Science.gov

Sample records for atomic structure chemical

  1. Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy.

    PubMed

    Krivanek, Ondrej L; Chisholm, Matthew F; Nicolosi, Valeria; Pennycook, Timothy J; Corbin, George J; Dellby, Niklas; Murfitt, Matthew F; Own, Christopher S; Szilagyi, Zoltan S; Oxley, Mark P; Pantelides, Sokrates T; Pennycook, Stephen J

    2010-03-25

    Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom. Recently the technique has advanced greatly owing to the introduction of aberration-corrected optics. However, neither electron microscopy nor any other experimental technique has yet been able to resolve and identify all the atoms in a non-periodic material consisting of several atomic species. Here we show that annular dark-field imaging in an aberration-corrected scanning transmission electron microscope optimized for low voltage operation can resolve and identify the chemical type of every atom in monolayer hexagonal boron nitride that contains substitutional defects. Three types of atomic substitutions were found and identified: carbon substituting for boron, carbon substituting for nitrogen, and oxygen substituting for nitrogen. The substitutions caused in-plane distortions in the boron nitride monolayer of about 0.1 A magnitude, which were directly resolved, and verified by density functional theory calculations. The results demonstrate that atom-by-atom structural and chemical analysis of all radiation-damage-resistant atoms present in, and on top of, ultra-thin sheets has now become possible. PMID:20336141

  2. Structural and chemical characterization of complex nanomaterials at atomic resolution

    NASA Astrophysics Data System (ADS)

    Sanchez, Sergio I.

    Catalytic and energetic nanomaterials are analyzed chemically and structurally in atomistic detail. Examination of the prototypical industrial catalyst Pt catalysts supported on gamma-Al2O3 using X-ray absorption spectroscopy (XAS) and scanning transmission electron microscopy (STEM) revealed non-bulk-like behavior. Anomalous, temperature-dependent structural dynamics were characterized in the form of negative thermal expansion (NTE) and abnormal levels of disorder. To examine a less complex system, electrocatalytically-active, core-shell nanostructures assembled from Pt and Pd were synthesized and subsequently examined using spherical aberration-corrected STEM (Cs-STEM) and high-energy X-ray diffraction (XRD). Atomically resolved micrographs provide significant insight into the differences in crystallinity and metal-atom bonding between Pt and Pd. The apparent structural dichotomy between Pt and Pd was extended to studying the differences in nanostructure between other third row fcc transition metals (3M -- Ir, Pt, and Au) and their second row counterparts (2M -- Rh, Pd, and Ag). With the use of Cs-STEM and atomic pair distribution function (PDF) measurements it was determined that the Au, Pt and Ir nanocrystals were more crystalline than their Ag, Pd and Rh analogues and that the 3M series was capable of imparting its crystal structure onto the atoms from the 2M series. Lastly, we looked at highly-reactive Al crystals and their successive passivation by secondary transition metals (Cu, Ni, Ag, Pd, Au and Pt). Rather than affording a uniform, monolayer coverage, C s-STEM, XRD and energy dispersive X-ray spectroscopy revealed unalloyed, particulate deposits of the secondary metal on the Al.

  3. 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.

  4. 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

  5. FROM THE CURRENT LITERATURE: Scanning tunneling microscopy of atomic structure, electronic properties, and surface chemical reactions

    NASA Astrophysics Data System (ADS)

    Maslova, N. S.; Panov, Vladimir I.

    1989-01-01

    This paper is a review of the application of scanning tunneling microscopy (STM) to the study of the electronic properties of clean surfaces, the changes in the electronic properties upon adsorption and surface chemical reactions, and the role that the electronic properties of a surface play in the formation of chemical bonds during reactions and in the formation of surface structures. The effect of the local density of electron states on the STM image of atoms of various elements is shown. A description is given of the electronic properties and the atomic structure of the reconstructed Si(111)-(7×7) surface. The example of the chemical reaction of NH3 with the Si(111)-(7×7) surface is used to show that the reactivity of various atoms is directly related to the presence of localized dangling bonds.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. 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; Ondráček, Martin; Jelínek, 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.

  9. 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.

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

    PubMed Central

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

    2014-01-01

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

  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 BΙ-sites and Fe0.20Ti0.80 at BΙΙ-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems.

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

    PubMed

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

    2014-01-01

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

  17. 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 BΙ-sites and Fe0.20Ti0.80 at BΙΙ-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems.

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

    SciTech Connect

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

    2014-01-01

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

  19. 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

  20. 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.

  1. 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.

  2. Structural and chemical characteristics of atomically smooth GaN surfaces prepared by abrasive-free polishing with Pt catalyst

    NASA Astrophysics Data System (ADS)

    Murata, Junji; Sadakuni, Shun; Okamoto, Takeshi; Hattori, Azusa N.; Yagi, Keita; Sano, Yasuhisa; Arima, Kenta; Yamauchi, Kazuto

    2012-06-01

    This paper reports the structural and chemical characteristics of atomically flat gallium nitride (GaN) surfaces prepared by abrasive-free polishing with platinum (Pt) catalyst. Atomic force microscopy revealed regularly alternating wide and narrow terraces with a step height equivalent to that of a single bilayer on the flattened GaN surfaces, which originate from the differences in etching rate of two neighboring terraces. The material removal characteristics of the method for GaN surfaces were investigated in detail. We confirmed that an atomically smooth GaN surface with an extremely small number of surface defects, including pits and scratches, can be achieved, regardless of the growth method, surface polarity, and doping concentration. X-ray photoelectron spectroscopy showed that the flattening method produces clean GaN surfaces with only trace impurities such as Ga oxide and metallic Ga. Contamination with the Pt catalyst was also evaluated using total-reflection X-ray fluorescence analysis. A wet cleaning method with aqua regia is proposed, which markedly eliminates this Pt contamination without affecting the surface morphology.

  3. Atomic scale chemical fabrication of metal surfaces

    NASA Astrophysics Data System (ADS)

    Tanaka, Ken-ichi; Okawa, Yuji

    1997-10-01

    Adsorption of an oxygen atom at the four-fold hollow site of a Cu(100) surface forces the displacement of the nearest four Cu atoms laterally away from the oxygen atom, which induces stress in the substrate surface. When oxygen coverage exceeds a critical value (ca 0.3 ML), Cu atoms are regularly missed and the (2√2 × √2)R45° reconstruction is established. Contrary to this, when a Cu(110) surface is exposed to O 2, the chemical reaction of Cu atoms produces a quasi-compound of (CuO) strings along the [001] direction which have a tendency to agglomerate into a (2 × 1) structure. The reconstruction assisted by chemical reaction is called "chemical reconstruction". By reacting a quasi-compound of (AgO) strings on Ag(110) with Cu atoms, a (CuO) string grows on the Ag(110) surface in a zigzag manner along the [11¯0] direction. The new quasi-compound of (CuO) strings grown on the Ag(110) surface undergo a reversible reaction of (CuO)⇄(Cu) 6+O 2. It was found that the chemical transportation of Cu atoms from a W-tip onto the Ag(110) surface is also assisted by the formation of a quasi-compound. Photo chemical reaction of quasi-compounds suggested the feasibility of the nano-scale photo fabrication of the surface.

  4. 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.

  5. 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

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

    PubMed

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

    2014-01-01

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

  7. 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.

  8. 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…

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

    ERIC Educational Resources Information Center

    Wang, Chia-Yu; Barrow, Lloyd H.

    2013-01-01

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

  10. 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.

  11. 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

  12. RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.

    SciTech Connect

    HOLDEN, N.E.

    2005-08-13

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

  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. 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

  15. Direct Atom Imaging by Chemical-Sensitive Holography.

    PubMed

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

    2016-05-11

    In order to understand the physical and chemical properties of advanced materials, functional molecular adsorbates, and protein structures, a detailed knowledge of the atomic arrangement is essential. Up to now, if subsurface structures are under investigation, only indirect methods revealed reliable results of the atoms' spatial arrangement. An alternative and direct method is three-dimensional imaging by means of holography. Holography was in fact proposed for electron waves, because of the electrons' short wavelength at easily accessible energies. Further, electron waves are ideal structure probes on an atomic length scale, because electrons have a high scattering probability even for light elements. However, holographic reconstructions of electron diffraction patterns have in the past contained severe image artifacts and were limited to at most a few tens of atoms. Here, we present a general reconstruction algorithm that leads to high-quality atomic images showing thousands of atoms. Additionally, we show that different elements can be identified by electron holography for the example of FeS2. PMID:27070050

  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 community. The book would also be useful to someone seeking a survey of the physics of atomic structure and how it can be calculated. A limitation of the book is that it covers only isolated atoms and ions. Density effects are not covered. Plasma physicists, especially spectroscopists, interested in calculating line positions, line strengths and other atomic properties will find this book and suite of codes useful.

  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. 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)

  20. Effects of nitrogen incorporation in HfO(2) grown on InP by atomic layer deposition: an evolution in structural, chemical, and electrical characteristics.

    PubMed

    Kang, Yu-Seon; Kim, Dae-Kyoung; Kang, Hang-Kyu; Jeong, Kwang-Sik; Cho, Mann-Ho; Ko, Dae-Hong; Kim, Hyoungsub; Seo, Jung-Hye; Kim, Dong-Chan

    2014-03-26

    We investigated the effects of postnitridation on the structural characteristics and interfacial reactions of HfO2 thin films grown on InP by atomic layer deposition (ALD) as a function of film thickness. By postdeposition annealing under NH3 vapor (PDN) at 600 °C, an InN layer formed at the HfO2/InP interface, and ionized NHx was incorporated in the HfO2 film. We demonstrate that structural changes resulting from nitridation of HfO2/InP depend on the film thickness (i.e., a single-crystal interfacial layer of h-InN formed at thin (2 nm) HfO2/InP interfaces, whereas an amorphous InN layer formed at thick (>6 nm) HfO2/InP interfaces). Consequently, the tetragonal structure of HfO2 transformed into a mixture structure of tetragonal and monoclinic because the interfacial InN layer relieved interfacial strain between HfO2 and InP. During postdeposition annealing (PDA) in HfO2/InP at 600 °C, large numbers of oxidation states were generated as a result of interfacial reactions between interdiffused oxygen impurities and out-diffused InP substrate elements. However, in the case of the PDN of HfO2/InP structures at 600 °C, nitrogen incorporation in the HfO2 film effectively blocked the out-diffusion of atomic In and P, thus suppressing the formation of oxidation states. Accordingly, the number of interfacial defect states (Dit) within the band gap of InP was significantly reduced, which was also supported by DFT calculations. Interfacial InN in HfO2/InP increased the electron-barrier height to ∼0.6 eV, which led to low-leakage-current density in the gate voltage region over 2 V. PMID:24467437

  1. 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.

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

    SciTech Connect

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

    1996-09-01

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

  3. 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

  4. 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.

  5. 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)

  6. Chemical reactivity of the spherically confined atoms

    NASA Astrophysics Data System (ADS)

    Chattaraj, P. K.; Sarkar, U.

    2003-05-01

    Softness, polarizability and mean excitation energy are calculated for several atoms confined in a spherical box, using numerical Hartree-Fock technique with a Dirichlet boundary condition. Both softness and polarizability increase and mean excitation energy decreases and ultimately level off when the size of the box increases. In general softness and polarizability decrease along a period and increase along a group of the periodic table. Softness varies linearly with the cuberoot of polarizability for all the confined systems. Energy, virial and various moments follow the expected trends.

  7. 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)

  8. 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.

  9. About the atomic structures of icosahedral quasicrystals

    NASA Astrophysics Data System (ADS)

    Quiquandon, Marianne; Gratias, Denis

    2014-01-01

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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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)

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

    NASA Astrophysics Data System (ADS)

    Chen, Hsin-Yi; Wei, Ching-Ming

    2007-03-01

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

  16. 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.

  17. Atomic vapor spectroscopy in integrated photonic structures

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  18. Atomic vapor spectroscopy in integrated photonic structures

    SciTech Connect

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

    2015-07-27

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

  19. Molecular beam studies of hot atom chemical reactions: Reactive scattering of energetic deuterium atoms

    SciTech Connect

    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/ /minus/> DH + H and the substitution reaction D + C/sub 2/H/sub 2/ /minus/> 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. 18 refs., 9 figs.

  20. 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.

  1. 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.

  2. 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.

  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. 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

  7. 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.

  8. Chemically induced magnetism in atomically precise gold clusters.

    PubMed

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

    2014-03-12

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

  9. 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.

  10. 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}.

  11. 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

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

    SciTech Connect

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

    2013-04-29

    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 La{sub 0.7}Sr{sub 0.3}MnO{sub 3} and antiferromagnetic BiFeO{sub 3} 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2016-04-13

    Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena. PMID:26943670

  15. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

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

    2016-05-11

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

  16. 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.

  17. 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.

  18. 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)

  19. 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.

  20. Hyperfine structure of hydrogenlike and lithiumlike atoms

    SciTech Connect

    Shabaev, V.M.; Shabaeva, M.B.; Tupitsyn, I.I.

    1995-11-01

    The hyperfine splitting values of the ground state of the hydrogenlike atoms {sup 13}C{sup 5+}, {sup 14}N{sup 6+}, {sup 17}O{sup 7+} and the lithiumlike atoms {sup 7}Li{sup 0}, {sup 14}N{sup 4+}, {sup 19}F{sup 6+}, {sup 23}Na{sup 8+}, {sup 25}Mg{sup 9+}, {sup 27}Al{sup 10+}, {sup 29}Si{sup 11+}, {sup 35}Cl{sup 14+}, {sup 57}Fe{sup 23+} are calculated. The calculations of the lithiumlike ions ({ital Z}{ge}7) are based on a combination of the 1/{ital Z} perturbation theory and the configuration interaction Hartree-Fock method. The relativistic corrections are calculated in the zeroth and first orders in 1/{ital Z}. The nuclear charge and magnetization distribution corrections and the radiative corrections are taken into account. The uncertainty of the calculations is estimated to be {similar_to}0.02% for the hydrogenlike ions and {similar_to}0.06% for the lithiumlike ions, except {sup 57}Fe{sup 23+}, for which the uncertainty is about 0.15%. The hyperfine structure constant of the ground state of Li is calculated to be {ital A}=401.5(4) MHz. The results of the calculations are compared with the theoretical values obtained with other methods and with experiment.

  1. Automated extraction of chemical structure information from digital raster images

    PubMed Central

    Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

    2009-01-01

    Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

  2. 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.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01403h

  6. 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.

  7. X-ray emission from chemically bound atoms

    NASA Astrophysics Data System (ADS)

    Günther, C.; Hartmann, E.; Lauterbach, Ch.; Hormes, J.

