, G.; Lazar, P.; Redinger, J.; Podloucky, R.

    2010-08-01

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

  20. The prediction of protein structural class using averaged chemical shifts.

    PubMed

    Lin, Hao; Ding, Chen; Song, Qiang; Yang, Ping; Ding, Hui; Deng, Ke-Jun; Chen, Wei

    2012-01-01

    Knowledge of protein structural class can provide important information about its folding patterns. Many approaches have been developed for the prediction of protein structural classes. However, the information used by these approaches is primarily based on amino acid sequences. In this study, a novel method is presented to predict protein structural classes by use of chemical shift (CS) information derived from nuclear magnetic resonance spectra. Firstly, 399 non-homologue (about 15% identity) proteins were constructed to investigate the distribution of averaged CS values of six nuclei ((13)CO, (13)C?, (13)C?, (1)HN, (1)H? and (15)N) in three protein structural classes. Subsequently, support vector machine was proposed to predict three protein structural classes by using averaged CS information of six nuclei. Overall accuracy of jackknife cross-validation achieves 87.0%. Finally, the feature selection technique is applied to exclude redundant information and find out an optimized feature set. Results show that the overall accuracy increased to 88.0% by using the averaged CSs of (13)CO, (1)H? and (15)N. The proposed approach outperformed other state-of-the-art methods in terms of predictive accuracy in particular for low-similarity protein data. We expect that our proposed approach will be an excellent alternative to traditional methods for protein structural class prediction. PMID:22545995

  1. Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

    PubMed Central

    Allali-Hassani, Abdellah; Pan, Patricia W; Dombrovski, Ludmila; Najmanovich, Rafael; Tempel, Wolfram; Dong, Aiping; Loppnau, Peter; Martin, Fernando; Thonton, Janet; Edwards, Aled M; Bochkarev, Alexey; Plotnikov, Alexander N; Vedadi, Masoud; Arrowsmith, Cheryl H

    2007-01-01

    The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique chemical fingerprints for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural priming of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone. PMID:17425406

  2. [Chemical Components, Mercury Coordination Structure and Micro-Morphology of Tibetan Medicine Zuotai].

    PubMed

    Li, Cen; Zhan, Dui; Leng-ben-cai-rang; Sang-lao; Suo-lang; Duo-jie-la-dan; Duo-ji; Du, Yu-zhi; Li, Lin-shuai; Zhang, Ming; Yang, Hong-xia; Bi, Hong-tao; Wei, Li-xin

    2015-04-01

    In order to reveal the chemical substance basis of pharmacodynamic effects of Zuotai, energy dispersive spectrometry of X-ray (EDX), X-ray fluorescence spectroscopy (XRF), synchrotron radiation X-ray absorption fine structure (SR-XAFS), X-ray diffraction (XRD), scanning electron microscope (SEM) and atomic force microscope (AFM) were used to analyze the elements, the chemical valence and local structure of mercury, and the chemical phase composition and micro-morphology of Zuotai. EDX and XRF analysis shows that the main elements in Zuotai are Hg and S, with some other minor elements, such as 0, Fe, Al, Cu, K, Ag, Ca, Mg etc. SR-XAFS analysis shows that: the oxidation state of mercury in Zuotai is divalence, its neighbor atoms are S, and its coordination number is four. XRD assay found that ?-HgS (cubic, F-43m 216) and S8 (orthorhombic, Fddd 70) are the main phase compositions in Zuotai. Besides, it also has a small amount of C (hexagonal, P63/mmc 194), Fel.05 S0.95 (hexagonal, P63/mmc 194), Cu6S6 (hexagonal, P63/mmc 194), Cu1.8 S (cubic, F-43m 216) and so on. And it was found that the crystallinity of Zuotai is about 59%, and the amorphous morphology substance in it is about 41%. SEM and AFM detection suggests that Zuotai is a kind of ancient micro-nano drug, and its particle size is mainly in the range of 100-600 nm, even less than 100 nm, which commonly further aggregate into several to 30 m loose amorphous particles. In summary, the present study elucidated physicochemical characterization(elements composition, coordination information of mercury, phase composition and micro-morphology) of Zuotai, and it will play a positive role in promoting the interpretation of this mysterious drug. PMID:26201098

  3. Chemical synthesis and structural characterization of small AuZn nanoparticles

    NASA Astrophysics Data System (ADS)

    Jurez-Ruiz, E.; Pal, U.; Lombardero-Chartuni, J. A.; Medina, A.; Ascencio, J. A.