    1996-04-01

    For the application of PIXE and related X-ray spectroscopic techniques to inferring ionization cross sections or elemental abundances from measured X-ray line intensities, precise knowledge of de-excitation parameters such as fluorescence yields and relative X-ray line intensities is indispensable. For a theoretical derivation of such quantities due consideration must be given to both intra- and interatomic relaxation which have different effects on radiative one-electron and nonradiative two-electron transitions. In particular, the scattered-wave approach to the electronic structure has proved exceedingly useful to simultaneously model X-ray and Auger transitions occurring in atoms embedded in their actual surroundings, thereby including the effects of both ordinary static as well as configuration-induced transitory covalency. Recent studies of environmental effects on S K-shell Auger satellite spectra disclosed some implications for X-ray spectroscopic measurements. Particular emphasis is laid on the relationship to the speciation of third-row atoms in samples of practical relevance.

  8. Chemical Structure Handling by Computer.

    ERIC Educational Resources Information Center

    Paris, C. Gregory

    1997-01-01

    Organized from the viewpoint of information retrieval theory, this review addresses issues of chemical information representation, comparison and matching, and retrieval strategies. Additional topics include similarity and clustering, visualization, and molecular diversity. Trends in research and application are identified, and gaps in the…

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

    PubMed

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

    2016-04-14

    Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces. PMID:27030282

  10. 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.

  11. 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

  12. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

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

    2014-01-01

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

  13. [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

  14. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

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

  15. Bulk chemical properties of new elements from one-atom-at-a-time data

    NASA Astrophysics Data System (ADS)

    Zvára, I.

    2006-01-01

    For the volatile (oxo)halides of known elements the energies of desorption from the surface of fused silica measured in radiochemical gas-solid chromatographic experiments proved close to the sublimation energies. This could hardly be expected for interaction of isolated molecules with bare surface of ionic SiO2. Because such regularity shows great promise for evaluation of bulk properties of transactinoid compounds we need to understand the origin of apparent inconsistency. The clue seems to be the real structure of the surface. It is initially rough (from µm down to nm scale), inherently heterogeneous at the molecular level, and contains atoms and groups with excessive energy. Exposing to ambient air produces numerous surface ≡SiOH groups. The halogenating agents employed in transactinoid studies chemically modify such surface: it gets tightly covered by halogen atoms and fragments of the agent molecule attached to the Si and O atoms. Now the molecules of new compounds cannot touch SiO2 lattice; moreover, in some initially geometric wells (due to roughness), they get surrounded by halogen atoms bonded to the surface — the situation resembling that in their own bulk condensed phase. Hence, there must be sites with desorption energies up to the sublimation energy.

  16. Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Kim, Duckhoe; Sahin, Ozgur

    2015-03-01

    Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

  17. 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.

  18. 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

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

    SciTech Connect

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

    2009-05-12

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

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

    NASA Astrophysics Data System (ADS)

    Ansari, Reza; Ajori, Shahram; Malakpour, Sina

    2016-04-01

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

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

    SciTech Connect

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

    2014-05-07

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

  2. 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.

  3. Ability to Control a Titanium-Alloy Structure by Atomic-Emission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Molchan, N. V.; Polkin, I. S.; Fertikov, V. I.

    2014-05-01

    The effect of material structure on the analytical signal was studied using atomic emission spectroscopy with spark excitation of solids. A method for assessing the structure of the titanium alloy was proposed. It consisted of repeated analysis of a series of samples before and after heat treatment with excitation and recording of the spectrum under identical conditions followed by statistical processing of the results. The effects on the alloy structure of two heattreatment regimes, quenching and annealing, were studied. Atomic-emission spectroscopy with inductively coupled plasma was used to control the homogeneity of the chemical composition in the test samples.

  4. 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.

  5. 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.

  6. 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

  7. 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…

  8. 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

  9. 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.

  10. 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…

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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)

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  1. Relating Dynamic Properties to Atomic Structure in Metallic Glasses

    SciTech Connect

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

    2012-07-18

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

  2. Atom-atom potentials and the crystal structure simulation of long linear chain carboxylic acids

    NASA Astrophysics Data System (ADS)

    Michopoulos, Yanos; Adam, Craig D.; Leslie, Maurice

    Using appropriate inter and intramolecular atom-atom potential functions we have simulated the crystal structures of the C-form of n-dodecanoic and B- and C-forms of n-octadecanoic acids by lattice energy minimization. The molecular packing, in particular the intermolecular hydrogen bonds, and the lattice energies are in good agreement with available experimental evidence while the relative energies of the two polymorphic phases of n-octadecanoic acid are correctly predicted. Full unit cell relaxation reveals a systematic discrepancy with experimental values which is interpreted in terms of recognized anisotropy in thermal expansion of such structures. This work confirms the transferability of atom-atom potentials from small molecular crystals to far larger related systems.

  3. Structural evolution during the reduction of chemically derived graphene oxide

    NASA Astrophysics Data System (ADS)

    Bagri, Akbar; Mattevi, Cecilia; Acik, Muge; Chabal, Yves J.; Chhowalla, Manish; Shenoy, Vivek B.

    2010-07-01

    The excellent electrical, optical and mechanical properties of graphene have driven the search to find methods for its large-scale production, but established procedures (such as mechanical exfoliation or chemical vapour deposition) are not ideal for the manufacture of processable graphene sheets. An alternative method is the reduction of graphene oxide, a material that shares the same atomically thin structural framework as graphene, but bears oxygen-containing functional groups. Here we use molecular dynamics simulations to study the atomistic structure of progressively reduced graphene oxide. The chemical changes of oxygen-containing functional groups on the annealing of graphene oxide are elucidated and the simulations reveal the formation of highly stable carbonyl and ether groups that hinder its complete reduction to graphene. The calculations are supported by infrared and X-ray photoelectron spectroscopy measurements. Finally, more effective reduction treatments to improve the reduction of graphene oxide are proposed.

  4. Atomic structure and dynamics of metal dopant pairs in graphene.

    PubMed

    He, Zhengyu; He, Kuang; Robertson, Alex W; Kirkland, Angus I; Kim, Dongwook; Ihm, Jisoon; Yoon, Euijoon; Lee, Gun-Do; Warner, Jamie H

    2014-07-01

    We present an atomic resolution structural study of covalently bonded dopant pairs in the lattice of monolayer graphene. Two iron (Fe) metal atoms that are covalently bonded within the graphene lattice are observed and their interaction with each other is investigated. The two metal atom dopants can form small paired clusters of varied geometry within graphene vacancy defects. The two Fe atoms are created within a 10 nm diameter predefined location in graphene by manipulating a focused electron beam (80 kV) on the surface of graphene containing an intentionally deposited Fe precursor reservoir. Aberration-corrected transmission electron microscopy at 80 kV has been used to investigate the atomic structure and real time dynamics of Fe dimers embedded in graphene vacancies. Four different stable structures have been observed; two variants of an Fe dimer in a graphene trivacancy, an Fe dimer embedded in two adjacent monovacancies and an Fe dimer trapped by a quadvacancy. According to spin-sensitive DFT calculations, these dimer structures all possess magnetic moments of either 2.00 or 4.00 μB. The dimer structures were found to evolve from an initial single Fe atom dopant trapped in a graphene vacancy. PMID:24945707

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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…

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

    Amorphous hydrogenated silicon nitride (SiNH) materials prepared by plasma-enhanced chemical vapor deposition (PECVD) are of high interest because of their suitability for diverse applications including optical coatings, gas/vapor permeation barriers, corrosion resistant, and protective coatings and numerous others. In addition, they are very suitable for structurally graded systems such as those with a graded refractive index. In parallel, modeling the PECVD process of SiN(H) of an a priori given SiN(H) ratio by atomistic calculations represents a challenge due to: (1) different (and far from constant) sticking coefficients of individual elements, and (2) expected formation of N2 (and H2) gas molecules. In the present work, we report molecular-dynamics simulations of particle-by-particle deposition process of SiNH films from SiHx and N radicals. We observe formation of a mixed zone (damaged layer) in the initial stages of film growth, and (under certain conditions) formation of nanopores in the film bulk. We investigate the effect of various PECVD process parameters (ion energy, composition of the SiHx+N particle flux, ion fraction in the particle flux, composition of the SiHx radicals, angle of incidence of the particle flux) on both (1) deposition characteristics, such as sticking coefficients, and (2) material characteristics, such as dimension of the nanopores formed. The results provide detailed insight into the complex relationships between these process parameters and the characteristics of the deposited SiNH materials and exhibit an excellent agreement with the experimentally observed results.

  12. 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,…

  13. 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,

  14. 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.

  15. 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).

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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: 2̂=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 π/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 π/2 pulses. Following this scheme, we have performed in 2010 a measurement of α with an uncertainty of 6.6 x10-10. Our final result is: 1/α= 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.

  5. 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.

  6. Hartree-Fock electronic structure calculations for free atoms and immersed atoms in an electron gas

    NASA Astrophysics Data System (ADS)

    Walsh, Kenneth Charles

    Electronic structure calculations for free and immersed atoms are performed in the context of unrestricted Hartree-Fock Theory. Spherical symmetry is broken, lifting degeneracies in electronic configurations involving the magnetic quantum number mℓ. Basis sets, produced from density functional theory, are then explored for completeness. Comparison to spectroscopic data is done by a configurational interaction of the appropriate L and S symmetry. Finally, a perturbation technique by Lowdin is used to couple the bound atomic states to a neutral, uniform background electronic gas (jellium).

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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)

  13. 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

  14. 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.

  15. Two-Atom Structures of Ge on Si(100): Dimers versus Adatom Pairs

    SciTech Connect

    da Silva, Antonio J. R.; Dalpian, G. M.; Janotti, A.; Fazzio, A.

    2001-07-16

    We present an ab initio study of the properties of structures composed of two and four Ge atoms adsorbed on the troughs of the Si(100) surface, and we conclude that these structures are all composed of dimers, with a chemical bonding between the adatoms. We compare our calculated local density of states with scanning tunneling microscope (STM) images, and we show that these Ge dimers adsorbed on the troughs between the substrate dimer rows can be identified with the adatom pairs observed experimentally. We also show that the local buckling of the substrate dimers can give rise to similar structures with very different STM images.

  16. Drop impact on chemically structured arrays

    NASA Astrophysics Data System (ADS)

    Mock, Ulrike; Michel, Tobias; Tropea, Cameron; Roisman, Ilia; Rühe, Jürgen

    2005-03-01

    We describe recent investigations on the impact behaviour of liquid drops onto chemically structured surfaces. The surface patterns were prepared via photochemical attachment of polymer molecules with different hydrophilicities using self-assembled monolayers of benzophenone bearing silanes. Immobilization of the polymer monolayers was followed by an ablation process to generate a chemical surface pattern. Impact experiments on systems consisting of very hydrophobic poly(perfluoroalkylethyl)acrylate coatings and hydrophilic areas show that within certain limitations the water drop has a strong tendency to reach the hydrophilic spots, even for inclined substrates. Impact experiments of drops on arrays of hydrophilic spots on the background of a perfluorinated polymer show that the drops spontaneously self-centre on the lithographically generated pattern. The obtained results suggest that the process can be used to circumvent some of the current problems in micro-array fabrication.

  17. 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.

  18. 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.

  19. Structure and dynamics in two-electron atoms

    NASA Astrophysics Data System (ADS)

    Shuman, Edward Somerville

    In this dissertation, I present experimental studies of two-electron atoms. I have been primarily concerned with the effects of external perturbations on dielectronic recombination (DR). Specifically I have examined dielectronic recombination in the presence of electric, microwave, and combined electric and magnetic fields. These measurements illustrate that any external perturbation must have a coupling in excess of the autoionization rate to affect the DR rate. I have also studied the structure of two-electron atoms using microwave resonance techniques. In particular I present experiments which provide new insight into the core polarization model and which provide techniques for measuring both bound and autoionizing energy levels with microwaves.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed Central

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

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. 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.

  6. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

    PubMed

    Hattori, Masahiro; Okuno, Yasushi; Goto, Susumu; Kanehisa, Minoru

    2003-10-01

    Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes. PMID:14505407

  7. 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

  8. 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.

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

    PubMed Central

    van den Bedem, Henry; Fraser, James S.

    2015-01-01

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

  10. 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

  11. Interfacial Atomic Structure of Twisted Few-Layer Graphene

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  12. 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 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

  13. 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

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

    PubMed

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

    2013-12-01

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

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

    PubMed Central

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

    2008-01-01

    The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS2 nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS2 nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism. PMID:18838681

  16. 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.

  17. 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.

  18. 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

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

    PubMed

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

    2014-04-01

    Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating ¹H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases. PMID:24584194

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

    SciTech Connect

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

    2007-01-01

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

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

    DOE PAGESBeta

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

    2016-01-05

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

  2. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

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

    2015-11-15

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

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

    SciTech Connect

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

    1997-11-01

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

  4. 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.

  5. 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.

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

    SciTech Connect

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

    2014-10-13

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

  7. 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

  8. 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

  9. 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.

  10. B-spline algorithm for magnetized multielectron atomic structures

    NASA Astrophysics Data System (ADS)

    Zhao, L. B.; Stancil, P. C.

    2008-03-01

    A B-spline algorithm has been developed to evaluate the electronic structure of multielectron atoms in a magnetic field. A generalized electron configuration concept, which is crucial to perform the current investigation, was introduced to solve Hartree-Fock equations. The wave functions for electron orbitals of the magnetized multielectron atom are expanded in terms of a B-spline basis in the radial direction and spherical harmonics in the angular direction. The developed algorithm has been applied to calculations of He in a magnetic field. Energy levels of magnetized He in the ground state are presented as a function of magnetic field strength with a range from zero up to 2.35×107T and compared with available theoretical data.

  11. 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.

  12. Absence of a stable atomic structure in fluorinated graphene.

    PubMed

    Boukhvalov, Danil W

    2016-05-21

    Based on the results of first-principles calculations we demonstrate that significant distortion of graphene sheets caused by adsorption of fluorine atoms leads to the formation of metastable patterns for which the next step of fluorination is considerably less energetically favorable. Existence of these stable patterns oriented along the armchair direction makes possible the synthesis of various CFx structures. The combination of strong distortion of the nonfluorinated graphene sheet with the doping caused by the polar nature of C-F bonds reduces the energy cost of migration and the energy of migration barriers, making possible the migration of fluorine atoms on the graphene surface as well as transformation of the shapes of fluorinated areas. The decreasing energy cost of migration with increasing fluorine content also leads to increasing numbers of single fluorine adatoms, which could be the source of magnetic moments. PMID:27116897

  13. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-05-28

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

  15. Atomic and electronic structure of decagonal Al-Ni-Co alloys and approximant phases

    NASA Astrophysics Data System (ADS)

    Krajčí, M.; Hafner, J.; Mihalkovič, M.

    2000-07-01

    Detailed investigations of the atomic and electronic structures of decagonal AlNiCo alloys have been performed. Several different models for the decagonal structure have been investigated: A model based on a rhombic-hexagon tiling proposed by Henley and models based on a cluster decoration of the Penrose tiling with large rhombus edge. The topology of the structural models has been refined on the basis of the existing x-ray-diffraction data which, however, do not allow us to specify the chemical decoration uniquely. The chemical order on the decagonal lattice has been optimized via the comparison of the calculated electronic spectra with photoemission and soft-x-ray data and using total-energy calculations. The electronic structure calculations for large periodic approximants with up to 1276 atoms/cell have been performed self-consistently using a real-space tight-binding linear muffin-tin orbital technique. The best agreement with the experimental spectra is achieved for a large-rhombus-tiling model with the innermost ring of the pentagonal columnar clusters occupied by Ni atoms only. This configuration also has the lowest total energy. As in decagonal AlCuCo we find a high density of states at the Fermi level, but the chemical ordering is very different: whereas in d-AlCuCo direct Cu-Cu neighbors are suppressed and there is a slight preference for Co-Co homocoordination, in d-AlNiCo a strong Ni-Ni interaction stabilizes the innermost Ni ring, direct Co-Co neighbors are suppressed and there is a strong Co-Al interaction.

  16. 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.

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

    PubMed

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

    2016-05-19

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

  18. Gas-phase silicon atom densities in the chemical vapor deposition of silicon from silane

    SciTech Connect

    Coltrin, M.E.; Breiland, W.G.; Ho, P.

    1993-12-31

    Silicon atom number density profiles have been measured using laser-induced fluorescence during the chemical vapor deposition of silicon from silane. Measurements were obtained in a rotating-disk reactor as a function of silane partial pressure and the amount of hydrogen added to the carrier gas. Absolute number densities were obtained using an atomic absorption technique. Results were compared with calculated density profiles from a model of the coupled fluid flow, gas-phase and surface chemistry for an infinite-radius rotating disk. An analysis of the reaction mechanism showed that the unimolecular decomposition of SiH{sub 2} is not the dominant source of Si atoms. Profile shapes and positions, and all experimental trends are well matched by the calculations. However, the calculated number density is up to 100 times smaller than measured.

  19. 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.

  20. Ordering of carbon atoms in boron carbide structure

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

    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.

  1. 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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

  4. 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.

  5. 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.

  6. 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.

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

    PubMed

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

    2014-04-30

    The complex coupling of atomic, chemical, and electronic transformations across multiple length scales underlies the performance of electrochemical energy storage devices. Here, the coupling of chemistry with atomic- and nanoscale structure in iron conversion electrodes is resolved by combining pair distribution function (PDF) and small-angle X-ray scattering (SAXS) analysis for a series of Fe fluorides, oxyfluorides, and oxides. The data show that the anion chemistry of the initial electrode influences the abundance of atomic defects in the Fe atomic lattice. This, in turn, is linked to different atom mobilities and propensity for particle growth. Competitive nanoparticle growth in mixed anion systems contributes to a distinct nanostructure, without the interconnected metallic nanoparticles formed for single anion systems. PMID:24735418

  8. 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.

  9. Chemical alteration of thin alumina films on aluminum during hydrogen-atom exposures

    NASA Astrophysics Data System (ADS)

    Epling, William S.; Mount, Charles K.; Hoflund, Gar B.; Young, Vaneica Y.

    1998-04-01

    Hot-rolled and partially oxidized Al foil surfaces were examined before and after H-atom exposures using X-ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy (ISS) to monitor the changes which occur at the sample surfaces. The near-surface region of the native oxide of the hot-rolled Al foil contains primarily C and O. Cl and Ca contamination also are present at the outermost atomic layer according to ISS. H-atom exposures reduce the amount of carbonates and hydrocarbons but causes an enrichment of sulfur in the outermost layer of the foil. The O-to-Al ratio is reduced, and the AlO x species initially present is converted to Al 2O 3. After sputtering the Al foil to remove the Cl, C, and Ca contaminants, the Al was exposed to oxygen at 10 -7 Torr for 10 min. The near-surface region of this re-oxidized surface contains both Al metal and Al 2O 3. Exposing this partially oxidized surface to H-atoms produces a chemically-induced driving force which causes subsurface O to migrate toward the surface of the foil. This results in an increase of the Al 2O 3 concentration at the sample surface. These results suggest that the thickness of Al oxide layers may be controlled using H-atom exposures. Furthermore, the amounts of carbon contamination can be decreased and possibly eliminated without reducing the alumina.

  10. Atomic structure and hierarchical assembly of a cross-β 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; Müller, 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-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-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-β 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 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. PMID:23513222

  11. Atomic structure and hierarchical assembly of a cross-β amyloid fibril

    PubMed Central

    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; Müller, 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.

    2013-01-01

    The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-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-β 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 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. PMID:23513222

  12. 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

  13. Atomic structure of amorphous shear bands in boron carbide

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-01-01

    Amorphous shear bands are the main deformation and failure mode of super-hard boron carbide subjected to shock loading and high pressures at room temperature. Nevertheless, the formation mechanisms of the amorphous shear bands remain a long-standing scientific curiosity mainly because of the lack of experimental structure information of the disordered shear bands, comprising light elements of carbon and boron only. Here we report the atomic structure of the amorphous shear bands in boron carbide characterized by state-of-the-art aberration-corrected transmission electron microscopy. Distorted icosahedra, displaced from the crystalline matrix, were observed in nano-sized amorphous bands that produce dislocation-like local shear strains. These experimental results provide direct experimental evidence that the formation of amorphous shear bands in boron carbide results from the disassembly of the icosahedra, driven by shear stresses. PMID:24052052

  16. 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.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  19. 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.

  20. 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

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  3. 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

  4. 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.

  5. 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

  6. An atomic force microscopy investigation of cyanophage structure.

    PubMed

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

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  8. 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.

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

    PubMed

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

    2015-12-01

    The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized. PMID:26627656

  10. Electronic Structure of Helium Atom in a Quantum Dot

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  11. 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

  12. 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)

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

    SciTech Connect

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

    2015-06-24

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

  14. 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 0.136 nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78 Å. Furthermore, the relative positions of the atoms in the chemical composition line scan signals could be directly interpreted from the corresponding incoherent high-angle annular dark-field image. PMID:25426003

  15. First Optical Hyperfine Structure Measurement in an Atomic Anion

    SciTech Connect

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

    2010-02-19

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

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

    PubMed

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

    2009-09-16

    A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content, where M is either niobium or tantalum. The glasses are found to consist of tetrahedral borate and phosphate with octahedral MO(6). As expected, B and P play the roles of tetrahedral network formers. At low M content there are isolated MO(6) units with [Formula: see text] and [Formula: see text] linkages that contribute to the glass network. As the M content increases, the number of [Formula: see text] links increases, and at the highest M content each MO(6) unit is connected to several others. The octahedra become significantly distorted as the niobium content increases, an effect that is not seen for tantalum. PMID:21832337

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

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

    A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content, where M is either niobium or tantalum. The glasses are found to consist of tetrahedral borate and phosphate with octahedral MO6. As expected, B and P play the roles of tetrahedral network formers. At low M content there are isolated MO6 units with \\mathrm {P{\\cdots }M} and \\mathrm {B{\\cdots }M} linkages that contribute to the glass network. As the M content increases, the number of \\mathrm {M{\\cdots }M} links increases, and at the highest M content each MO6 unit is connected to several others. The octahedra become significantly distorted as the niobium content increases, an effect that is not seen for tantalum.

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

    PubMed

    Villarreal, R; Longobardi, M; Köster, 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

  19. 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.

  20. 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.

  1. 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

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

    PubMed

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

    2016-05-01

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species. PMID:27070292

  3. The grasp2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

    This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectra—atomic energy levels, oscillator strengths, and radiative decay rates—using a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator Π=βπ. 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)

  4. 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.

  5. Chemically gated electronic structure of a superconducting doped topological insulator system

    NASA Astrophysics Data System (ADS)

    Wray, L. A.; Xu, S.; Neupane, M.; Fedorov, A. V.; Hor, Y. S.; Cava, R. J.; Hasan, M. Z.

    2013-07-01

    Angle resolved photoemission spectroscopy is used to observe changes in the electronic structure of bulk-doped topological insulator CuxBi2Se3 as additional copper atoms are deposited onto the cleaved crystal surface. Carrier density and surface-normal electrical field strength near the crystal surface are estimated to consider the effect of chemical surface gating on atypical superconducting properties associated with topological insulator order, such as the dynamics of theoretically predicted Majorana Fermion vortices.

  6. 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.

  7. An atomic structure of human γ-secretase.

    PubMed

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

    2015-09-10

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

  8. An atomic structure of human γ-secretase

    PubMed Central

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

    2015-01-01

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

  9. Chemical structure representations and applications in computational toxicity.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

  11. 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.

  12. 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.

  13. Colloidal palladium—a promising chemical modifier for electrothermal atomic absorption spectrometry

    NASA Astrophysics Data System (ADS)

    Volynsky, Anatoly B.; Krivan, Viliam

    1997-07-01

    The efficiencies of chemical modifiers based on palladium for electrothermal atomic absorption spectrometry (ETAAS) were compared. The main attention was devoted to the comparison of two types of colloidal palladium with a mixture of palladium nitrate and magnesium nitrate or a mixture of ammonium dihydrogenphosphate and magnesium nitrate. The modifiers were applied to model solutions of the analytes Se, Cd, Te and Sn containing sodium sulphate, sodium chloride and glucose as matrix components. In general, no significant difference in effectiveness was found between the polymer-stabilized colloidal palladium and other chemical modifiers studied. Colloidal palladium stabilized with polyvinylpyrrolidone ( Mr ˜ 360 000) has proved to be as effective as colloidal palladium stabilized with the surfactant lauryldimethylcarboxymethylammonium betaine. However, concentrated solutions of the former modifier can be prepared easily and kept for a long time at room temperature. The increase in the palladium particle size in solution from 2-10 nm to 20-2000 nm resulting from storage for 16 months did not significantly influence the effectiveness of the modifier. Colloidal palladium can be considered as a prospective aid to the investigation of processes in graphite atomizers.

  14. 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.

  15. Drawing Chemical Structures with the Apple Macintosh.

    ERIC Educational Resources Information Center

    Kauffman, Joel M.; Zogott, Joyce D.

    1985-01-01

    A Macintosh microcomputer and MacPaint program can be used to quickly make charts of structural formulas that fill standard-sized paper with a minimum of instruction, and smaller drawings or structures or fragments may be inserted into text composed with a word processing program. Shows how this is done. (JN)

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

    SciTech Connect

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

    1993-12-01

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

  17. 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

  18. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    A revised version of GRASP2K [P. Jönsson, 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, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A 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.

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

    SciTech Connect

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

    2010-05-17

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

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

    PubMed Central

    Buehler, Markus J.

    2013-01-01

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

  1. 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.…

  2. 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

  3. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  4. 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

  5. Correlating Atomic Structure and Transport in Suspended Graphene Nanoribbons

    PubMed Central

    2015-01-01

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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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.

  13. 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.

  14. 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.

  15. Laser-controlled moving atomic structures for microelectronics

    NASA Astrophysics Data System (ADS)

    Sovetov, Nikolay M.; Nikonov, Anatoly V.; Naumova, Elena V.; Moskovsky, Victor A.; Grigoriev, Dmitry A.

    1997-05-01

    One proposes the method of neutral atom beam formation due to effect of neutral atoms long-time localization in the minimums of potentials of intense standing wave of resonant light with simultaneous influence of cooling radiation. For fields of complicated configurati on the resonant light pressure force and the momentum diffusion tensor of two-level atom ensemble are presented. Mathematical modeling is based on the solving of equations for their spatial terms. One shows that with cooling time about 2 - 3 ms and with manipulation of intensity of co-propagated light wave, the arbitrary given cross-section atom density distribution with the contrast up to 1000 can be produced. One demonstrates that size of localization region can be essentially decreased by sweeping of cooling light carrier frequency in the range about 2 - 3 widths of moving atoms spectral transition lines. Low temperature cooling of atoms in the beam and 'soft' output from interaction region allow us to produce the well-manipulated practically aberration-off process. In this case transverse compression of image in cross-section of atomic beam can reach to 106 with given level of contrast. Calculations shows that at modern level of laser technique the spatial resolution of such process can reach to 30 - 50 A. The possibility of using of given method for high-resolution development and the analyses of micro-object surfaces is discussed.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. Influence of the chemical structure of functional monomers on their adhesive performance.

    PubMed

    Van Landuyt, K L; Yoshida, Y; Hirata, I; Snauwaert, J; De Munck, J; Okazaki, M; Suzuki, K; Lambrechts, P; Van Meerbeek, B

    2008-08-01

    Functional monomers in adhesive systems can improve bonding by enhancing wetting and demineralization, and by chemical bonding to calcium. This study tested the hypothesis that small changes in the chemical structure of functional monomers may improve their bonding effectiveness. Three experimental phosphonate monomers (HAEPA, EAEPA, and MAEPA), with slightly different chemical structures, and 10-MDP (control) were evaluated. Adhesive performance was determined in terms of microtensile bond strength of 4 cements that differed only for the functional monomer. Based on the Adhesion-Decalcification concept, the chemical bonding potential was assessed by atomic absorption spectrophotometry of the dissolution rate of the calcium salt of the functional monomers. High bond strength of the adhesive cement corresponded to low dissolution rate of the calcium salt of the respective functional monomer. The latter is according to the Adhesion-Decalcification concept, suggestive of a high chemical bonding capacity. We conclude that the adhesive performance of an adhesive material depends on the chemical structure of the functional monomer. PMID:18650548

  1. 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

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

    SciTech Connect

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

    2015-08-29

    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.

  3. 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.

  4. 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.

    2015-01-01

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

  5. 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.

  6. Drug-induced changes of cytoskeletal structure and mechanics in fibroblasts: an atomic force microscopy study.

    PubMed Central

    Rotsch, C; Radmacher, M

    2000-01-01

    The effect of various drugs affecting the integrity of different components of the cytoskeleton on the elasticity of two fibroblast cell lines was investigated by elasticity measurements with an atomic force microscope (AFM). Disaggregation of actin filaments always resulted in a distinct decrease in the cell's average elastic modulus indicating the crucial importance of the actin network for the mechanical stability of living cells. Disruption or chemical stabilization of microtubules did not affect cell elasticity. For the f-actin-disrupting drugs different mechanisms of drug action were observed. Cytochalasins B and D and Latrunculin A disassembled stress fibers. For Cytochalasin D this was accompanied by an aggregation of actin within the cytosol. Jasplakinolide disaggregated actin filaments but did not disassemble stress fibers. Fibrous structures found in AFM images and elasticity maps of fibroblasts could be identified as stress fibers by correlation of AFM data and fluorescence images. PMID:10620315

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

    NASA Astrophysics Data System (ADS)

    Zhang, Yin; Murphy, Kevin D.