    2007-03-01

    In this paper, we report the aqueous synthesis of bimetallic Au-Zn nanoparticles of different compositions by the simultaneous reduction technique. The stability and atomic configuration of the particles are studied through high-resolution transmission electron microscopy (HRTEM) and UV-Vis optical absorption techniques. Depending on the composition, small bimetallic nanoparticles of 1 15 nm in size were obtained. The average size and size distribution of the bimetallic nanoparticles are seen to be critically dependent on the atomic ratio of the constituting elements Au and Zn. While a 1:1 atomic proportion of Au and Zn produced most stable nanoparticles of smallest average size, nanoparticles produced with higher content of either of the component elements are unstable, inducing agglomeration and coalescence to form elongated structures with uneven morphologies. Au3Zn1 nanoparticles followed a directional growth pattern, producing bimetallic nanorods with multiple crystalline domains. Interestingly, in these rod-like nanostructures, the domains are in well array of solid solution-like bimetallic and pure mono-metallic regions alternatively. Such nanostructures with uneven morphology and compositions might show distinct catalytic selectivity in chemical reactions.

  4. 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

    Bikup, Neven; lvarez-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. PMID:24690379

  5. Smooth and filamental structures in chaotically advected chemical fields.

    PubMed

    Tzella, Alexandra; Haynes, Peter H

    2010-01-01

    This paper studies the spatial structure of decaying chemical fields generated by a chaotic-advection flow and maintained by a spatially smooth chemical source. Previous work showed that in a regime where diffusion can be neglected (large Pclet number), the structures are filamental or smooth depending on the relative strength of the chemical dynamics and the stirring induced by the flow. The scaling exponent, gamma(q), of the qth -order structure function depends, at leading order, linearly on the ratio of the rate of decay of the chemical processes, alpha , and the average rate of divergence of neighboring fluid parcel trajectories (Lyapunov exponent), h. Under a homogeneous stretching approximation, gamma(q)/q=max[alpha/h,1] which implies that a well-defined filamental-smooth transition occurs at alpha=h. This approximation has been improved by using the distribution of finite-time Lyapunov exponents to characterize the inhomogeneous stretching of the flow. However, previous work focused more on the behavior of the exponents as q varies and less on the effects of alpha and hence the implications for the filamental-smooth transition. Here we set out the precise relation between the stretching rate statistics and the scaling exponents and emphasize that the latter are determined by the distribution of the finite-size (rather than finite-time) Lyapunov exponents. We clarify the relation between the two distributions. We show that the corrected exponents, [symbol: see text] depend nonlinearly on alpha with [formula: see text]. The magnitude of the correction to the homogeneous stretching approximation, [formula: see text], grows as alpha increases, reaching a maximum when the leading-order transition is reached (alpha=h). The implication of these results is that there is no well-defined bulk filamental-smooth transition. Instead it is the case that the chemical field is unambiguously smooth for alpha>h(max), where h(max) denotes the maximum finite-time Lyapunov exponent and unambiguously filamental for alpha

  6. 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 ?m(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

  7. Surface structure of MX-chains studied by atomic force microscopy

    SciTech Connect

    Bar, G.; Scott, B.; Johnson, S.R.; Kanner, G.S.; Swanson, B.I.

    1995-03-01

    The surfaces of mixed-valence halogen-bridged transition metal linear chain compounds [[Pt(en){sub 2}][Pt(en)]{sub 2}(X{sub 1-y}X{prime}{sub y}){sub 2}](ClO{sub 4}){sub 4} (X, X{prime} = Cl, Br, or I; en = C{sub 2}H{sub 8}N{sub 2}; y = 0.0 - 1.0) were examined by atomic force microscopy (AFM). The AFM images are consistent with the surfaces expected from the bulk crystal structure. The surface unit cell parameters of the images correspond to the lattice constants of the bulk crystals. The patterns of the atomic-scale AFM images are dominated by the most protruded H atoms of the en ligands and the most protruded O atoms of the ClO{sub 4}{sup -} anions.

  8. On the atomic structure of Zr60Cu20Fe20 metallic glass

    NASA Astrophysics Data System (ADS)

    Kaban, I.; Jvri, P.; Stoica, M.; Mattern, N.; Eckert, J.; Hoyer, W.; Beuneu, B.