    As a cantilever structure, atomic force microscope (AFM) can be either modeled as a beam, plate or a simple one degree-of-freedom (DOF) system depending on its geometry and application scenario. The AFM structure can experience the deformation shapes of vertical bending, lateral bending, torsion, extension and couplings between these four deformations depending on the excitation mode. As a small structure of micron scale, forces like van der Waals (vdW) force, surface stress, electrostatic force and residual stress can have significant influence on the AFM deflection. When the AFM tip is in contact with the sample surface, different contact mechanics models are needed depending on the tip geometry, AFM operating mode and tip, sample surface material properties. In dynamic mode, the AFM tip-sample surface intermittent contact is a complicated nonlinear dynamics problem. As a powerful tool, the AFM application is already beyond the stage of being used to image the sample surface topography. Nowadays, AFM is used more often to extract the sample materials properties such as Young's modulus, surface energy/adhesion and viscosity. How to properly model the AFM structure with different deformations and their coupling under different forces and the tip-sample surface interaction is vital to linking the experimentally measured data correctly with the sample surface material properties. This chapter reviews the different models concerning the AFM structure (static) deformations, external residual forces modeling, tip-surface contact and the AFM dynamics. This chapter is intended to provide a comprehensive review rather than an in-depth discussion on those models. Because there are too many factors influencing the experimentally measured data during the application of AFM, it is extremely difficult to consider all these factors in one model for AFM if not impossible. Because there are too many factors influencing the AFM deformations/dynamics, it will be extremely difficult if not impossible to link all of the influencing factors to the experimental data. Therefore, in the modeling aspect, certain assumptions must be made to render the problem solvable. One of the major purposes of this chapter is to discuss and analyze the assumptions of those models and by doing so we try to outline the applicability ranges of those models. At the same time by analyzing the assumptions of the models applied to the AFM, the limitations of some models are also presented. Pointing out the limitations of those models which work fine with certain application scenarios is intended to make the applicability ranges of the models clearer and also helps to better interpret the experimental data. Only the dominant factors should be considered in a model and the other factors must be neglected to have a workable model. However, for different AFM applications the dominant factors are varied and thus transferring the model developed for one AFM application to another one can be inappropriate or even wrong. The analysis on the model assumption thus plays an important role of applying one model developed for certain application scenario to other applications.

  8. 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.

  9. 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.

  10. 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.

  11. Structure, Thermodynamics and Kinetics of Chemically Heterogeneous Interfaces

    NASA Astrophysics Data System (ADS)

    Palafox Hernandez, Jesus Pablo

    2011-12-01

    In this work we have used atomistic computer simulations to examine the structure, thermodynamics and transport properties, for two models of chemically heterogeneous interfaces: an ideal model (repulsive soft spheres against a potential wall), and a metal alloy interface (Cu-Pb). In both systems, interfacial prefreezing (crystal formation above the melting point of the fluid) was observed and this prefreezing was seen to promote heterogeneous nucleation, when the systems were cooled below the melting temperature. In our study of inverse-power repulsive soft spheres, we found that the soft-sphere fluid exhibited prefreezing at the wall surface. Similar behavior was previously observed in hard-sphere fluids at hard wall [17, 18, 20], however, to our knowledge, this the first time that prefreezing is reported for soft spheres. The prediction of prefreezing is based on the calculation of interfacial free energies wall-crystal (gammawc) and wall-fluid (gammawf) using a variant of the cleaving wall method. With the calculated, gammawc and gamma wf together with gammacf, previously computed [79], the tendency to prefreeze was quantified by the wetting angle formed between the metastable crystal phase on the wall and the soft-sphere fluid. We found that all the closest packing orientations [(111) FCC and (110) BCC] developed prefreezing (complete wetting). A detailed atomic-level characterization of the structure, energetics and transport properties of the planar Cu/Pb solid-liquid interface in equilibrium was performed at a several temperatures (625K and 750K) above the melting point of Pb and for two Cu crystal orientations [(111) and (100)]. Among the most relevant findings are that the Cu(100)/Pb interfaces presents surfaces alloying and the Cu(111)/Pb exhibits a prefreezing layer of Pb crystal. It was also observed that both interfaces have a nucleation barrier that prevents heterogeneous nucleation and that the mechanisms by which each structure promotes heterogeneous nucleation are different. Both models, the inverse-power soft spheres and the EAM Cu-Pb, showed the connection between atomistic behavior and prefreezing. The crystalline layer formed above the melting point of the fluids showed to be influential in heterogeneous nucleation in both cases. In this way, the study of basic properties shed new light on the atomistic underlying nature of macroscopic events, such as wetting and nucleation.

  12. 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.

  13. 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

  14. 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

  15. Chemical structure of Bacteriovorax stolpii lipid A.

    PubMed

    Beck, Sebastian; Müller, Frederic D; Strauch, Eckhard; Brecker, Lothar; Linscheid, Michael W

    2010-02-01

    Bdellovibrionales is a phylogenetically diverse group of predatory prokaryotes, which consists of the two families Bdellovibrionaceae and Bacteriovoracaceae. We describe LPS and lipid A of the type strain Bacteriovorax stolpii DSM 12778, representing the first characterized endotoxin of a Bacteriovoracaceae member. It has a smooth form LPS, which was identified by SDS-polyacrylamide gel electrophoresis. The lipid A structure was determined by combined gas chromatography-mass spectrometry, electrospray ionization mass spectrometry and NMR spectroscopy. Its backbone consists of two beta-(1-->6)-linked 2,3-diamino-2,3-dideoxy-D-glucopyranoses (GlcpN3N) carrying a pyrophosphoethanolamine at O-4' of the non-reducing sugar and a phosphate group linked to O-1 of the reducing GlcpN3N. Positions 2, 3, 2' and 3' of the two GlcpN3N are acylated with primary 3-hydroxy fatty acids and one of those carries a secondary fatty acid. PMID:20094810

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2015-08-01

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

  3. Study of the structure and chemical bonding of crystalline Ge4Sb2Te7 using first principle calculations

    NASA Astrophysics Data System (ADS)

    Singh, Janpreet; Singh, Satvinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

    2016-05-01

    The atomic arrangements and chemical bonding of stable Ge4Sb2Te7 (GeTe rich), a phase-change material, have been investigated by means of ab initio total energy calculations. To study the atomic arrangement, GeTe block is considered into -TeSbTeSbTe- block and -Te-Te- layer in the stacking I and II respectively. The stacking I is energetically more stable than the stacking II. The reason for more stability of the stacking I has been explained. The chemical bonding has been studied with the electronic charge density distribution around the atomic bonds. The quantity of electronic charge loosed or gained by atoms has been calculated using the Bader charge analysis. The metallic character has been studied using band structures calculations. The band gap for the stacking I and II is 0.463 and 0.219 eV respectively.

  4. Low-temperature chemically-driven atomic layer epitaxy for II-VI material growth

    NASA Astrophysics Data System (ADS)

    Luo, Yi

    2000-10-01

    In this thesis, I present the results of three surface science studies on (1) II-VI semiconductor surface preparation, (2) low-temperature chemically driven atomic layer epitaxy, and (3) investigations of surface chemistry for material deposition with chemical precursors. First, in Chapter 3, I present results of using combination of atomic hydrogen and oxygen plasma to removal surface contaminants such as O, C, S, Cl, etc. from CdTe and Cd1-xZnxTe surfaces at room temperature. XPS, AES, and LEED measurements showed that this method is very effective in removing common surface contaminants via low temperature surface reactions. The surface damage cause by the reactions is much lower than high temperature thermal annealing and ion sputtering. In addition, in situ photoluminescence results shows about three orders of magnitude increase of near band-gap feature intensity after the sample went through H cleaning and annealing to a proper temperature. Second, in Chapter 4, an in situ molecular-level study of material growth using a binary reaction sequence of hydride and metalorganic precursors is presented. The study used a model material system of CdS/ZnSe (100) and focused on the material chemistry of heteroepitaxy growth. In the growth process, dimethylcadmium and H2S precursors were sequentially dosed onto a c(2x2) ZnSe (100) substrate under high-vacuum conditions. At temperatures of ˜300K, saturated chernisorption of a Cd and a S monolayer occurred during each cycle of the binary reaction sequence. Characterization of the growth surface was accomplished in the growth chamber using AES, XPS and LEIS for probing surface chemical composition and LEED for determining surface order. These measurements showed layer-by-layer growth at a substrate temperature of ˜300 K, yielding an ordered stoichiometric US film. Strong variations in the composition of the grown surface layer were observed at different substrate temperatures; these variations were found to be related to the temperature dependence of the precursor reactions with the growth surfaces. Finally, in Chapter 5, I will discuss the detail surface chemical investigation using TPD and NEXAFS for atomic layer epitaxy of CdS on ZnSe(100) surface. Both TPD and NEXAFS results show that either a monolayer of surface methyl or hydrogen termination exists after the growth surface is dosed with DMCd or H2S. Both precursors adsorb on the surface dissociatively. The terminating groups (CH3 and H) are thermally stable on the surface in a certain temperature range, thus passivate the growth surfaces preventing further uptake of materials after monolayer-coverage is reached. However, surface CH3 or H is reactive to the alternative precursor, so the other constituent material can be deposited subsequently. This methyl or hydrogen passivation provides a satisfactory self-limiting material deposition mechanism to allow the growth proceed in a layer-by-layer manner. TPD and NEXAFS results obtained after different reaction steps are presented separately in details.

  5. 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.

  6. 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.

  7. 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 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. Electronic supplementary information (ESI) available: Additional HE-XRD/PDFs, XPS, and other experimental data. See DOI: 10.1039/c5nr04535e

  8. 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

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

    SciTech Connect

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

    2005-01-01

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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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).

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

    PubMed Central

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

    2013-01-01

    Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The Cα and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments. PMID:23897468

  16. 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

  17. 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.

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

  19. 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.

  20. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    PubMed

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  1. 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.

  2. Theoretical and Experimental Studies of the Structures of 12-, 13-, and 14-atom Bimetallic Ni/Al Clusters.

    NASA Astrophysics Data System (ADS)

    Rexer, Eric F.; Parks, Eric K.; Riley, Stephen J.; Krissinel, Evgueni B.; Jellinek, Julius

    2002-03-01

    Results of a combined experimental/theoretical study of the structures of isolated 12-, 13-, and 14-atom mixed Ni/Al clusters are presented and discussed. All the possible compositions are considered for each cluster size. The experimental probes capitalize on the fact that N2 molecules adsorb on Ni but not on Al within the time and temperature regimes of the flow tube reactor cluster source. The theoretical predictions of the cluster structures are derived from a semi-empirical many-body potential. The measurements are consistent with icosahedral-based conformations obtained in computations. Moreover, the experimental measurements are in remarkable accord with the detailed theoretically determined distribution of the Ni and Al atoms within the clusters. --------------------- *Work supported by: U.S. Dept. of Energy, Division of Chemical Sciences, Contract No. W-31-109-Eng-38

  3. [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

  4. 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.

  5. Investigation of the mechanisms of the action of chemical modifiers for electrothermal atomic absorption spectrometry: what for and how?

    NASA Astrophysics Data System (ADS)

    Volynsky, Anatoly B.

    1998-01-01

    Modern trends in the research of the action of chemical modifiers for electrothermal atomic absorption spectrometry (ETAAS) are discussed critically. The most prolific approach is that of investigation of processes occurring during the drying and pyrolysis stages with wide application of data from different fields of chemistry and physics.

  6. 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)

  7. 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.

  8. On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO.

    PubMed

    Baysal, C; Meirovitch, H

    2000-11-01

    A statistical mechanics methodology for predicting the solution structures and populations of peptides developed recently is based on a novel method for optimizing implicit solvation models, which was applied initially to a cyclic hexapeptide in DMSO (C. Baysal and H. Meirovitch, Journal of American Chemical Society, 1998, vol. 120, pp. 800-812). Thus, the molecule has been described by the simplified energy function E(tot) = E(GRO) + summation operator(k) sigma(k)A(k), where E(GRO) is the GROMOS force-field energy, sigma(k) and A(k) are the atomic solvation parameter (ASP) and the solvent accessible surface area of atom k, respectively. In a more recent study, these ASPs have been found to be transferable to the cyclic pentapeptide cyclo(D-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO (C. Baysal and H. Meirovitch, Biopolymers, 2000, vol. 53, pp. 423-433). In the present paper, our methodology is applied to the cyclic heptapeptides axinastatin 2 [cyclo(Asn(1)-Pro(2)-Phe(3)-Val(4)-Leu(5)-Pro(6)-Val(7))] and axinastatin 3 [cyclo(Asn(1)-Pro(2)-Phe(3)-Ile(4)-Leu(5)-Pro(6)-Val(7))], in DMSO, which were studied by nmr by Mechnich et al. (Helvetica Chimica Acta, 1997, vol. 80, pp. 1338-1354). The calculations for axinastatin 2 show that special ASPs should be optimized for the partially charged side-chain atoms of Asn while the rest of the atoms take their values derived in our previous work; this suggests that similar optimization might be needed for other side chains as well. The solution structures of these peptides are obtained ab initio (i.e., without using experimental restraints) by an extensive conformational search based on E(GRO) alone and E(*)(tot), which consists of the new set of ASPs. For E(*)(tot), the theoretical values of proton-proton distances, (3)J coupling constants, and other properties are found to agree very well with the nmr results, and they are always better than those based on E(GRO). PMID:10951328

  9. Epitaxial B-Graphene: Large-Scale Growth and Atomic Structure.

    PubMed

    Usachov, Dmitry Yu; Fedorov, Alexander V; Petukhov, Anatoly E; Vilkov, Oleg Yu; Rybkin, Artem G; Otrokov, Mikhail M; Arnau, Andrés; Chulkov, Evgueni V; Yashina, Lada V; Farjam, Mani; Adamchuk, Vera K; Senkovskiy, Boris V; Laubschat, Clemens; Vyalikh, Denis V

    2015-07-28

    Embedding foreign atoms or molecules in graphene has become the key approach in its functionalization and is intensively used for tuning its structural and electronic properties. Here, we present an efficient method based on chemical vapor deposition for large scale growth of boron-doped graphene (B-graphene) on Ni(111) and Co(0001) substrates using carborane molecules as the precursor. It is shown that up to 19 at. % of boron can be embedded in the graphene matrix and that a planar C-B sp(2) network is formed. It is resistant to air exposure and widely retains the electronic structure of graphene on metals. The large-scale and local structure of this material has been explored depending on boron content and substrate. By resolving individual impurities with scanning tunneling microscopy we have demonstrated the possibility for preferential substitution of carbon with boron in one of the graphene sublattices (unbalanced sublattice doping) at low doping level on the Ni(111) substrate. At high boron content the honeycomb lattice of B-graphene is strongly distorted, and therefore, it demonstrates no unballanced sublattice doping. PMID:26121999

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

    SciTech Connect

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

    2015-09-14

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

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Fine structure in a strong magnetic field: Paschen-Back effect reconsidered in Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Liu, Wenyu; Gu, Sihong; Li, Baiwen

    1996-05-01

    Using a kind of potential model wave function for alkali metal atoms, we nonperturbatively study the effect of fine structure on the Rydberg spectra of Cs atom in a strong magnetic field. Our numerical results reveal spectral structure dramatically different from the well-established Paschen-Back effect, and we argue that the fine structure of the Rydberg Cs atom cannot be neglected even in a magnetic field as strong as several teslas. We also give an error estimate of our results and a word on possible experimental verification.