    2010-10-01

    The structure of Zr60Cu20Fe20 metallic glass has been studied with high-energy x-ray diffraction, neutron diffraction and extended x-ray absorption spectroscopy and modelled with the reverse Monte Carlo simulation technique. It is found that Cu and Fe atoms prefer Zr as a nearest neighbour. The mean interatomic distance between Cu/Fe and Zr atoms in the glass is remarkably shorter than the sum of the respective atomic radii. The coordination numbers for Cu/Fe-Cu/Fe pairs are very close to each other, suggesting a regular distribution of Cu and Fe atoms in the Zr60Cu20Fe20 metallic glass.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  10. Interplay between bulk atomic clusters and surface structure in complex intermetallic compounds: The case study of the Al5Co2 (001 ) surface

    NASA Astrophysics Data System (ADS)

    Meier, M.; Ledieu, J.; De Weerd, M.-C.; Huang, Ying-Tzu; Abreu, G. J. P.; Pussi, K.; Diehl, R. D.; Mazet, T.; Fournée, V.; Gaudry, É.

    2015-02-01

    The Al5Co2 crystal is a complex intermetallic compound, whose structure can be described by a stacking of chemically bonded atomic motifs. It is a potentially new catalytic material for heterogeneous hydrogenation. A single crystal of this phase has been grown by the Czochralski technique in order to study the influence of the three-dimensional bulk substructure on the two-dimensional surface using both experimental ultrahigh vacuum surface techniques and ab initio methods based on the density functional theory. Some bulk properties are first presented, focusing on chemical bond strengths, the determination of the Al and Co chemical potentials in Al5Co2 , the vibrational properties, and the specific heat. Then, the combination of experimental and computational approaches allows the identification of the surface structure, which was found to depend on the surface preparation conditions. In all cases, the surface terminates at specific bulk layers (Al-rich puckered layers) where various fractions of specific sets of Al atoms are missing, identified as Al3 atoms left at the surface resulting from cluster truncation. Finally, electron density of states calculations and spectroscopic measurements were compared and indicate a strong s p -d hybridization of the topmost pure Al layer with subsurface Co atoms. This could influence the surface reactivity and the catalytic performances of this material.

  11. Direct detection of H atoms in the catalytic chemical vapor deposition of the SiH4/H2 system

    NASA Astrophysics Data System (ADS)

    Umemoto, Hironobu; Ohara, Kentaro; Morita, Daisuke; Nozaki, Yoshitaka; Masuda, Atsushi; Matsumura, Hideki

    2002-02-01

    The absolute densities of H atoms produced in catalytic chemical vapor deposition (Cat-CVD or hot-wire CVD) processes were determined by employing two-photon laser-induced fluorescence and vacuum ultraviolet absorption techniques. The H-atom density in the gas phase increases exponentially with increases in the catalyzer temperature in the presence of pure H2. When the catalyzer temperature was 2200 K, the absolute density in the presence of 5.6 Pa of H2 (150 sccm in flow rate) was as high as 1.5×1014 cm-3 at a point 10 cm from the catalyzer. This density is one or two orders of magnitude higher than those observed in typical plasma-enhanced chemical vapor-deposition processes. The H-atom density decreases sharply with the addition of SiH4. When 0.1 Pa of SiH4 was added, the steady-state density decreased to 7×1012 cm-3. This sharp decrease can primarily be ascribed to the loss processes on chamber walls.

  12. Structural, chemical and optical evaluation of Cu-doped ZnO nanoparticles synthesized by an aqueous solution method

    SciTech Connect

    Iribarren, A.; Hernández-Rodríguez, E.; Maqueira, L.

    2014-12-15

    Highlights: • Cu-doped ZnO nanoparticles obtained by chemical synthesis. • Substitutional or interstitial Cu into ZnO lead specific structural, chemical, and optical changes. • Incorporation efficiency of Cu atoms in ZnO as a function of the Cu concentration in the precursor dissolution. - Abstract: In this work a study of ZnO and Cu-doped ZnO nanoparticles obtained by chemical synthesis in aqueous media was carried out. Structural analysis gave the dominant presence of wurtzite ZnO phase forming a solid solution Zn{sub 1−x}Cu{sub x}O. For high Cu doping CuO phase is also present. For low Cu concentration the lattice shrinks due to Cu atoms substitute Zn atoms. For high Cu concentration the lattice enlarges due to predominance of interstitial Cu. From elemental analysis we determined and analyzed the incorporation efficiency of Cu atoms in Zn{sub 1−x}Cu{sub x}O as a function of the Cu concentration in the precursor dissolution. Combining structural and chemical results we described the Cu/Zn precursor concentrations r{sub w} in which the solid solution of Cu in ZnO is predominant. In the region located at r{sub w} ≈ 0.2–0.3 it is no longer valid. For Cu/Zn precursor concentration r{sub w} > 0.3 interstitial Cu dominates, and some amount of copper oxide appears. As the Cu concentration increases, the effective size of nanoparticles decreases. Photoluminescence (PL) measurements of the Cu-doped ZnO nanoparticles were carried out and analyzed.

  13. 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 ?B , whereas for Pt atoms it is 1 ?B. 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 strong magnets without rare earths as well as Pt alloy catalysts.

  14. 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 ?1 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 for 350 sites, better than 0.3 for another 150, and 1.0 for 150 distances in the range of 5-8 . 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 0.250.09 ), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.790.03 ). Moreover, side chain heavy atoms are well restrained (0.760.06 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.

  15. 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

  16. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06mmolgdry(-1) and a maximal adsorption capacity of 0.93-1.25mmolgdry(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+). PMID:26852210

  17. X-Ray photoelectron diffraction and photoelectron holography as methods for investigating the local atomic structure of the surface of solids

    NASA Astrophysics Data System (ADS)

    Kuznetsov, M. V.; Ogorodnikov, I. I.; Vorokh, A. S.

    2014-01-01

    The state-of-the-art theory and experimental applications of X-ray photoelectron diffraction (XPD) and photoelectron holography (PH) are discussed. These methods are rapidly progressing and serve to examine the surface atomic structure of solids, including nanostructures formed on surfaces during adsorption of gases, epitaxial film growth, etc. The depth of analysis by these methods is several nanometres, which makes it possible to characterize the positions of atoms localized both on and beneath the surface. A remarkable feature of the XPD and PH methods is their sensitivity to the type of examined atoms and, in the case of high energy resolution, to the particular chemical form of the element under study. The data on experimental applications of XPD and PH to studies of various surface structures are analyzed and generalized. The bibliography includes 121 references.

  18. Chemical analysis at atomic resolution of isolated extended defects in an oxygen-deficient, complex manganese perovskite.

    PubMed

    Ruiz-Gonzlez, M Luisa; Corts-Gil, Raquel; Torres-Pardo, Almudena; Gonzlez-Merchante, Daniel; Alonso, Jos M; Gonzlez-Calbet, Jos M

    2014-01-27

    A general approach to the structural and analytical characterization of complex bulk oxides that exploits the advantage of the atomic spatial resolution and the analytical capability of aberration-corrected microscopy is described. The combined use of imaging and spectroscopic techniques becomes necessary to the complete characterization of the oxygen-deficient colossal magnetoresistant La(0.56)Sr(0.44)MnO(2.5)-related perovskite. In this compound, the formation of isolated (La/Sr)O and MnO rock-salt-type planar defects are identified from atomically resolved High Angle Annular Dark Field (HAADF) images. The location of the oxygen atomic columns from Annular Bright Field (ABF) images indicates edge-sharing MnO6 octahedra in the MnO planes and the study performed by Electron Energy Loss Spectroscopy (EELS) reveals different Mn oxidation states derived from the corner- or edge-sharing MnO6 octahedra environment. PMID:24375704

  19. Electronic structure and anisotropic chemical bonding in TiNF from ab initio study

    SciTech Connect

    Matar, Samir F.