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

    PubMed Central

    Tan, J.; Wang, G.; Liu, Z. Y.; Bednarčík, 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. Phosphorus-doped graphene and (8, 0) carbon nanotube: Structural, electronic, magnetic properties, and chemical reactivity

    NASA Astrophysics Data System (ADS)

    Wang, Hong-mei; Wang, Hong-xia; Chen, Ying; Liu, Yue-jie; Zhao, Jing-xiang; Cai, Qing-hai; Wang, Xuan-zhang

    2013-05-01

    Recently, doping non-carbon atoms into graphene or carbon nanotube (CNT) has attracted considerable attention due to its effectiveness to change or tailor their electronic and magnetic properties as well as chemical reactivity. In this work, we present a density functional theory study of the recently synthesized phosphorus (P) doped graphene and CNT. Particular attention is paid to studying the effects of P-doping on the structural, electronic, and magnetic properties as well as chemical reactivity of graphene or CNT. The results show that P dopant drastically changes the geometrical structure of graphene or CNT, rendering P and its neighboring C atoms protrude from the sidewall of CNT and graphene. Moreover, P-doping induces localized electronic states into graphene and CNTs, thus modifying the electronic properties by producing n-type behavior. Meanwhile, due to P doping, the graphene and CNT exhibit magnetic nature with spin net moment of 1.02 and 0.99 μB, respectively. In order to evaluate the chemical reactivity of the two nanostructures, their interactions with several gas molecules, including NH3, H2O, O2, NO2, and NO, are further calculated. Our results may be useful not only for deeply understanding the properties of CNTs and graphenes, but also for developing various novel nanodevices.

  2. 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'…

  3. 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…

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

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

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

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

    ERIC Educational Resources Information Center

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

    2002-01-01

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

  6. 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.

  7. 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

  8. 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.

  9. Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.

    PubMed

    Serrano, Jorge; Moros, Javier; Laserna, J Javier

    2015-03-01

    Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule. PMID:25668318

  10. Atomic structure calculations for F-like tungsten

    NASA Astrophysics Data System (ADS)

    Sunny, Aggarwal

    2014-09-01

    Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

  11. Chemical Structure-Related Drug-Like Criteria of Global Approved Drugs.

    PubMed

    Mao, Fei; Ni, Wei; Xu, Xiang; Wang, Hui; Wang, Jing; Ji, Min; Li, Jian

    2016-01-01

    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

  12. Atomic-level investigation of the growth of Si/Ge by ultrahigh vacuum chemical vapor deposition

    SciTech Connect

    Lin, D.; Miller, T.; Chiang, T.

    1997-05-01

    Si and Ge films can be prepared under ultrahigh vacuum conditions by chemical vapor deposition using disilane and digermane as source gases. These gases offer a high sticking probability, and are suitable for atomic layer epitaxy. Using synchrotron radiation photoemission spectroscopy and scanning tunneling microscopy, we have examined the surface processes associated with the heteroepitaxial growth of Ge/Si. The measured surface-induced shifts and chemical shifts of the Si 2p and Ge 3d core levels allow us to identify the surface species and to determine the surface chemical composition, and this information is correlated with the atomic features observed by scanning tunneling microscopy. Issues related to precursor dissociation, attachment to dangling bonds, diffusion, surface segregation, growth morphology, and pyrolytic reaction pathways will be discussed. {copyright} {ital 1997 American Vacuum Society.}

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

    PubMed

    Stashans, Arvids; Chamba, Gaston; Pinto, Henry

    2008-02-01

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

  14. 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

  15. The Flexible Pocketome Engine for Structural Chemical Genomics

    PubMed Central

    Abagyan, Ruben; Kufareva, Irina

    2010-01-01

    Biological metabolites, substrates, cofactors, chemical probes, and drugs bind to flexible pockets in multiple biological macromolecules to exert their biological effect. The rapid growth of the structural databases, sequence data, including SNPs and disease-related genome modifications, complemented by the new cutting-edge 3D docking, scoring and profiling methods created a unique opportunity to develop a comprehensive structural map of interactions between any small molecule and biopolymers. Here we demonstrated that a comprehensive structural genomics engine can be built using multiple pocket conformations, experimentally determined or generated with a variety of modeling methods, and new efficient ensemble docking algorithms. In contrast to traditional ligand-activity based engines trained on known chemical structures and their activities, the structural pocketome and docking engine will allow to predict poses and activities for new, previously unknown, protein binding sites, and new, previously uncharacterized, chemical scaffolds. This de novo structure-based activity prediction engine may dramatically accelerate the discovery of potent and specific therapeutics with reduced side effects. PMID:19727619

  16. Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering

    NASA Astrophysics Data System (ADS)

    Ha, N.-B.; Jeong, S.; Yu, S.; Ihm, H.-I.; Kim, J.-S.

    2015-01-01

    Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates.

  17. Topological structure and chemical composition of inner surfaces of borosilicate vials.

    PubMed

    Schwarzenbach, Monica S; Reimann, Peter; Thommen, Verena; Hegner, Martin; Mumenthaler, Marco; Schwob, Jacky; Güntherodt, Hans-Joachim

    2004-01-01

    The use of atomic force microscopy (AFM) and x-ray photoelectron spectroscopy (XPS) is described to characterize the inner surfaces of pharmaceutical vials. The two type I borosilicate glasses included in this study slightly differ in their amounts of alkaline oxides. The topography and chemistry of the inner surfaces of vials are predominantly caused by the forming process. A structural and chemical modification of the inner surface of vials was also observed when exposing the surface to different pH conditions and special treatment like washing and sterilization, which are routine operation steps during galenical manufacturing. PMID:15233256

  18. 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.

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

    ERIC Educational Resources Information Center

    Lo, Mei Ling

    1997-01-01

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

  20. 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'...

  1. 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...

  2. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  3. 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.

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Wang, H.; Lu, Y. F.

    2008-01-01

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

  6. Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Ponomareva, A. A.; Moshnikov, V. A.; Suchaneck, G.

    2013-12-01

    In this work, we evaluate the hierarchical surface topography of reactively sputtered nanocrystalline Pb(Zr,Ti)O3 and TiO2 thin films as well as plasma-treated antireflective PET films by means of determining the fractal dimension and power spectral density (PSD) of surface topography recorded by atomic force microscopy (AFM). Local fractal dimension was obtained using the triangulation method. The PSDs of all samples were fitted to the k-correlation model (also called ABC model) valid for a self-affine surface topography. Fractal analysis of AFM images was shown to be an appropriate and easy to use tool for the characterization of hierarchical nanostructures.

  7. Unexpected Symmetry in the Nodal Structure of the He Atom

    NASA Astrophysics Data System (ADS)

    Bressanini, Dario; Reynolds, Peter J.

    2005-09-01

    The nodes of even simple wave functions are largely unexplored. Motivated by their importance to quantum simulations of fermionic systems, we have found unexpected symmetries in the nodes of several atoms and molecules. Here, we report on helium. We find that in both ground and excited states the nodes have simple forms. In particular, they have higher symmetry than the wave functions they come from. It is of great interest to understand the source of these new symmetries. For the quantum simulations that motivated the study, these symmetries may help circumvent the fermion sign problem.

  8. 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).

  9. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces. PMID:26444084

  10. [Physico-chemical properties of microbial and plant polysaccharides structurants].

    PubMed

    Votselko, S K; Dankevytch, L A; Lytvynchuk, O O

    2012-01-01

    The comparative investigation of physico-chemical properties of plant (guar gum, konjac-mannan) and microbial (xanthan gum) origin structurants have been carried out. Among them, xanthan sigma (1544 mPa) and konjac-mannan (5000 mPa) have the best initial viscosity. It has been shown that due to molecular-mass characteristics xanthan (74.3%) gum, ksampan (39%) and konjac-mannan (42.1%) have the highest percentage of high-weight fractions. It has been established that mannose, glucose and galactose as well as unidentified substances are presented in different concentrations in the structure of structurants. PMID:22686017

  11. High-precision atomic structure measurements in thallium

    NASA Astrophysics Data System (ADS)

    Burkhardt, M. H.; Holmes, C. D.; Uhl, R.; Majumder, P. K.

    2004-05-01

    Using a thallium atomic beam apparatus, we are undertaking a series of laser spectroscopy measurements with the goal of providing precise, independent cross-checks on the accuracy of new calculations of parity nonconservation in thallium(M. Kozlov et al.), Phys Rev. A64, 053107 (2001). In our apparatus, a laser beam interacts transversely with a dense, 2-cm-wide thallium beam and reveals roughly tenfold Doppler narrowing of the absorption profile. Having completed a new 0.4% measurement of the Stark shift within the 378 nm 6P_1/2-7S_1/2 E1 transition, we have now begun to study the weak 1283 nm 6P_1/2-6P_3/2 transition in the atomic beam. We seek to determine both Stark shift components, as well as the various components of the Stark-induced amplitude within this mixed M1/E2 transition. Using these existing laser systems, we have also begun a vapor cell spectroscopy study of the 1301 nm 7S_1/2-7P_1/2 E1 transition by means of a two-step excitation from the ground state. To enhance the visibility of these weak absorption signals, we are employing an FM spectroscopy technique. The demodulated laser transmission spectrum provides a low-noise, zero-background signal, and includes replicas of the absorption spectrum separated by the well-known RF sideband frequency, offering built-in frequency scale calibration.

  12. 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.

  13. Xas Studies of Chemical Bonding of Nitrogen And Oxygen Atoms in Ti/ZrHf High-K Gate Dielectrics

    SciTech Connect

    Seo, H.; Lee, S.; Ju, B.; Lucovsky, G.; Luning, J.

    2009-06-05

    Near edge x-ray absorption spectroscopy (NEXAS) has been used to study bonding in Ti/Zr/Hf (hereafter TM) Si oxynitrides and silicates. Comparisons between O K{sub 1} and N K{sub 1} spectra are particularly informative since O and N anti-bonding molecular orbitals (MO) display distinct features from nearest- and next-nearest-neighbor TM and Si atoms. MO TM-atom spectral features are qualitatively different in TM silicates and Si oxynitrides. NEXAS studies of TM silicates identity chemical phase separation (CPS) into TM-dioxides and SiO{sub 2} for annealing to 900{sup o}C.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Quantum Chemical Insight into the LiF Interlayer Effects in Organic Electronics: Reactions between Al Atom and LiF Clusters.

    PubMed

    Wu, Shui-Xing; Kan, Yu-He; Li, Hai-Bin; Zhao, Liang; Wu, Yong; Su, Zhong-Min

    2015-08-01

    It is well known that the aluminum cathode performs dramatically better when a thin lithium fluoride (LiF) layer inserted in organic electronic devices. The doping effect induced by the librated Li atom via the chemical reactions producing AlF3 as byproduct was previously proposed as one of possible mechanisms. However, the underlying mechanism discussion is quite complicated and not fully understood so far, although the LiF interlayer is widely used. In this paper, we perform theoretical calculations to consider the reactions between an aluminum atom and distinct LiF clusters. The reaction pathways of the Al-(LiF)n (n = 2, 4, 16) systems were discovered and the energetics were theoretically evaluated. The release of Li atom and the formation of AlF3 were found in two different chemical reaction routes. The undissociated Al-(LiF)n systems have chances to change to some structures with loosely bound electrons. Our findings about the interacted Al-(LiF)n systems reveal new insights into the LiF interlayer effects in organic electronics applications. PMID:26267187

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Element-resolved atomic structure imaging of rocksalt Ge2Sb2Te5 phase-change material

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Zhang, Wei; Shen, Zhenju; Chen, Yongjin; Li, Jixue; Zhang, Shengbai; Zhang, Ze; Wuttig, Matthias; Mazzarello, Riccardo; Ma, Evan; Han, Xiaodong

    2016-05-01

    Disorder-induced electron localization and metal-insulator transitions (MITs) have been a very active research field starting from the seminal paper by Anderson half a century ago. However, pure Anderson insulators are very difficult to identify due to ubiquitous electron-correlation effects. Recently, an MIT has been observed in electrical transport measurements on the crystalline state of phase-change GeSbTe compounds, which appears to be exclusively disorder driven. Subsequent density functional theory simulations have identified vacancy disorder to localize electrons at the Fermi level. Here, we report a direct atomic scale chemical identification experiment on the rocksalt structure obtained upon crystallization of amorphous Ge2Sb2Te5. Our results confirm the two-sublattice structure resolving the distribution of chemical species and demonstrate the existence of atomic disorder on the Ge/Sb/vacancy sublattice. Moreover, we identify a gradual vacancy ordering process upon further annealing. These findings not only provide a structural underpinning of the observed Anderson localization but also have implications for the development of novel multi-level data storage within the crystalline phases.

  5. Atomic 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.

  6. (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…

  7. Atomic partial charges on CH3NH3PbI3 from first-principles electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Madjet, Mohamed E.; El-Mellouhi, Fedwa; Carignano, Marcelo A.; Berdiyorov, Golibjon R.