    2012-01-15

    Accounting for disorder in anatase titanium nitride fluoride TiNF is done through atoms re-distributions based on geometry optimizations using ultra soft pseudo potentials within density functional theory DFT. The fully geometry relaxed structures are found to keep the body centering of anatase (I4{sub 1}/amd No. 141). The new structural setups are identified with space groups I-4m2 No. 119 and Imm2 No. 44 which obey the 'group to subgroup' relationships with respect to anatase. In the ground state Imm2 structure identified from energy differences, TiNF is found semi-conducting with similar density of states features to anatase TiO{sub 2} and a chemical bonding differentiated between covalent like Ti-N versus ionic like Ti-F. Inter-anion N-F bonding is also identified. - Graphical Abstract: The geometry optimized ground state anatase derived TiNF structure with arrangement of open faceted TiN3F3 distorted octahedra. The insert shows the arrangement of octahedra in anatase TiO{sub 2}. Highlights: Black-Right-Pointing-Pointer Original approach of TiNF structure for addressing the electronic band structure. Black-Right-Pointing-Pointer Based on anatase, two different ordering scheme models with geometry optimization. Black-Right-Pointing-Pointer New structures obeying the group{yields}subgroup relationships with Imm2 ground state from energy. Black-Right-Pointing-Pointer In the ground state TiNF is found semi-conducting with similar density of states to anatase TiO{sub 2}. Black-Right-Pointing-Pointer Chemical bonding differentiated between covalent like Ti-N and ionic Ti-F.

  20. 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 ?(B) and of the 3d magnetic moment with an average accuracy of 0.07 ?(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 /?(B) for magnetic moments up to 3.0 ?(B). Further, the 3d exchange splitting changes nearly linearly in the region of higher magnetic moments (3.0-4.0 ?(B)) and the corresponding Stoner exchange parameter equals I(h)(3d) = (0.272 0.006) eV /?(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 ?(B). Then, when the volume further increases, the 4s bands start to separate, increasing thus the 4s magnetic moment. Surprisingly, in the region of higher magnetic moments (?3.0 ?(B)), there is also a linear relationship between the 4s exchange splitting and the total magnetic moment with a slope of I(h)(4s) = (1.053 0.016) eV /?(B), which is nearly identical to I(3d) for magnetic moments up to 3.0 ?B. These linear relations can be considered as an extension of the Stoner model for low-dimensional systems. PMID:24501204

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

    NASA Astrophysics Data System (ADS)

    Rondinelli, James

    2015-03-01

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

  2. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    PubMed Central

    Giordano, V. M.; Ruta, B

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization. PMID:26787443

  3. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    NASA Astrophysics Data System (ADS)

    Giordano, V. M.; Ruta, B.

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization.

  4. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging.

    PubMed

    Giordano, V M; Ruta, B

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization. PMID:26787443

  5. On the physical and chemical details of alumina atomic layer deposition: A combined experimental and numerical approach

    SciTech Connect

    Pan, Dongqing; Ma, Lulu; Xie, Yuanyuan; Yuan, Chris; Jen, Tien Chien

    2015-03-15

    Alumina thin film is typically studied as a model atomic layer deposition (ALD) process due to its high dielectric constant, high thermal stability, and good adhesion on various wafer surfaces. Despite extensive applications of alumina ALD in microelectronics industries, details on the physical and chemical processes are not yet well understood. ALD experiments are not able to shed adequate light on the detailed information regarding the transient ALD process. Most of current numerical approaches lack detailed surface reaction mechanisms, and their results are not well correlated with experimental observations. In this paper, the authors present a combined experimental and numerical study on the details of flow and surface reactions in alumina ALD using trimethylaluminum and water as precursors. Results obtained from experiments and simulations are compared and correlated. By experiments, growth rate on five samples under different deposition conditions is characterized. The deposition rate from numerical simulation agrees well with the experimental results. Details of precursor distributions in a full cycle of ALD are studied numerically to bridge between experimental observations and simulations. The 3D transient numerical model adopts surface reaction kinetics and mechanisms based on atomic-level studies to investigate the surface deposition process. Surface deposition is shown as a strictly self-limited process in our numerical studies. ALD is a complex strong-coupled fluid, thermal and chemical process, which is not only heavily dependent on the chemical kinetics and surface conditions but also on the flow and material distributions.