    2016-04-01

    We calculated the partial charges in methylammonium (MA) lead-iodide perovskite CH3NH3PbI3 in its different crystalline phases using different first-principles electronic charge partitioning approaches, including the Bader, ChelpG, and density-derived electrostatic and chemical (DDEC) schemes. Among the three charge partitioning methods, the DDEC approach provides chemically intuitive and reliable atomic charges for this material, which consists of a mixture of transition metals, halide ions, and organic molecules. The DDEC charges are also found to be robust against the use of hybrid functionals and/or upon inclusion of spin-orbit coupling or dispersive interactions. We calculated explicitly the atomic charges with a special focus on the dipole moment of the MA molecules within the perovskite structure. The value of the dipole moment of the MA is reduced with respect to the isolated molecule due to charge redistribution involving the inorganic cage. DDEC charges and dipole moment of the organic part remain nearly unchanged upon its rotation within the octahedral cavities. Our findings will be of both fundamental and practical importance, as the accurate and consistent determination of the atomic charges is important in order to understand the average equilibrium distribution of the electrons and to help in the development of force fields for larger scale atomistic simulations to describe static, dynamic, and thermodynamic properties of the material.

  8. Neutron Diffraction and Local Atomic Structure of Fontainebleau Sandstone: Evidence for an Amorphous Phase?

    NASA Astrophysics Data System (ADS)

    Page, K.; Proffen, T.; Darling, T. W.; Tencate, J. A.

    2004-12-01

    Total neutron scattering measurements of solid Fontainebleau sandstone were carried out. Standard Rietveld analysis, yielding only average structural information, reveals that the long range average structure of this sandstone is pure quartz. Atomic pair distribution function (PDF) analysis, however, shows significant local structural deviations from the quartz structure. These deviations manifest themselves as an excess of 5-10% of nearest neighbor (NN) Si-O and O-O bonds. No evidence of deviations from the average quartz structure can be found for atom-atom separations larger that the NN O-O bond. This could be understood as an additional glassy SiO2 phase being present in the sandstone. [Work supported by Los Alamos Institutional Support (LDRD) and the DOE Office of Basic Energy Sciences. The Manuel Lujan Jr. Neutron Scattering Center is a national user facility funded in part by the U.S. DOE.

  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 π bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is ~100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. Understanding the NMR chemical shifts for 6-halopurines: role of structure, solvent and relativistic effects.

    PubMed

    Standara, Stanislav; Malináková, Katerina; Marek, Radek; Marek, Jaromír; Hocek, Michal; Vaara, Juha; Straka, Michal

    2010-05-21

    A prototypical study of NMR chemical shifts in biologically relevant heteroaromatic compounds containing a heavy halogen atom is presented for two isomers of halogen-substituted purines. Complete sets of (1)H-, (13)C- and (15)N-NMR chemical shifts are determined experimentally in solution. Experimental results are complemented by quantum-chemical calculations that provide understanding of the trends in the chemical shifts for the studied compounds and which show how different physical effects influence the NMR parameters. Chemical shifts for isolated molecules are calculated using density-functional theory methods, the role of solvent effects is studied using polarised continuum models, and relativistic corrections are calculated using the leading-order Breit-Pauli perturbation theory. Calculated values are compared with the experimental data and the effects of structure, solvent and relativity are discussed. Overall, we observe a good agreement of theory and experiment. We find out that relativistic effects cannot be neglected even in the chlorine species when aiming at high precision and a good agreement with the experimental data. Relativity plays a crucial role in the bromine and iodine species. Solvent effects are of smaller importance for (13)C shifts but are shown to be substantial for particular (15)N shifts. The test of method performance shows that the BLYP and B3LYP functionals provide the most reliable computational results after inclusion of the solvent and relativistic effects while BHandHLYP may--depending on atom in question--slightly improve but mostly deteriorate the data. Ab initio Hartree-Fock suffers from triplet instability in the Breit-Pauli relativistic part while MP2 provides no clear improvement over DFT in the nonrelativistic region. This work represents the first full application of the Breit-Pauli perturbation theory to an organic chemistry problem. PMID:20445915

  16. 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

  17. 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

  18. 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

  19. Structural and electronic properties of atomically thin germanium selenide polymorphs

    NASA Astrophysics Data System (ADS)

    Hu, Ziyu

    Using comprehensive density functional theory calculations, we systematically investigate the structure, stability, and electronic properties of five polymorphs of GeSe monolayer, and highlight the differences in their structural and electronic properties. Our calculations show that the five free-standing polymorphs of GeSe are stable semiconductors. β-GeSe, γ-GeSe, δ-GeSe, and ɛ-GeSe are indirect gap semiconductors, whereas α-GeSe is a direct gap semiconductor. We calculated Raman spectra and scanning tunneling microscopy images for the five polymorphs. Our results show that the β-GeSe monolayer is a candidate for water splitting.

  20. 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.

  1. 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.

  2. Structure and Chemistry of Atomic Clusters from Supersonic Beams.

    NASA Astrophysics Data System (ADS)

    Yang, Shi-He.

    A tandem time-of-flight (TOF) apparatus was designed to study the structure and chemistry of cold transition metal cluster ions from supersonic beams. By means of a photodissociation laser fluence dependence technique, binding energies of Nb_{rm x }^{+} (x = 2 - 20), Co_{rm x}^{+ } (x = 4 - 20) and etc. were found to generally increase with cluster size. The desorption energies of Nb_{rm x}N _2^{+} (x = 2 - 17) and Nb_{rm x} CO^{+} (x = 2 - 10) also increase with cluster size with some oscillations similar to the size dependent reactivities of these clusters. Photodetachment studies revealed that electron affinities of copper clusters increase with cluster size with a sharp even/odd alternation. Unlike other noble metals, Ag_{rm x}^ {-} clusters display two competing processes: photodissociation and photodetachment. Relative reactivities of cluster ions of Nb, Co, Ag, and etc. have been measured using a fast flow cluster reactor, displaying a similar function of cluster size to that of the neutrals. In addition, preliminary photoelectron experiments have been performed on Cu_{ rm x}^{-} and Nb _{rm x}^{-}. A magnetic Time-of-flight ultraviolet photoelectron spectrometer (MTOFUPS) has been developed to study electronic structures of cold metal and semiconductor cluster anions prepared in supersonic beams. Application of this spectrometer to carbon clusters with a F_2 laser (7.9 eV) allowed their electron affinities and UPS patterns to be measured,demonstrating a remarkable structural evolution of these clusters: Chains (C_2^{ -}-C_9^{-} ) - Rings (C_{10}^ {-}-C_{29}^ {-}) - Cages (C_{38 }^{-}-C_{84 }^{-}). In particular, the UPS of C_{60}^{-} is in excellent agreement with the CNDO/S calculation, providing a striking spectral evidence for the highly symmetric icosahedral soccer ball structure--Buckminsterfullerene. For comparison, the UPS of Si_ {rm x}^{-} and Ge_{rm x}^{ -} are presented. Unlike carbon clusters which prefer structures of low dimensionality, these clusters tend to take a network structure. In conjunction with calculations, some tentative structural assignments were possible.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  4. Structure of intracellular mature vaccinia virus visualized by in situ atomic force microscopy.

    PubMed

    Malkin, A J; McPherson, A; Gershon, P D

    2003-06-01

    Vaccinia virus, the basis of the smallpox vaccine, is one of the largest viruses to replicate in humans. We have used in situ atomic force microscopy (AFM) to directly visualize fully hydrated, intact intracellular mature vaccinia virus (IMV) virions and chemical and enzymatic treatment products thereof. The latter included virion cores, core-enveloping coats, and core substructures. The isolated coats appeared to be composed of a highly cross-linked protein array. AFM imaging of core substructures indicated association of the linear viral DNA genome with a segmented protein sheath forming an extended approximately 16-nm-diameter filament with helical surface topography; enclosure of this filament within a 30- to 40-nm-diameter tubule which also shows helical topography; and enclosure of the folded, condensed 30- to 40-nm-diameter tubule within the core by a wall covered with peg-like projections. Proteins observed attached to the 30- to 40-nm-diameter tubules may mediate folding and/or compaction of the tubules and/or represent vestiges of the core wall and/or pegs. An accessory "satellite domain" was observed protruding from the intact core. This corresponded in size to isolated 70- to 100-nm-diameter particles that were imaged independently and might represent detached accessory domains. AFM imaging of intact virions indicated that IMV underwent a reversible shrinkage upon dehydration (as much as 2.2- to 2.5-fold in the height dimension), accompanied by topological and topographical changes, including protrusion of the satellite domain. As shown here, the chemical and enzymatic dissection of large, asymmetrical virus particles in combination with in situ AFM provides an informative complement to other structure determination techniques. PMID:12743290

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

    SciTech Connect

    Ho, P.; Coltrin, M.E.; Breiland, W.G. )

    1994-10-06

    An extensive set of laser-induced fluorescence (LIF) measurements of Si atoms during the chemical vapor deposition (CVD) of silicon from silane and disilane in a research rotating disk reactor are presented. The experimental results are compared in detail with predictions from a numerical model of CVD from silane and disilane that treats the fluid flow coupled to gas-phase and gas-surface chemistry. The comparisons showed that the unimolecular decomposition of SiH[sub 2] could not account for the observed gas-phase Si atom density profiles. The H[sub 3]SiSiH [leftrightarrow] Si + SiH[sub 4] and H[sub 3]SiSiH + SiH[sub 2] [leftrightarrow] Si + Si[sub 2]H[sub 6] reactions are proposed as the primary Si atom production routes. The model is in good agreement with the measured shapes of the Si atom profiles and the trends in Si atom density with susceptor temperature, pressure, and reactant gas mixture. 33 refs., 12 figs., 3 tabs.

  6. First-principles calculation of atomic forces and structural distortions in strongly correlated materials.

    PubMed

    Leonov, I; Anisimov, V I; Vollhardt, D

    2014-04-11

    We introduce a novel computational approach for the investigation of complex correlated electron materials which makes it possible to evaluate interatomic forces and, thereby, determine atomic displacements and structural transformations induced by electronic correlations. It combines ab initio band structure and dynamical mean-field theory and is implemented with the linear-response formalism regarding atomic displacements. We apply this new technique to explore structural transitions of prototypical correlated systems such as elemental hydrogen, SrVO3, and KCuF3. PMID:24765993

  7. 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

  8. 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.

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

    SciTech Connect

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

  10. 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.

  11. 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.

  12. 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

  13. 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

  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. 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.

  16. 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.

  17. 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.

  18. Chemical and physical structures of proteinoids and related polyamino acids

    NASA Astrophysics Data System (ADS)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  19. Towards chemical identification in atomic-resolution noncontact AFM imaging with silicon tips

    NASA Astrophysics Data System (ADS)

    Foster, A. S.; Gal, A. Y.; Airaksinen, J. M.; Pakarinen, O. H.; Lee, Y. J.; Gale, J. D.; Shluger, A. L.; Nieminen, R. M.

    2003-11-01

    In this study we use ab initio calculations and a pure silicon tip to study the tip-surface interaction with four characteristic insulating surfaces: (i) the narrow gap TiO2 (110) surface, (ii) the classic oxide MgO (001) surface, (iii) the ionic solid CaCO3 (101¯4) surface with molecular anion, and (iv) the wide gap CaF2 (111) surface. Generally we find that the tip-surface interaction strongly depends on the surface electronic structure due to the dominance of covalent bond formation with the silicon tip. However, we also find that in every case the strongest interaction is with the highest anion of the surface. This result suggests that, if the original silicon tip can be carefully controlled, it should be possible to immediately identify the species seen as bright in images of insulating surfaces. In order to provide a more complete picture we also compare these results to those for contaminated tips and suggest how applied voltage could also be used to probe chemical identity.

  20. Chemical structure of odorants and perceptual similarity in ants.

    PubMed

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity. PMID:23685976

  1. 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

  2. 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

  3. 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.}

  4. 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.

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

    PubMed Central

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

    1996-01-01

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

  6. 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.

  7. Modelling the atomic structure of Al92U8 metallic glass.

    PubMed

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

    2010-10-13

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

  8. 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)

  9. Structure-chemical approach to organization of information on metabolic charts.

    PubMed

    Malygin, A G

    2004-12-01

    A nontraditional approach to construction of metabolic charts is proposed. It is based on the discovery of symmetry in the structure of the network of metabolic reactions. So if compounds and reactions are located on the metabolic chart according to their chemical features, the chart structure will acquire a periodic pattern. The charts thus created have a natural two-dimensional coordinate system of the metabolic network. Points on the X-axis correspond to number of carbon atoms in the carbon skeleton of compounds in columns and points on the Y-axis correspond to number of -COOH groups in compounds filing in series of rows on the charts. As a result this coordinate system sections the field of the charts into rectangular blocks each of which containing compounds with the same numbers of carbon atoms and the same numbers of -COOH groups. The latter substantially improves the charts and makes them a more valid source of metabolic data possessing heuristic properties. The periodicity of the metabolic network structure enables us easily to remember information about biochemical reactions and their products. The charts can also be used as a universal key for any biological database information that is systematically connected with the metabolic information. The charts can be important for medicine and pharmacology because they can help to understand the metabolic processes involved in decomposition of a particular drug or to find the chain of reactions blocked or initiated by administering this drug into a living organism. PMID:15627394

  10. Novel mesoscale defect structure on NiO(1 0 0) surfaces by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Petitto, S. C.; Berrie, C. L.; Langell, M. A.

    2006-09-01

    Cleaved NiO(1 0 0) surfaces were imaged with atomic force microscopy (AFM) to determine defect concentrations and morphology. Random <0 1 0> and <0 0 1> oriented steps, which have been previously characterized, were the most common defect observed on the cleaved surface and formed with step heights in multiples of 2.1 Å, the Ni-O nearest-neighbor distance, and terrace widths in the range of 25-100 nm. In addition, the surface showed novel mesoscale (˜0.5-2 μm) square pyramidal defects with the pyramid base oriented along <1 0 0> symmetry related directions. Upon etching, the pyramidal defects converted to more stable cubic pits, consistent with (1 0 0) symmetry related walls. The square pyramidal pits tended to cluster or to form along step edges, where the weakened structure is more susceptible to surface deformations. Also, a small concentration of square pyramidal pits, oriented with the base of the pyramid along <0 1 1>, was observed on the cleaved NiO surfaces. For comparison purposes, chemical mechanical polished (CMP) NiO(1 0 0) substrates were imaged with AFM. Defect concentrations were of comparable levels to the cleaved surface, but showed a different distribution of defect types. Long-ranged stepped defects were much less common on CMP substrates, and the predominant defects observed were cubic pits with sidewalls steeper than could be accurately measured by the AFM tip. These defects were similar in size and structure to those observed on cleaved NiO(1 0 0) surfaces that had been acid etched, although pit clustering was more pronounced for the CMP surfaces.

  11. On the Mechanisms of Hydrogen-Atom Transfer from Water to the Heteronuclear Oxide Cluster [Ga2 Mg2 O5 ](.+) : Remarkable Electronic Structure Effects.