  6. Aromatic rings in chemical and biological recognition: energetics and structures.

    PubMed

    Salonen, Laura M; Ellermann, Manuel; Diederich, Franois

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S???aromatic, cation-?, and anion-? interactions, as well as hydrogen bonding to ? systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

  7. Characterization of Atomic Structure, Relaxation and Phase Transformation Mechanisms in Bulk and Thin Film Amorphous Chalcogenides and Gallium Antimonide

    NASA Astrophysics Data System (ADS)

    Edwards, Trenton Gerard

    This dissertation details the characterization of the atomic structure, relaxation processes and phase transformation mechanisms in a variety of chalcogenide (selenides and tellurides) and other non-oxide (Ga-Sb alloys) glasses which are highly relevant to optoelectronic and phase change memory applications. One of the principal goals of these studies is to develop a fundamental, atomistic understanding of the structure-property relationships in these materials. Variable temperature Raman spectroscopy is used to the study the structure and its temperature dependent relaxation in GexSe100-x glasses and supercooled liquids with x ≤ 33.33 %. It is shown that the compositional dependence of the relative fractions of the edge- and corner-shared GeSe4 tetrahedra is fully consistent with a structural model based on random connectivity between the tetrahedral and chain elements. Temperature-dependent structural changes involve a progressive conversion of edge-shared to corner shared GeSe4 tetrahedra with decreasing equilibration temperature. The time scale of this structural conversion agrees with both enthalpy and shear relaxation near the glass transition. The temperature dependent change in the edge- vs. corner- sharing tetrahedral speciation is shown to be related to the production of configurational entropy, indicating a connection between structural relaxation, configurational entropy, and viscous flow. A combination of Raman and 77Se nuclear magnetic resonance (NMR) spectroscopy is applied to study the structure of a series of Se-deficient GexSe100-x glasses, with 42 ≥ x ≥ 33.33. Considerable violation of chemical order in the nearest-neighbor coordination environments of the constituent atoms is observed in the stoichiometric GeSe2 glass. On the other hand, the presence of a random distribution of Ge-Ge bonds can be inferred in the Se-deficient glasses. Furthermore, the results of this study conclusively indicate that the structure of these glasses is intermediate between a randomly connected and a fully clustered network of GeSe4 tetrahedra and Se chains. Additionally, a new two-dimensional NMR spectroscopic technique is developed and applied to Ge-Se glasses that allowed the separation of isotropic and anisotropic chemical shifts. Through the analysis of the anisotropic sideband pattern in the second dimension it is possible to detect up to four distinct types of Se environments in the glass structure on the basis of their characteristic chemical shift anisotropies. 125Te NMR chemical shift systematics is established for coordination environments of Te atoms in a wide range of crystalline and glassy tellurides in the Ga-As-Sb-Te system. 125Te NMR spectroscopy is then used to investigate the short-range structure of amorphous and crystalline Ge1Sb2 Te4 and Ge2Sb2Te5 phase change alloys. Both alloys are found to consist of only heteropolar Ge/Sb-Te bonds in the amorphous and crystalline state and strong vacancy clustering in the nanocrystalline state that may facilitate a rapid displacive transformation between the amorphous and crystalline states without the need of significant atomic rearrangement or diffusion. Based on these 125Te NMR results a Te-centric model of the phase change mechanism in GST alloys is proposed. Structure and phase changes in amorphous Ga-Sb alloys are studied using synchrotron x-ray diffraction and 71Ga and 121Sb NMR spectroscopy. Pressure induced phase transformations in amorphous GaSb is shown to be consistent with the existence of an underlying polyamorphic phase transition between a low and a high-density amorphous phase. NMR results for amorphous Ga46Sb54 indicate that both Ga and Sb atoms are fourfold coordinated with 40% of these atoms participating in homopolar bonding in the as-deposited film. Subsequent crystallization into the zinc blend structure therefore requires extensive bond switching and elimination of homopolar bonds. For amorphous Ga14Sb86 both Ga and Sb atoms are found to be threefold coordinated allowing for a fast phase change kinetics although crystallization of this alloy leads to phase separation of GaSb domains in an Sb matrix, whereby all Ga becomes 4 coordinated. These structural characteristics of the amorphous and crystalline Ga-Sb alloys may have important implications in understanding the kinetics of the associated phase change process that defines the suitability of these materials for non-volatile memory applications.

  8. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    PubMed

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory. PMID:22999222

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

    EPA Science Inventory

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

  10. STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

    EPA Science Inventory

    Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

    Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

  11. What a difference a bond makes: the structural, chemical, and physical properties of methyl-terminated Si(111) surfaces.

    PubMed

    Wong, Keith T; Lewis, Nathan S

    2014-10-21

    The chemical, electronic, and structural properties of surfaces are affected by the chemical termination of the surface. Two-step halogenation/alkylation of silicon provides a scalable, wet-chemical method for grafting molecules onto the silicon surface. Unlike other commonly studied wet-chemical methods of surface modification, such as self-assembly of monolayers on metals or hydrosilylation on silicon, the two-step method enables attachment of small alkyl chains, even methyl groups, to a silicon surface with high surface coverage and homogeneity. The methyl-terminated Si(111) surface, by comparison to hydrogen-terminated Si(111), offers a unique opportunity to study the effects of the first surface bond connecting the overlayer to the surface. This Account describes studies of methyl-terminated Si(111), which have shown that the H-Si(111) and CH3-Si(111) surfaces are structurally nearly identical, yet impart significantly different chemical and electronic properties to the resulting Si surface. The structure of methyl-terminated Si(111) formed by a two-step halogenation/methylation process has been studied by a variety of spectroscopic methods. A covalent Si-C bond is oriented normal to the surface, with the methyl group situated directly atop a surface Si atom. Multiple spectroscopic methods have shown that methyl groups achieve essentially complete coverage of the surface atoms while maintaining the atomically flat, terraced structure of the original H-Si(111) surface. Thus, the H-Si(111) and CH3-Si(111) surface share essentially identical structures aside from the replacement of a Si-H bond with a Si-C bond. Despite their structural similarity, hydrogen and methyl termination exhibit markedly different chemical passivation. Specifically, CH3-Si(111) exhibits significantly greater oxidation resistance than H-Si(111) in air and in aqueous electrolyte under photoanodic current flow. Both surfaces exhibit similar thermal stability in vacuum, and the Si-H and Si-C bond strengths are expected to be very similar, so the results suggest that methyl termination presents a greater kinetic barrier to oxidation of the underlying Si surface. Hydrogen termination of Si(111) provides nearly perfect electronic passivation of surface states (i.e., less than 1 electronic defect per 40 million surface atoms), but this electronic passivation is rapidly degraded by oxidation in air or under electrochemical conditions. In contrast, methyl termination provides excellent electronic passivation that resists degradation due to oxidation. Moreover, alkylation modifies the surface electronic structure by creating a surface dipole that effectively changes the electron affinity of the Si surface, facilitating modification of the charge-transfer kinetics across Si/metal or Si/electrolyte junctions. This Account also briefly describes recent studies of mixed monolayers formed by the halogenation/alkylation of silicon. Mixed monolayers allow attachment of bulkier groups that enable secondary chemistry at the surface (e.g., attachment of molecular catalysts or seeding of atomic layer deposition) to be combined with methyl termination of remaining unreacted surface sites. Thus, secondary chemistry can be enabled while maintaining the chemical and electronic passivation provided by complete termination of surface atoms with Si-C bonds. Such studies of mixed monolayers demonstrate the potential use of a wet-chemical surface modification scheme that combines both chemical and electronic passivation. PMID:25192516

  12. Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

    SciTech Connect

    Saito, M.; Suzuki, S. . E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

    2005-11-15

    Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The two rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.

  13. Structural and chemical trends in doped silicon nanocrystals: First-principles calculations

    NASA Astrophysics Data System (ADS)

    Zhou, Zhiyong; Steigerwald, Michael L.; Friesner, Richard A.; Brus, Louis; Hybertsen, Mark S.

    2005-06-01

    Electronic and structural properties of substitutional group-V donors (N, P, As, Sb) and group-III acceptors (B, Al, Ga, In) in silicon nanocrystals with hydrogen passivation are explored using first-principles calculations based on hybrid density functional theory with complete geometrical optimization. The bonding near the impurity is similar to that found for the impurity in bulk crystalline silicon, with some quantitative differences. The N case shows large local distortions, as it does in the bulk, characteristic of a deep trap. For the other impurities, no evidence is found for a transition to atomic scale localization induced by the small size of the nanocrystal. The chemical trends of the donor and acceptor binding energies and the donor excited state energies in doped nanocrystals are similar to those in the bulk; however, the absolute magnitudes are substantially larger. The increase in the magnitude of the binding energy is mainly due to the quantum confinement effect combined with the reduced screening of the impurity potential in small nanocrystals. The screening of the impurity potential is carefully examined using the self-consistent electrostatic potential from the full calculations. Strong chemical and local-field effects are seen within the radius of the first neighbor bonds to the impurity atom. This explains the large increase in the donor excited state energy level splittings and the relative importance of the central cell contributions to the binding energies. The acceptor and donor orbitals have different atomic character on the impurity site, leading to substantially different acceptor and donor energy level splittings.