    PubMed

    Li, Jilai; Zhou, Shaodong; Wu, Xiao-Nan; Tang, Shiya; Schlangen, Maria; Schwarz, Helmut

    2015-09-28

    Mechanistic insight into the homolytic cleavage of the O-H bond of water by the heteronuclear oxide cluster [Ga2 Mg2 O5 ](.+) has been derived from state-of-the-art gas-phase experiments in conjunction with quantum chemical calculations. Three pathways have been identified computationally. In addition to the conventional hydrogen-atom transfer (HAT) to the radical center of a bridging oxygen atom, two mechanistically distinct proton-coupled electron-transfer (PCET) processes have been identified. The energetically most favored path involves initial coordination of the incoming water ligand to a magnesium atom followed by an intramolecular proton transfer to the lone-pair of the bridging oxygen atom. This step, which is accomplished by an electronic reorganization, generates two structurally equivalent OH groups either of which can be liberated, in agreement with labeling experiments. PMID:26277446

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

    SciTech Connect

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

    2011-01-01

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

  13. 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.

  14. 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.

  15. 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

  16. [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

  17. 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.

  18. 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.

  19. 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.

  20. Breit–Pauli atomic structure calculations for Fe XI

    SciTech Connect

    Aggarwal, Sunny Singh, Jagjit; Mohan, Man

    2013-11-15

    Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many of the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.

  1. 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.

  2. Structural, electronic and optical properties of 7-atom Ag-Cu nanoclusters from density functional theory

    NASA Astrophysics Data System (ADS)

    Li, Weiyin; Chen, Fuyi

    2014-04-01

    The structures and electronic properties of 7-atom silver and copper bimetallic clusters are systematically investigated by density functional theory (DFT) in the theoretical frame of the generalised gradient approximation (GGA) exchange-correlation functional. Optical absorption, Raman spectra, as well as vibrational spectra are calculated by DFT/GGA and semi-core pseudopotentials. The lowest-energy stable motifs are primarily related to the quantity of Cu-Cu bonds and Ag-Cu bonds. The Ag5Cu2 2-I with D 5 h symmetry cluster is the lowest energy cluster in the family of the 7-atom Ag-Cu nanoclusters, but has the lowest electronic stability. The Ag5Cu2 2-I, Ag4Cu3 3-I and Ag3Cu4 4-I clusters with mixed motifs indicate that silver and copper may be miscible on the nanoscale but not in bulk. Overall, with increasing Cu atoms, for the lowest energy nanoclusters, blue-shift of the maximum absorption peaks presents in the UV-Vis wavelength range, the intensities of the maximum peak of the Raman spectra weaken, the Cu atom(s) introduced make the vibrational spectra complex, and the intensities of the vibrational spectra strengthen. The calculated vibrational and Raman spectroscopy of 7-atom Ag-Cu clusters may be helpful in determining the size and structure of the experimental cluster.

  3. 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.

  4. In situ investigation of surface chemistry for chemically driven atomic layer epitaxy of II-VI semiconductor thin films

    NASA Astrophysics Data System (ADS)

    Han, Ming

    2000-10-01

    Atomic Layer Epitaxy (ALE) can provide atomic scale control of the growth of ultra thin semiconductor films. This thesis presents an overview of an in situ molecular-level study of surface chemistry for heteroepitaxy of II-VI semiconductor by using a binary reaction sequence with hydride and metalorganic precursors. The study focused primarily on developing a fundamental understanding of surface chemistry in a model material system: the growth of US on ZnSe (100). Dimethylcadmium and H2S precursors were sequentially dosed onto a c(2x2) ZnSe (100) substrate and characterization of the growth surface at each growth step was accomplished in the growth chamber under UHV conditions. The surface chemical composition was probed by Auger electron spectroscopy (AES) and low energy ion scattering spectroscopy (LEIS) and the surface order was determined by low energy electron diffraction (LEED). These measurements showed that, at a substrate temperature of ˜300 K, self-limiting reactions resulted in saturated chemisorption of one Cd and one S monolayer during each cycle of the binary reaction sequence, yielding the layer-by-layer growth of an ordered stoichiometric US film. We investigated surface chemistry of our model system in further detail using near edge X-ray fine structure (NEXAFS) spectroscopy and temperature programmed desorption (TPD) spectroscopy. NEXAFS and TPD results revealed that the growth surface is terminated by either a monolayer of surface methyl or hydrogen subsequent to saturation with either DMCd or H2S respectively, at ˜300 K. These surface terminating groups (CH3 or H) passivate the growth surface, preventing further uptake of the precursors once monolayer coverage is reached. However, surface CH3 or H is reactive to the alternative precursor, so the other constituent can be deposited subsequently. Therefore, both methyl and hydrogen termination provide satisfactory self-limiting reactions that allow the growth to proceed in a layer-by-layer manner. Heteroepitaxy of ZnS on Si(100) using a similar binary reaction sequence has also been proposed. The initial stage of our study has focused on the interactions of potential precursors with Si(100). Adsorption and desorption mechanisms of H2S on Si(100) have been investigated by using AES, TPD and LEED. The surface is saturated by 0.5 ML of H2S for all substrate exposure temperatures, i.e. -145°C -425°C. Desorption of hydrogen and diffusion of sulfur occur almost simultaneously after dissociative adsorption of H2S on Si(100). This process makes it impossible to form 1.0 ML of surface sulfur without a separate means of H-atom removal. Alternative approaches to initiating the growth of a II-VI semiconductor on Si(100), such as the use of a group III or group V intermediary layer, are discussed.

  5. 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.

  6. Surface characterization study of the chemical alteration of an air-exposed polycrystalline tin foil during H-atom exposures

    NASA Astrophysics Data System (ADS)

    Epling, William S.; Mount, Charles K.; Hoflund, Gar B.

    1998-09-01

    An air-exposed polycrystalline Sn foil surface has been examined before and after exposure to H atoms using X-ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy (ISS). The foil initially contains large amounts of oxygen and carbon at the surface. C is present mostly as hydrocarbon contamination, and O is present as Sn hydroxide and surface water in addition to SnO, SnO 2 and transitional oxide (possibly Sn 3O 4), which has an O content between SnO and SnO 2. The C and O contents of the near-surface region are significantly reduced by exposure to the H-atom flux. The large hydroxyl group concentration is reduced through formation and desorption of water. A short 1-min exposure results in reduction of some of the SnO 2 or transitional oxide to SnO. Longer reduction periods result in the formation of a large amount of transitional oxide and some metallic Sn. ISS data indicate that the O and C contents of the outermost atomic layer initially increase upon exposure to H atoms due to a chemically induced driving force and then decrease. Migration of subsurface C and O becomes the rate-limiting step with regard to further removal of these species at room temperature.

  7. 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.

  8. Real-space imaging of atomic structure with white x rays.

    PubMed

    Korecki, P; Materlik, G

    2001-03-12

    The first real-space x-ray image of an atomic structure was obtained by illuminating a crystal with white synchrotron radiation. The internal photocurrent signal served as a probe of the x-ray interference field strength at the atomic sites and was accordingly measured as a function of illumination direction to record the two-dimensional image. This novel method of real-space imaging makes use of the fact that the interference field intensity is energy independent with respect to contributions from those scattering atoms which are brought via sample rotation into the forward scattering condition. In contrast, contributions from other atoms oscillate with energy and vanish for broadband illumination. PMID:11289922

  9. 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

  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. 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

  12. Interfacial diffusion of metal atoms during air annealing of chemically deposited ZnS-CuS and PbS-CuS thin films

    SciTech Connect

    Huang, L.; Zingaro, R.A.; Meyers, E.A. . Dept. of Chemistry); Nair, P.K.; Nair, M.T.S. . Lab. de Energia Solar)

    1994-09-01

    The authors report on the interfacial diffusion of metal ions occurring during air annealing of multilayer CuS films (0.15-0.6[mu]m) deposited on thin coating of ZnS or PbS ([approximately]0.06 [mu]m) on glass substrates. All the films are deposited from chemical baths at room temperature. The interfacial diffusion on the metal atoms during the air annealing is illustrate by X-ray photoelectron spectroscopy studies. A multilayer of 0.3 [mu]m thick CuS film deposited over a thin film of ZnS upon annealing at 150 C shows atomic ratios of Zn to Cu of [approximately]0.15 and [approximately]0.48 at the surface layers of the samples annealed for 12 and 24 h, respectively. In the case of CuS on PbS film, the corresponding Pb to Cu atomic ratios at the surface layers are 0.43 and 0.83. The optical transmittance spectra and sheet resistance of these multilayer films indicate thermal stabilities superior to that of the CuS-only coatings. Application of the interfacial diffusion process in the production of thermally stable solar control coatings, solar absorber coating, or p-type films for solar cell structures is discussed.

  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 μB , whereas for Pt atoms it is 1 μB. These are quite high compared with the values for bulk Fe as well as bulk FePt and F e3Pt phases while bulk Pt is nonmagnetic. There is significant charge transfer from those Fe atoms that interact directly with Pt atoms. We discuss the hybridization between the electronic states of Pt and Fe atoms as well as the variation in the magnetic moments on Fe and Pt atoms. Our results provide insight into the understanding of the nanoalloy behavior of Fe-Pt and we hope that this would help to design Fe based nanoalloys and their assemblies with high magnetic moments for strong magnets without rare earths as well as Pt alloy catalysts.

  14. 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.

  15. A neutral atom-molecular ion collider: progress towards state-to-state resolution in a chemical reaction

    NASA Astrophysics Data System (ADS)

    Tu, Ming-Feng; Tung, Shih-Kuang; Odom, Brian

    2015-05-01

    In our recent experiment, we demonstrated a scheme to prepare AlH+ molecules in a single quantum state. This new development opens up new possibilities to study chemical reactions with state-to-state resolution. Moving towards this new direction, we designed an experimental apparatus to study reactive interactions between neutral Rb atoms and AlH+ molecules. Our hybrid machine consists of a Rb MOT and a spatially separated AlH+ ion trap. A translatable dipole trap will be used to bring the Rb atoms to interact with the trapped AlH+ molecules and will allow us to accurately control the collisional energies. Here we report our progress on building this experimental apparatus. This work is supported by ARO MURI.

  16. Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Nieuwkoop, Andrew J.; Wylie, Benjamin J.; Franks, W. Trent; Shah, Gautam J.; Rienstra, Chad M.

    2009-09-01

    We show that quantitative internuclear N15-C13 distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of C13 sites in the ?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.

  17. Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

    PubMed Central

    Nieuwkoop, Andrew J.; Wylie, Benjamin J.; Franks, W. Trent; Shah, Gautam J.; Rienstra, Chad M.

    2009-01-01

    We show that quantitative internuclear 15N–13C 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 13C sites in the β1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-13C or 2-13C-glycerol as the 13C source. Quantitative dipolar trajectories are extracted from two-dimensional 15N–13C planes, in which ∼750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one 13C and several 15N each), yielding quantitative precision as good as 0.1 Å for ∼350 sites, better than 0.3 Å for another 150, and ∼1.0 Å for 150 distances in the range of 5–8 Å. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25±0.09 Å), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79±0.03 Å). Moreover, side chain heavy atoms are well restrained (0.76±0.06 Å total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure. PMID:19739873

  18. 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

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

    SciTech Connect

    Schnohr, C. S.

    2015-09-15

    Compound semiconductor alloys such as In{sub x}Ga{sub 1−x}As, GaAs{sub x}P{sub 1−x}, or CuIn{sub x}Ga{sub 1−x}Se{sub 2} are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI{sub 2} chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family.

  20. 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.

  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. Chemical Structural Novelty: On-Targets and Off-Targets

    PubMed Central

    Yera, Emmanuel R.; Cleves, Ann. E.; Jain, Ajay N.

    2011-01-01

    Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3D similarity, or their combination. For prediction of primary targets, the benefit of 3D over 2D was relatively small, but for prediction of off-targets, the added benefit was large. In addition to assessing prediction, the relationship between chemical similarity and pharmacological novelty was studied. Drug pairs that shared high 3D similarity but low 2D similarity (i.e. a novel scaffold) were shown to be much more likely to exhibit pharmacologically relevant differences in terms of specific protein target modulation. PMID:21916467

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

    PubMed

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

    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-π, and anion-π interactions, as well as hydrogen bonding to π 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

  4. Behaviour of chemical modifiers in the determination of arsenic by electrothermal atomic absorption spectrometry in petroleum products.

    PubMed

    Reboucas, Marcio V; Ferreira, Sergio L C; de Barros Neto, Benicio

    2005-07-15

    Most comparative studies on the efficiency of chemical modifiers have been conducted in aqueous media. In the present work, we proposed a detailed study of the use of different chemical modifiers for direct determination of arsenic in complex organic matrices by electrothermal atomic absorption spectrometry (ETAAS). Palladium, rhodium, tungsten, silver, lanthanum and a mixture of palladium and magnesium were tested. The figures of merit used for evaluation and comparison were acquired in the optimal conditions for each modifier, established by multivariate optimization of the main variables based on Doehlert designs. Singular features were observed for the chemical behaviour of some modifiers in organic matrices compared to aqueous media, such as the worse performance of Pd+Mg modifier and no notice of severe tube corrosion from La application. Lanthanum was chosen as the best chemical modifier for the present application, according to predefined criteria. Lanthanum showed the minimum limit of detection, characteristic concentration and blank signal among all tested species and no effect of the concomitants usually present in petrochemical feedstocks. Using a 200mgL(-1) lanthanum solution as a chemical modifier, the average relative standard deviations of 7 and 16% (at 3-15mugL(-1) level) and characteristic concentrations of 0.47 and 0.77mugL(-1) for naphtha and petroleum condensates, respectively, were observed. PMID:18970155

  5. Evaluating and interpreting the chemical relevance of the linear response kernel for atoms II: open shell.

    PubMed

    Boisdenghien, Zino; Fias, Stijn; Van Alsenoy, Christian; De Proft, Frank; Geerlings, Paul

    2014-07-28

    Most of the work done on the linear response kernel χ(r,r') has focussed on its atom-atom condensed form χAB. Our previous work [Boisdenghien et al., J. Chem. Theory Comput., 2013, 9, 1007] was the first effort to truly focus on the non-condensed form of this function for closed (sub)shell atoms in a systematic fashion. In this work, we extend our method to the open shell case. To simplify the plotting of our results, we average our results to a symmetrical quantity χ(r,r'). This allows us to plot the linear response kernel for all elements up to and including argon and to investigate the periodicity throughout the first three rows in the periodic table and in the different representations of χ(r,r'). Within the context of Spin Polarized Conceptual Density Functional Theory, the first two-dimensional plots of spin polarized linear response functions are presented and commented on for some selected cases on the basis of the atomic ground state electronic configurations. Using the relation between the linear response kernel and the polarizability we compare the values of the polarizability tensor calculated using our method to high-level values. PMID:24837234

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

    NASA Technical Reports Server (NTRS)

    Ross, H. Richard

    1993-01-01

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

  7. 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

  8. 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...