  14. An Analysis of Taiwanese Eighth Graders' Science Achievement, Scientific Epistemological Beliefs and Cognitive Structure Outcomes After Learning Basic Atomic Theory.

    ERIC Educational Resources Information Center

    Tsai, Chin-Chung

    1998-01-01

    Explores the interrelationships between students' general science achievement, scientific epistemological beliefs, and cognitive structure outcomes derived from instruction of basic atomic theory. Contains 19 references. (DDR)

  15. A theoretical study of the structures and chemical bonds of neptunium (III) molecules by a density functional method

    NASA Astrophysics Data System (ADS)

    Yin, Yao-Peng; Dong, Chen-Zhong; Du, Lei-Qiang; Wu, Fang-Xian; Ding, Xiao-Bin

    2014-10-01

    In this paper, equilibrium structures and chemical bond characteristics of neptunium trihalide molecules NpX3 (X = F, Cl, Br and I) have been investigated by using density functional theory (DFT). The influences of the size of the relativistic effective core potential (RECP) have been examined on the molecular structures. The chemical bond characteristics have also been systematically studied by calculating the density of states (DOS), bond length differences and electronic charge distributions. We have determined that the chemical bonds are mainly ionic in those molecules, and the covalency is enhancing while ionicity decreases from NpF3 to NpI3. The calculated bond energies show that the interaction strength in NpX3 molecules becomes weaker as the halogen atoms becoming heavier.

  16. An x ray scatter approach for non-destructive chemical analysis of low atomic numbered elements

    NASA Technical Reports Server (NTRS)

    Ross, H. Richard

    1993-01-01

    A non-destructive x-ray scatter (XRS) approach has been developed, along with a rapid atomic scatter algorithm for the detection and analysis of low atomic-numbered elements in solids, powders, and liquids. The present method of energy dispersive x-ray fluorescence spectroscopy (EDXRF) makes the analysis of light elements (i.e., less than sodium; less than 11) extremely difficult. Detection and measurement become progressively worse as atomic numbers become smaller, due to a competing process called 'Auger Emission', which reduces fluorescent intensity, coupled with the high mass absorption coefficients exhibited by low energy x-rays, the detection and determination of low atomic-numbered elements by x-ray spectrometry is limited. However, an indirect approach based on the intensity ratio of Compton and Rayleigh scattered has been used to define light element components in alloys, plastics and other materials. This XRS technique provides qualitative and quantitative information about the overall constituents of a variety of samples.

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

    PubMed

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

    2012-02-28

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

  18. The chemical structure of the Hawaiian mantle plume.

    PubMed

    Ren, Zhong-Yuan; Ingle, Stephanie; Takahashi, Eiichi; Hirano, Naoto; Hirata, Takafumi

    2005-08-11

    The Hawaiian-Emperor volcanic island and seamount chain is usually attributed to a hot mantle plume, located beneath the Pacific lithosphere, that delivers material sourced from deep in the mantle to the surface. The shield volcanoes of the Hawaiian islands are distributed in two curvilinear, parallel trends (termed 'Kea' and 'Loa'), whose rocks are characterized by general geochemical differences. This has led to the proposition that Hawaiian volcanoes sample compositionally distinct, concentrically zoned, regions of the underlying mantle plume. Melt inclusions, or samples of local magma 'frozen' in olivine phenocrysts during crystallization, may record complexities of mantle sources, thereby providing better insight into the chemical structure of plumes. Here we report the discovery of both Kea- and Loa-like major and trace element compositions in olivine-hosted melt inclusions in individual, shield-stage Hawaiian volcanoes--even within single rock samples. We infer from these data that one mantle source component may dominate a single lava flow, but that the two mantle source components are consistently represented to some extent in all lavas, regardless of the specific geographic location of the volcano. We therefore suggest that the Hawaiian mantle plume is unlikely to be compositionally concentrically zoned. Instead, the observed chemical variation is probably controlled by the thermal structure of the plume. PMID:16100780

  19. Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

    ERIC Educational Resources Information Center

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

    The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

  20. Do General Physics Textbooks Discuss Scientists' Ideas about Atomic Structure? A Case in Korea

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Kwon, Sangwoon; Kim, Nahyun; Lee, Gyoungho

    2013-01-01

    Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general…