  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. 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

  11. Passivation of structured p-type silicon interfaces: Effect of surface morphology and wet-chemical pre-treatment

    NASA Astrophysics Data System (ADS)

    Angermann, H.

    2008-10-01

    The effect of both surface morphology and wet-chemical pre-treatment on electronic surface and interface properties was investigated for mono- and polycrystalline silicon substrates with special surface structures. Surface charge, energetic distribution, and density of rechargeable states on these surfaces were determined by surface photovoltage (SPV) measurements. These results were correlated to previously reported findings on atomically flat Si(111) and Si(100) surfaces of monocrystalline wafers. In this paper, a specially optimised sequence of cleaning, wet-chemical oxidation, and oxide removal procedures is described in detail for the first time. This method was successfully applied in order to remove contaminations and damaged surface layers and to obtain atomically flat areas on substrates with evenly distributed atomic steps, polycrystalline and monocrystalline substrates with randomly distributed pyramids. A significant reduction in surface micro-roughness, interface state density, and recombination loss was achieved. Using passivation by wet-chemical oxidation or H-termination, respectively, the optimised surface state can be preserved by the time of following preparation steps and during subsequent a-Si:H plasma enhanced chemical vapour deposition (PECVD).

  12. 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.

  13. 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

  14. 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

  15. Chemical and structural modifications in the UV ablation of polymers

    NASA Astrophysics Data System (ADS)

    Georgiou, Savas K.; Bounos, John; Athanassiou, Athanassia; Anglos, Dmitrios; Tornari, Vivi; Fotakis, Costas

    2002-09-01

    The study examines chemical and structural modifications effected in the UV ablation of polymers. For the study of the chemical processes, aromatic photosensitive compounds with well-defined photochemistry are employed as dopants and their reactivity is examined as a function of laser parameters (fluence, wavelength and laser pulse width). A 'pump-probe' scheme based on laser-induced fluorescence is employed for monitoring photoproduct formation in the polymeric substrate following UV irradiation. Ablation is shown to result in a change of the photolysis degree of the dopant and in the efficient formation of bi-aryl compounds, indicative of a high species mobility. Furthermore, kinetics of photoproduct formation in the ablative regime is shown to differ distinctly from that in the irradiation at low laser fluences. However, the quantitative extent of these changes is critically affected by the absorptivity of the substrate at the irradiation wavelength. On the other hand, structural modifications induced in polymer films are probed via holographic interferometry. Deformations are shown to be induced at distances far away (approximately 2-3 cm) from the irradiation spot. The implications for UV laser material processing schemes are briefly discussed.

  16. Determination of airblast atomized spray structure using state-of-the-art laser diagnostics

    NASA Astrophysics Data System (ADS)

    Jasuja, A. K.; Tam, C. K.

    1992-07-01

    This paper presents the results of an integrated qualitative-quantitative investigation into the detailed structure of an airblast atomized gas turbine spray at near atmospheric pressure and temperature conditions. Pre-filming airblast atomizer was studied with aviation kerosine as the test fuel. Phase Doppler anemometry was utilized to interrogate droplet size, velocity and number density characteristics while high-energy, pulsed laser sheet illumination technique enabled the visualization of the condition of the liquid at atomizer exit as well as variations in droplet concentration. The spray is found to be generally inhomogeneous in structure and the extent of size, velocity, number density inhomogeneity increases as the axial distance of the measurement plane diminishes. This has implications for the attainment of a satisfactory combustion-emissions performance from modern combustors with compact reaction zones.

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

    SciTech Connect

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

    2013-05-01

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

  18. Atomic Structure and Charge Density Waves of Blue Bronze by Variable Temperature Scanning Tunneling Microscopy

    SciTech Connect

    Nikiforov,M.; Isakovic, A.; Bonnell, D.

    2007-01-01

    Blue bronze (K{sub 0.3}MoO{sub 3}) has been the focus of a number of scattering, transport, scanning tunneling microscopy (STM), and theoretical studies that have provided insight into the relation between atomic structure and charge-density wave (CDW) formation. However, the full extent of a relation of the CDWs to the atomic lattice and the microscopic origin of CDW pinning are still not completely resolved. In this study STM is used to distinguish the atomic structure and CDWs at the (20{bar 1}) surface. Within the STM's spatial resolution, the CDWs are incommensurate with the lattice at midrange temperatures and approach commensurability at low temperatures. Incommensurate CDWs are present on the surface and the degree of the incommensurability between blue bronze lattice and CDW lattice agree well with those determined from bulk scattering techniques.

  19. 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

  20. 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

  1. 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.

  2. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are then used to construct a hierarchical framework for uncertainty quantification.

  3. 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.

  4. Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

    NASA Astrophysics Data System (ADS)

    Okada, H.; Kato, M.; Ishimaru, T.; Furukawa, M.; Sekiguchi, H.; Wakahara, A.

    2014-02-01

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

  5. Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

    SciTech Connect

    Okada, H.; Kato, M.; Ishimaru, T.; Sekiguchi, H.; Wakahara, A.; Furukawa, M.

    2014-02-20

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

  6. Interaction of diatomic germanium with lithium atoms: Electronic structure and stability

    NASA Astrophysics Data System (ADS)

    Gopakumar, G.; Lievens, Peter; Nguyen, Minh Tho

    2006-06-01

    Quantum chemical calculations were applied to investigate the electronic structure of mono-, di-, and trilithiated digermanium (Ge2Lin) and their cations (n=0-3). Computations using a multiconfigurational quasidegenerate perturbation approach based on complete active space self-consistent-field wave functions, and density functional theory reveal that Ge2Li has a B12 ground state with a doublet-quartet energy gap of 33kcal/mol. Ge2Li2 has a singlet ground state with a Au3-A11 gap of 29kcal/mol, and Ge2Li3 a doublet ground state with a B24-A22 separation of 22kcal/mol. The cation Ge2Li+ has a B13 ground state, being 13kcal/mol below the open-shell B11 state. The computed electron affinities for diatomic germanium are EA(1)=1.9eV, EA(2)=-2.5eV, and EA(3)=-6.0eV, for Ge2-, Ge22-, and Ge23-, respectively, indicating that only the monoanion is stable with respect to electron detachment, in such a way that Ge2Li is composed by Ge2-•Li+ ions. An "atoms-in-molecules" analysis shows the absence of a ring critical point in Ge2Li. An electron localization function analysis on Ge2Li supports the view that the Ge-Li bond is predominantly ionic; however, a small covalent character could be anticipated from the analysis of the Laplacian at the Ge-Li bond critical point. The ionic picture of the Ge-Li bond is further supported by a natural-bond-order analysis and the Laplacian of the electron density. The calculated Li affinity value for Ge2 is 2.08eV, while the Li+ cation affinity value for Ge2- is 5.7eV. The larger Li+ cation affinity value of Ge2- suggests a Ge2-Li+ interaction and thus supports the ionic nature of Ge-Li bond. In GeLi4 and Ge2Li, the presence of trisynaptic basins indicates a three-center bond connecting the germanium and lithium atoms.

  7. A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems.

    PubMed

    De Souza, Douglas G; Cezar, Henrique M; Rondina, Gustavo G; de Oliveira, Marcelo F; Da Silva, Juarez L F

    2016-05-01

    We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard's law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy. PMID:27045947

  8. A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems

    NASA Astrophysics Data System (ADS)

    De Souza, Douglas G.; Cezar, Henrique M.; Rondina, Gustavo G.; de Oliveira, Marcelo F.; Da Silva, Juarez L. F.

    2016-05-01

    We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard’s law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy.

  9. Three-Dimensional Imaging of the Local Structure of Materials at Atomic Resolution by Electron Tomography

    NASA Astrophysics Data System (ADS)

    Zhu, Chun

    Electron tomography was originally developed in 1968, and has been primarily applied to determine the three-dimensional (3D) structure of biological systems. In the last decade, the application of electron tomography in materials science and nanoscience has revived due to the utilization of scanning transmission electron microscopy (STEM) in the high-angle annular dark-field (HAADF) mode, and a highest resolution of ˜1 nm3 has been achieved. However, improving the resolution from ˜1 nm 3 to the atomic level remains a challenging task, which requires new tomographic reconstruction algorithms, better projection alignment methods, state-of-the-art STEM instruments, and more accurate data-acquisition procedures. In this thesis, important progress has been made in all these four areas. First, a novel tomographic method, termed equally sloped tomography (EST), was developed and allows the 3D image reconstruction of tilt series with a limited number projections and a "missing wedge" (i.e. specimens cannot usually be tilted beyond +/-70°). Second, an alignment method which can be used to align the projections of a tilt series at atomic-level resolution was developed based on center of mass. Finally, by using a Titan 80-300 STEM instrument at the California NanoSystems Institute, UCLA, more accurate data acquisition procedures were developed and a number of tomographic tilt series of atomic resolution projections from different nanoparticles have been obtained. With all these combinations, the 3D structure of a 10 nm gold nanoparticle was determined at 2.4 A resolution, the highest resolution ever achieved in any general tomography method. More recently, this novel electron tomography method has been applied to observe nearly all the atoms in a Pt nanoparticle, and imaged for the first time the 3D core structure of edge and screw dislocations at atomic resolution. Furthermore, through numerical simulations the feasibility of determining the 3D atomic structure of amorphous materials by the Electron Tomography method has been demonstrated.

  10. Chemical vapor generation of silver for atomic absorption spectrometry with the multiatomizer: Radiotracer efficiency study and characterization of silver species

    NASA Astrophysics Data System (ADS)

    Musil, Stanislav; Kratzer, Jan; Vobecký, Miloslav; Hovorka, Jan; Benada, Oldřich; Matoušek, Tomáš

    2009-11-01

    Volatile Ag species were generated in flow injection arrangement from nitric acid environment in the presence of surfactants (Triton X-100 and Antifoam B) and permanent Pd deposits as the reaction modifiers. Atomic absorption spectrometry (AAS) with multiple microflame quartz tube atomizer heated to 900 °C was used for atomization; evidence was found for thermal mechanism of atomization. Relative and absolute limits of detection (3 σ, 250 μl sample loop) measured under optimized conditions were: 1.4 μg l - 1 and 0.35 ng, respectively. The efficiency of chemical vapor generation (CVG) as well as spatial distribution of residual analyte in the apparatus was studied by 111Ag radioactive indicator (half-life 7.45 days) of high specific activity. It was found out that 23% of analyte was released into the gaseous phase. However, only 8% was found on filters placed at the entrance to the atomizer due to transport losses. About 40% of analyte remained in waste liquid, whereas the rest was found deposited over the CVG system. Presented study follows the hypothesis that the "volatile" Ag species are actually metallic nanoparticles formed upon reduction in liquid phase and then released with good efficiency to the gaseous phase. Number/charge size distributions of dry aerosol were determined by Scanning Mobility Particle Sizer. Ag was detected in 40-45 nm particles holding 10 times more charge if compared to Boltzmann equilibrium. At the same time, Ag was also present on 150 nm particles, the main size mode of the CVG generator. The increase of Ag in standards was reflected by proportional increase in particle number/charge for 40-45 nm size particles only. Transmission electron microscopy revealed particles of 8 ± 2 nm sampled from the gaseous phase, which were associated in isolated clusters of few to few tens of nanometres. Ag presence in those particles was confirmed by Energy Dispersive X-ray Spectroscopy (EDS) analysis.

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

    PubMed

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

    2013-05-30

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

  12. 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)

  13. The Structure of the Atom: Teacher's Guide Levels A, B, and C. Preliminary Limited Edition.

    ERIC Educational Resources Information Center

    Cambridge Physics Outlet, Woburn, MA. Education Programs Dept.

    This is a two-part curriculum package for teaching the structure of atoms. The first part--the Teacher's Guide--contains information necessary for using the equipment in a typical classroom including learning goals, vocabulary, math skills, and sample data for each activity. The second part of the package consists of photocopy masters for a set of…

  14. Imaging the atomic surface structures of CeO2 nanoparticles

    SciTech Connect

    Lin, Yuyuan; Wu, Zili; Wen, Jianguo; Poeppelmeier, Kenneth R; Marks, Laurence D

    2014-01-01

    Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear experimental determination of the positions of the surface oxygen atoms. Particularly controversial is the (100) surface structure of this material. In this study, with oxygen atoms clearly observed using aberration corrected high resolution electron microscopy, we determined the atomic structures of the (100), (110) and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has a mixture of Ce, O, and reduced CeO terminations, underscoring the complex structures of this polar surface that previously was often oversimplified. The (110) surface shows saw-like (111) nanofacets and flat CeO2-x terminations with oxygen vacancies. The (111) surface has an O termination. As these three low index surfaces are the most often exposed facets in the majority of CeO2 nanoparticles, these findings can be extended to the surfaces of differently shaped CeO2 nanoparticles as well as provide insight about face-selective catalysis.

  15. 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…

  16. Current State of Web Sites in Science Education--Focus on Atomic Structure.

    ERIC Educational Resources Information Center

    Tuvi, Inbal; Nachmias, Rafi

    2001-01-01

    Explores to what extent the web's advanced graphical tools and computational power are implemented in science education. Focuses on the pedagogical and technological characteristics of web sites attempting to teach the subject of atomic structure. (Contains 33 references.) (Author/YDS)

  17. 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…

  18. 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

  19. Boron carbides formed by coevaporation of B and C atoms: Vapor reactivity, BxC1-x composition, and bonding structure

    NASA Astrophysics Data System (ADS)

    Caretti, I.; Gago, R.; Albella, J. M.; Jiménez, I.

    2008-05-01

    Boron carbides (BxC1-x) in thin film form have been synthesized in a high vacuum by coevaporation of B and C atoms from independent sources, allowing a study of the whole composition range from pure B films to pure C films. The relationship between the impinging B/C atomic fluxes and the film composition has been studied, providing information on the chemical reactivity between the B and C vapors. The composition was determined with x-ray emission energy dispersion spectroscopy and x-ray absorption near edge spectroscopy (XANES). Finally, the bonding structure of the films has been determined by XANES, showing a change from structures based on B12 -icosahedral units for the B-rich samples to hexagonal-like structures for the C-rich samples. The study shows that the structural transition takes place for xtilde 0.5 .

  20. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    SciTech Connect

    Xiong, L.H.; Lou, H.B.; Wang, X.D.; Debela, T.T.; Cao, Q.P.; Zhang, D.X.; Wang, S.Y.; Wang, C.Z.; Jiang, J.Z.

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.